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kantale/lesson_7_draft.ipynb

Created November 23, 2018 18:31
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Πρόχειρες σημειώσεις από το μάθημα python, 7η διάλεξη, 23 Νοεμβρίου 2018
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lesson_7_draft.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" 12\r\n"
]
}
],
"source": [
"!ls -l | wc -l"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"-rw-r--r-- 1 antonakd staff 12 Nov 23 10:31 test.txt\r\n"
]
}
],
"source": [
"!ls -l test.txt"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA\r\n",
"BBB\r\n",
"CCC\r\n"
]
}
],
"source": [
"!cat test.txt"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"_io.TextIOWrapper"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"type(f)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"content = f.read()"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA\n",
"BBB\n",
"CCC\n",
"\n"
]
}
],
"source": [
"print (content)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"''"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.read()"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"''"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.read()"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"ename": "ValueError",
"evalue": "I/O operation on closed file.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-20-571e9fb02258>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mValueError\u001b[0m: I/O operation on closed file."
]
}
],
"source": [
"f.read()"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'AAA\\nBBB\\nCCC\\n'"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.read()"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [],
"source": [
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [],
"source": [
"g = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'AAA\\nBBB\\nCCC\\n'"
]
},
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.read()"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"''"
]
},
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.read()"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'AAA\\nBBB\\nCCC\\n'"
]
},
"execution_count": 37,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"g.read()"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {},
"outputs": [],
"source": [
"g.close()"
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {},
"outputs": [],
"source": [
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {},
"outputs": [],
"source": [
"c = f.read()"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA\n",
"BBB\n",
"CCC\n",
"\n"
]
}
],
"source": [
"print (c)"
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"3\n"
]
}
],
"source": [
"a=3\n",
"b=a\n",
"a=4\n",
"print (b)"
]
},
{
"cell_type": "code",
"execution_count": 47,
"metadata": {},
"outputs": [],
"source": [
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 48,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AA\n"
]
}
],
"source": [
"c = f.read(2)\n",
"print (c)"
]
},
{
"cell_type": "code",
"execution_count": 49,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"A\n",
"\n"
]
}
],
"source": [
"c = f.read(2)\n",
"print (c)"
]
},
{
"cell_type": "code",
"execution_count": 50,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'A\\n'"
]
},
"execution_count": 50,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"c"
]
},
{
"cell_type": "code",
"execution_count": 51,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"BB\n"
]
}
],
"source": [
"c = f.read(2)\n",
"print (c)"
]
},
{
"cell_type": "code",
"execution_count": 52,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 53,
"metadata": {},
"outputs": [],
"source": [
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 54,
"metadata": {},
"outputs": [],
"source": [
"line = f.readline()"
]
},
{
"cell_type": "code",
"execution_count": 56,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'AAA\\n'"
]
},
"execution_count": 56,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"line"
]
},
{
"cell_type": "code",
"execution_count": 57,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"BBB\n",
"\n"
]
}
],
"source": [
"line = f.readline()\n",
"print (line)"
]
},
{
"cell_type": "code",
"execution_count": 58,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CCC\n",
"\n"
]
}
],
"source": [
"line = f.readline()\n",
"print (line)"
]
},
{
"cell_type": "code",
"execution_count": 59,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"line = f.readline()\n",
"print (line)"
]
},
{
"cell_type": "code",
"execution_count": 60,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 60,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"line == ''"
]
},
{
"cell_type": "code",
"execution_count": 61,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"B\n"
]
}
],
"source": [
"if line:\n",
" print ('A')\n",
"else:\n",
" print ('B')"
]
},
{
"cell_type": "code",
"execution_count": 62,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 66,
"metadata": {},
"outputs": [],
"source": [
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 67,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA\n",
"\n",
"BBB\n",
"\n",
"CCC\n",
"\n"
]
}
],
"source": [
"for l in f:\n",
" print(l)"
]
},
{
"cell_type": "code",
"execution_count": 68,
"metadata": {},
"outputs": [],
"source": [
"f.close()\n",
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 69,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['AAA\\n', 'BBB\\n', 'CCC\\n']"
]
},
"execution_count": 69,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.readlines()"
]
},
{
"cell_type": "code",
"execution_count": 73,
"metadata": {},
"outputs": [],
"source": [
"f.close()\n",
"f = open('test.txt')"
]
},
{
"cell_type": "code",
"execution_count": 74,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA\n",
"\n",
"BBB\n",
"\n",
"CCC\n",
"\n"
]
}
],
"source": [
"counter = 0\n",
"for line in f:\n",
" counter += 1\n",
" if counter > 100:\n",
" break\n",
"\n",
" print(line)\n"
]
},
{
"cell_type": "code",
"execution_count": 75,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# WITH "
]
},
{
"cell_type": "code",
"execution_count": 76,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA\n",
"\n",
"BBB\n",
"\n",
"CCC\n",
"\n"
]
}
],
"source": [
"with open('test.txt') as f:\n",
" for l in f:\n",
" print (l)\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 77,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<_io.TextIOWrapper name='test.txt' mode='r' encoding='UTF-8'>"
]
},
"execution_count": 77,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f"
]
},
{
"cell_type": "code",
"execution_count": 83,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA KKK\n",
"BBB LLL\n",
"CCC MMM\n"
]
}
],
"source": [
"with open('test.txt') as f1, open('test2.txt') as f2:\n",
" for l1,l2 in zip(f1, f2):\n",
" l1=l1.replace('\\n', '')\n",
" l2=l2.replace('\\n', '')\n",
" \n",
" print (l1 + ' ' + l2)\n",
" \n",
" \n",
" "
]
},
{
"cell_type": "code",
"execution_count": 87,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA KKK\n",
"BBB LLL\n",
"CCC MMM\n"
]
}
],
"source": [
"with open('test.txt') as f1:\n",
" with open('test2.txt') as f2:\n",
" for l1,l2 in zip(f1, f2):\n",
" l1=l1.replace('\\n', '')\n",
" l2=l2.replace('\\n', '')\n",
" \n",
" print (l1 + ' ' + l2)"
]
},
{
"cell_type": "code",
"execution_count": 89,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA KKK\n",
"BBB LLL\n",
"CCC MMM\n"
]
}
],
"source": [
"f1 = open('test.txt')\n",
"f2 = open('test2.txt')\n",
"for l1,l2 in zip(f1, f2):\n",
" l1=l1.replace('\\n', '')\n",
" l2=l2.replace('\\n', '')\n",
" print (l1 + ' ' + l2)\n",
"f1.close()\n",
"f2.close()"
]
},
{
"cell_type": "code",
"execution_count": 92,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"AAA KKK\n",
"BBB LLL\n",
"CCC MMM\n"
]
}
],
"source": [
"f1 = open('test.txt')\n",
"f2 = open('test2.txt')\n",
"while True: # Otan sbhsei o hlios (h' brei to break)\n",
" \n",
" l1 = f1.readline()\n",
" l2 = f2.readline()\n",
" \n",
" if not l1 or not l2:\n",
" break\n",
" \n",
" #if not all([l1, l2]):\n",
" # break\n",
" \n",
" l1=l1.replace('\\n', '')\n",
" l2=l2.replace('\\n', '')\n",
" print (l1 + ' ' + l2)\n",
"f1.close()\n",
"f2.close()"
]
},
{
"cell_type": "code",
"execution_count": 93,
"metadata": {},
"outputs": [
{
"ename": "FileNotFoundError",
"evalue": "[Errno 2] No such file or directory: 'myfile.txt'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-93-0f22dbd670d4>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'myfile.txt'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: 'myfile.txt'"
]
}
],
"source": [
"f = open('myfile.txt')"
]
},
{
"cell_type": "code",
"execution_count": 94,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'w')"
]
},
{
"cell_type": "code",
"execution_count": 95,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"11"
]
},
"execution_count": 95,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.write('hello world')"
]
},
{
"cell_type": "code",
"execution_count": 96,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 106,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'w')"
]
},
{
"cell_type": "code",
"execution_count": 107,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"12"
]
},
"execution_count": 107,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.write('hello world\\n') "
]
},
{
"cell_type": "code",
"execution_count": 99,
"metadata": {},
"outputs": [],
"source": [
"# DO NOT DO IT \n",
"f.flush()"
]
},
{
"cell_type": "code",
"execution_count": 108,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# DO NOT OPEN A FILE THAT ALREDY EXISTS BECUSE YOY KILL IT!"
]
},
{
"cell_type": "code",
"execution_count": 105,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'r') # READ"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'w') # WRITE "
]
},
{
"cell_type": "code",
"execution_count": 109,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'a') # APPEND "
]
},
{
"cell_type": "code",
"execution_count": 110,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"12"
]
},
"execution_count": 110,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.write('Hello again\\n')"
]
},
{
"cell_type": "code",
"execution_count": 112,
"metadata": {},
"outputs": [],
"source": [
"f.close()"
]
},
{
"cell_type": "code",
"execution_count": 114,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'r') # READ"
]
},
{
"cell_type": "code",
"execution_count": 115,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'he'"
]
},
"execution_count": 115,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.readline(2)"
]
},
{
"cell_type": "code",
"execution_count": 118,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'world\\n'"
]
},
"execution_count": 118,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.readline(10)"
]
},
{
"cell_type": "code",
"execution_count": 119,
"metadata": {},
"outputs": [],
"source": [
"with open('myfile.txt', 'w') as f:\n",
" f.write('Hello World\\n')"
]
},
{
"cell_type": "code",
"execution_count": 120,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<function TextIOWrapper.seek(cookie, whence=0, /)>"
]
},
"execution_count": 120,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.seek"
]
},
{
"cell_type": "code",
"execution_count": 121,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'r')"
]
},
{
"cell_type": "code",
"execution_count": 122,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Hello World\r\n"
]
}
],
"source": [
"!cat myfile.txt"
]
},
{
"cell_type": "code",
"execution_count": 123,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"5"
]
},
"execution_count": 123,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.seek(5)"
]
},
{
"cell_type": "code",
"execution_count": 124,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"' '"
]
},
"execution_count": 124,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.read(1)"
]
},
{
"cell_type": "code",
"execution_count": 126,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2"
]
},
"execution_count": 126,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.seek(2)"
]
},
{
"cell_type": "code",
"execution_count": 127,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'l'"
]
},
"execution_count": 127,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.read(1)"
]
},
{
"cell_type": "code",
"execution_count": 130,
"metadata": {},
"outputs": [],
"source": [
"f = open('myfile.txt', 'br') # RANDOM ACCESS "
]
},
{
"cell_type": "code",
"execution_count": 131,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2"
]
},
"execution_count": 131,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.seek(2)"
]
},
{
"cell_type": "code",
"execution_count": 132,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"1"
]
},
"execution_count": 132,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f.seek(1)"
]
},
{
"cell_type": "code",
"execution_count": 133,
"metadata": {},
"outputs": [
{
"ename": "OSError",
"evalue": "[Errno 22] Invalid argument",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mOSError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-133-8500f1a071a0>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mseek\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mOSError\u001b[0m: [Errno 22] Invalid argument"
]
}
],
"source": [
"f.seek(-1)"
]
},
{
"cell_type": "code",
"execution_count": 135,
"metadata": {},
"outputs": [],
"source": [
"fn = '/Users/antonakd/Downloads/SnpEff_vcf.vcf'"
]
},
{
"cell_type": "code",
"execution_count": 137,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" 197 /Users/antonakd/Downloads/SnpEff_vcf.vcf\r\n"
]
}
],
"source": [
"!wc -l $fn"
]
},
{
"cell_type": "code",
"execution_count": 143,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"197\n"
]
}
],
"source": [
"with open(fn) as f:\n",
" c = 0\n",
" for l in f:\n",
" c+=1\n",
"print (c)\n"
]
},
{
"cell_type": "code",
"execution_count": 142,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"197"
]
},
"execution_count": 142,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(open(fn).readlines())"
]
},
{
"cell_type": "code",
"execution_count": 145,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"37\n"
]
}
],
"source": [
"with open(fn) as f:\n",
" c = 0\n",
" for l in f:\n",
" if l[0] == '#':\n",
" continue\n",
" c +=1 \n",
"print (c)"
]
},
{
"cell_type": "code",
"execution_count": 148,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['chr19', '617614', '.', 'G', 'A', '39.2648', '.', 'AB=0.6;ABP=3.44459;AC=1;AF=0.166667;AN=6;AO=3;CIGAR=1X;DP=13;DPB=13;DPRA=1.25;EPP=3.73412;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=4.75716;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=108;QR=396;RO=10;RPL=2;RPP=3.73412;RPPR=3.87889;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=6;SRP=3.87889;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=A|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|19/21|c.3537C>T|p.Ile1179Ile|3622/3829|3537/3693|1179/1230||,A|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding|4/6|c.276C>T|p.Ile92Ile|277/429|276/428|92/141||WARNING_TRANSCRIPT_INCOMPLETE,A|sequence_feature|LOW|POLRMT|ENSG00000099821|helix:combinatorial_evidence_used_in_manual_assertion|ENST00000588649|protein_coding|19/21|c.3537C>T||||||,A|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-455C>T|||||455|,A|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*1140G>A|||||455|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*3986C>T|||||3986|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*4921C>T|||||4921|,A|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron|2/4|n.254C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron|2/4|n.1020C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron|1/3|n.189C>T||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:26.7276:5:5,0:5:198:0:0:0,-1.50515,-18.1978', '0/1:39.2625:5:2,3:2:78:3:108:-8.56857,0,-5.89832', '0/0:20.707:3:3,0:3:120:0:0:0,-0.90309,-11.1879']\n",
"['chr19', '617804', '.', 'G', 'A', '0.309945', '.', 'AB=0.4;ABP=3.44459;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=15;DPB=15;DPRA=1;EPP=7.35324;EPPR=4.51363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=2.60418;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=51;QR=408;RO=13;RPL=1;RPP=3.0103;RPPR=4.51363;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=A|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|3SPA:A_829-A_1156:ENST00000588649|protein_coding|18/21|c.3468C>T||||||,A|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|4BOC:A_829-A_1156:ENST00000588649|protein_coding|18/21|c.3468C>T||||||,A|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|18/21|c.3468C>T|p.His1156His|3553/3829|3468/3693|1156/1230||,A|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding|3/6|c.207C>T|p.His69His|208/429|207/428|69/141||WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-645C>T|||||645|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2C>T|||||2|,A|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*1330G>A|||||645|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*3796C>T|||||3796|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*4731C>T|||||4731|,A|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron|1/4|n.185C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron|2/4|n.830C>T||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/1:0.309894:5:3,2:3:81:2:51:-3.33658,0,-6.05049', '0/0:52.6447:5:5,0:5:136:0:0:0,-1.50515,-12.503', '0/0:52.6447:5:5,0:5:191:0:0:0,-1.50515,-17.5583']\n",
"['chr19', '617959', '.', 'A', 'C', '0.0608339', '.', 'AB=0.666667;ABP=3.73412;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0.75;EPP=7.35324;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=4.26547;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=345;RO=9;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=9.04217;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-800T>G|||||800|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-157T>G|||||157|,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*1485A>C|||||800|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*3641T>G|||||3641|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*4576T>G|||||4576|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|17/20|c.3423-110T>G||||||,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding|2/5|c.141-89T>G||||||WARNING_TRANSCRIPT_INCOMPLETE,C|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron|1/4|n.30T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron|2/4|n.675T>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:43.2077:3:3,0:3:114:0:0:0,-0.90309,-10.6322', '0/1:0.0605699:3:1,2:1:36:2:43:-3.18125,0,-2.69518', '0/0:49.2283:5:5,0:5:195:0:0:0,-1.50515,-17.9233']\n",
"['chr19', '618159', '.', 'A', 'G', '193.704', '.', 'AB=0.333333;ABP=3.73412;AC=5;AF=0.833333;AN=6;AO=7;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.32051;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=1.41038;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=265;QR=50;RO=2;RPL=2;RPP=5.80219;RPPR=7.35324;RPR=5;RUN=1;SAF=5;SAP=5.80219;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-1000T>C|||||1000|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-171T>C|||||171|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-357T>C|||||357|,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*1685A>G|||||1000|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*3441T>C|||||3441|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*4376T>C|||||4376|,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|17/20|c.3423-310T>C||||||,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding|2/5|c.141-289T>C||||||WARNING_TRANSCRIPT_INCOMPLETE,G|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron|2/4|n.475T>C||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '1/1:48.5333:5:0,5:0:0:5:191:-17.5572,-1.50515,0', '1/1:36.4921:1:0,1:0:0:1:35:-3.49863,-0.30103,0', '0/1:0.948127:3:2,1:2:50:1:39:-2.99347,0,-3.84484']\n",
"['chr19', '618428', '.', 'T', 'G', '1.87498E-5', '.', 'AB=0;ABP=0;AC=0;AF=0;AN=6;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=1.06667;EPP=7.35324;EPPR=5.59539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=12.5477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=673;RO=21;RPL=0;RPP=7.35324;RPPR=3.94093;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=11;SRP=3.1137;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-1269A>C|||||1269|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-440A>C|||||440|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-626A>C|||||626|,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*1954T>G|||||1269|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*3172A>C|||||3172|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*4107A>C|||||4107|,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|17/20|c.3422+60A>C||||||,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding|2/5|c.140+60A>C||||||WARNING_TRANSCRIPT_INCOMPLETE,G|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron|2/4|n.206A>C||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:61.6796:6:6,0:6:210:0:0:0,-1.80618,-19.2357', '0/0:70.7105:9:9,0:9:253:0:0:0,-2.70927,-23.0382', '0/0:54.4939:8:6,2:6:210:2:24:0,-0.128252,-16.9518']\n",
"['chr19', '618851', '.', 'T', 'C', '74.4613', '.', 'AB=0.555556;ABP=3.25157;AC=1;AF=0.166667;AN=6;AO=5;CIGAR=1X2M1X;DP=15;DPB=15;DPRA=3;EPP=3.44459;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=2.67772;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=169;QR=312;RO=10;RPL=3;RPP=3.44459;RPPR=6.48466;RPR=2;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;technology.ILLUMINA=1;Split', 'primitives;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-1692A>G|||||1692|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-4668T>C|||||4668|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-863A>G|||||863|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-100A>G|||||100|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-1049A>G|||||1049|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-106A>G|||||105|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*2377T>C|||||1692|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*2749A>G|||||2749|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*3684A>G|||||3684|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*4610A>G|||||4610|WARNING_TRANSCRIPT_INCOMPLETE,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|15/20|c.3268-91A>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0|0:11.9871:2:2,0:2:75:0:0:0,-0.60206,-7.11959', '0|1:74.4611:9:4,5:4:142:5:169:-12.8298,0,-10.417', '0|0:18.0077:4:4,0:4:95:0:0:0,-1.20412,-8.78697']\n",
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"['chr19', '618911', '.', 'T', 'G', '2.88308E-4', '.', 'AB=0.5;ABP=3.0103;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=15;DPB=15;DPRA=0.727273;EPP=7.35324;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=10.0709;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=434;RO=13;RPL=2;RPP=7.35324;RPPR=4.51363;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-1752A>C|||||1752|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-4608T>G|||||4608|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-923A>C|||||923|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-160A>C|||||160|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-1109A>C|||||1109|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-166A>C|||||165|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*2437T>G|||||1752|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*2689A>C|||||2689|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*3624A>C|||||3624|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*4550A>C|||||4550|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|15/20|c.3267+86A>C||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:46.3144:3:3,0:3:117:0:0:0,-0.90309,-10.9104', '0/0:61.3659:8:8,0:8:245:0:0:0,-2.40824,-22.3421', '0/1:0.000183661:4:2,2:2:72:2:20:-0.695873,0,-5.6326']\n",
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"['chr19', '619408', '.', 'A', 'G', '207.722', '.', 'AB=0.285714;ABP=5.80219;AC=4;AF=0.666667;AN=6;AO=8;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=4.09604;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=4.61534;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=312;QR=191;RO=5;RPL=5;RPP=4.09604;RPPR=3.44459;RPR=3;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=2;SRP=3.44459;SRR=3;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-2249T>C|||||2249|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-4111A>G|||||4111|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-1420T>C|||||1420|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-657T>C|||||657|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-1606T>C|||||1606|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-663T>C|||||662|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*2934A>G|||||2249|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*2192T>C|||||2192|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*3127T>C|||||3127|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*4053T>C|||||4053|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|13/20|c.3067-112T>C||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '1/1:20.0884:6:0,6:0:0:6:232:-21.2475,-1.80618,0', '0/1:35.7986:4:3,1:3:112:1:40:-2.79156,0,-9.24161', '0/1:40.7778:3:2,1:2:79:1:40:-3.09259,0,-6.59454']\n",
"['chr19', '619574', '.', 'T', 'G', '594.095', '.', 'AB=0;ABP=0;AC=6;AF=1;AN=6;AO=18;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=4.9405;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=3;NUMALT=1;ODDS=10.8827;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=679;QR=0;RO=0;RPL=9;RPP=3.0103;RPPR=0;RPR=9;RUN=1;SAF=12;SAP=7.35324;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-2415A>C|||||2415|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3945T>G|||||3945|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-1586A>C|||||1586|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-823A>C|||||823|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-1772A>C|||||1772|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-829A>C|||||828|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3100T>G|||||2415|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*2026A>C|||||2026|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2961A>C|||||2961|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3887A>C|||||3887|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|13/20|c.3066+12A>C||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '1/1:62.3145:7:0,7:0:0:7:270:-24.6643,-2.10721,0', '1/1:68.3351:9:0,9:0:0:9:329:-29.9508,-2.70927,0', '1/1:47.263:2:0,2:0:0:2:80:-7.59179,-0.60206,0']\n",
"['chr19', '619772', '.', 'G', 'C', '612.352', '.', 'AB=0.75;ABP=5.18177;AC=5;AF=0.833333;AN=6;AO=20;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=9.95901;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=9.77621;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=709;QR=16;RO=1;RPL=10;RPP=3.0103;RPPR=5.18177;RPR=10;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C|splice_region_variant&intron_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|12/20|c.2887-7C>G||||||,C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-2613C>G|||||2613|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3747G>C|||||3747|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-1784C>G|||||1784|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1021C>G|||||1021|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-1970C>G|||||1970|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1027C>G|||||1026|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3298G>C|||||2613|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1828C>G|||||1828|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2763C>G|||||2763|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3689C>G|||||3689|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4953C>G|||||4953|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '1/1:45.8366:1:0,1:0:0:1:38:-3.79727,-0.30103,0', '1/1:90.9911:16:0,16:0:0:16:556:-50.351,-4.81648,0', '0/1:0.000246608:4:1,3:1:16:3:115:-9.51987,0,-0.395863']\n",
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"['chr19', '620004', '.', 'T', 'C', '0.00524165', '.', 'AB=0.375;ABP=4.09604;AC=2;AF=0.333333;AN=6;AO=3;CIGAR=1X;DP=17;DPB=17;DPRA=0.444444;EPP=3.73412;EPPR=8.59409;GTI=1;LEN=1;MEANALT=1;MQM=55.3333;MQMR=60;NS=3;NUMALT=1;ODDS=6.80257;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=473;RO=14;RPL=3;RPP=9.52472;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|12/21|c.2840A>G|p.Glu947Gly|2925/3829|2840/3693|947/1230||,C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-2845A>G|||||2845|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3515T>C|||||3515|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2016A>G|||||2016|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1253A>G|||||1253|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2202A>G|||||2202|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1259A>G|||||1258|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3530T>C|||||2845|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1596A>G|||||1596|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2531A>G|||||2531|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3457A>G|||||3457|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4721A>G|||||4721|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/1:0.000418338:3:2,1:2:50:1:12:-0.296904,0,-3.84636', '0/0:65.173:9:9,0:9:314:0:0:0,-2.70927,-28.5884', '0/1:0.00482153:5:3,2:3:109:2:32:-1.53443,0,-8.66185']\n",
"['chr19', '620045', '.', 'A', 'T', '15.5734', '.', 'AB=0.4;ABP=3.44459;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=19;DPB=19;DPRA=0.714286;EPP=3.0103;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.125;NS=3;NUMALT=1;ODDS=3.55758;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=489;RO=16;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=3.55317;SRR=9;TYPE=snp;technology.ILLUMINA=1;ANN=T|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|12/21|c.2799T>A|p.Ala933Ala|2884/3829|2799/3693|933/1230||,T|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-2886T>A|||||2886|,T|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3474A>T|||||3474|,T|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2057T>A|||||2057|,T|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1294T>A|||||1294|,T|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2243T>A|||||2243|,T|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1300T>A|||||1299|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3571A>T|||||2886|,T|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1555T>A|||||1555|,T|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2490T>A|||||2490|,T|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3416T>A|||||3416|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4680T>A|||||4680|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/1:15.5734:5:3,2:3:80:2:80:-6.08664,0,-5.9578', '0/0:41.6492:7:7,0:7:217:0:0:0,-2.10721,-19.8258', '0/0:38.6389:7:6,0:6:192:0:0:0,-1.80618,-17.4415']\n",
"['chr19', '620201', '.', 'A', 'C', '5.61107E-5', '.', 'AB=0.333333;ABP=4.45795;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0.75;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=11.2888;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=641;RO=20;RPL=2;RPP=7.35324;RPPR=3.44459;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3042T>G|||||3042|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3318A>C|||||3318|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2213T>G|||||2213|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1450T>G|||||1450|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2399T>G|||||2399|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1456T>G|||||1455|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3727A>C|||||3042|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1399T>G|||||1399|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2334T>G|||||2334|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3260T>G|||||3260|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4524T>G|||||4524|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/20|c.2764-121T>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:66.9084:8:8,0:8:239:0:0:0,-2.40824,-21.794', '0/0:66.9084:8:8,0:8:278:0:0:0,-2.40824,-25.3466', '0/1:5.43407e-05:6:4,2:4:124:2:23:-0.378809,0,-9.65542']\n",
"['chr19', '620210', '.', 'A', 'C', '1.63995E-5', '.', 'AB=0;ABP=0;AC=0;AF=0;AN=6;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=1.2;EPP=7.35324;EPPR=6.56362;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=12.6061;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=658;RO=22;RPL=1;RPP=3.0103;RPPR=3.40511;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=12;SRP=3.40511;SRR=10;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3051T>G|||||3051|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3309A>C|||||3309|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2222T>G|||||2222|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1459T>G|||||1459|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2408T>G|||||2408|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1465T>G|||||1464|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3736A>C|||||3051|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1390T>G|||||1390|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2325T>G|||||2325|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3251T>G|||||3251|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4515T>G|||||4515|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/20|c.2764-130T>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:54.7475:9:7,2:7:215:2:21:0,-0.714278,-17.6473', '0/0:68.492:8:8,0:8:271:0:0:0,-2.40824,-24.7089', '0/0:65.4817:7:7,0:7:172:0:0:0,-2.10721,-15.7183']\n",
"['chr19', '620214', '.', 'T', 'C', '3.42253E-5', '.', 'AB=0.285714;ABP=5.80219;AC=1;AF=0.166667;AN=6;AO=3;CIGAR=1X;DP=25;DPB=25;DPRA=0.888889;EPP=9.52472;EPPR=9.32731;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=11.9498;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=723;RO=22;RPL=3;RPP=9.52472;RPPR=3.40511;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3055A>G|||||3055|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3305T>C|||||3305|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2226A>G|||||2226|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1463A>G|||||1463|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2412A>G|||||2412|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1469A>G|||||1468|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3740T>C|||||3055|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1386A>G|||||1386|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2321A>G|||||2321|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3247A>G|||||3247|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4511A>G|||||4511|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/20|c.2764-134A>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:71.5023:9:9,0:9:270:0:0:0,-2.70927,-24.5838', '0/0:58.6976:9:8,1:8:275:1:16:0,-1.10929,-23.4748', '0/1:2.80562e-05:7:5,2:5:178:2:24:-0.172778,0,-14.2578']\n",
"['chr19', '620228', '.', 'A', 'C', '8.62681E-4', '.', 'AB=0.176471;ABP=18.4661;AC=2;AF=0.333333;AN=6;AO=3;CIGAR=1X;DP=26;DPB=26;DPRA=0.944444;EPP=3.73412;EPPR=7.63648;GTI=1;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=8.73081;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=791;RO=23;RPL=2;RPP=3.73412;RPPR=3.10471;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=12;SRP=3.10471;SRR=11;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3069T>G|||||3069|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3291A>C|||||3291|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2240T>G|||||2240|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1477T>G|||||1477|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2426T>G|||||2426|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1483T>G|||||1482|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3754A>C|||||3069|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1372T>G|||||1372|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2307T>G|||||2307|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3233T>G|||||3233|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4497T>G|||||4497|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/20|c.2763+137T>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:72.2949:9:9,0:9:283:0:0:0,-2.70927,-25.763', '0/1:0.000160961:9:8,1:8:298:1:31:-0.390184,0,-24.4572', '0/1:0.000701438:8:6,2:6:210:2:36:-1.0117,0,-16.8236']\n",
"['chr19', '620299', '.', 'C', 'A', '6.06919', '.', 'AB=0.25;ABP=7.35324;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=20;DPB=20;DPRA=1.33333;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=1.11328;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=79;QR=682;RO=18;RPL=0;RPP=7.35324;RPPR=4.9405;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=12;SRP=7.35324;SRR=6;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3140G>T|||||3140|,A|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3220C>A|||||3220|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2311G>T|||||2311|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1548G>T|||||1548|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2497G>T|||||2497|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1554G>T|||||1553|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3825C>A|||||3140|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1301G>T|||||1301|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2236G>T|||||2236|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3162G>T|||||3162|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4426G>T|||||4426|,A|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/20|c.2763+66G>T||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:44.6987:7:7,0:7:275:0:0:0,-2.10721,-25.1191', '0/0:38.6781:5:5,0:5:183:0:0:0,-1.50515,-16.8258', '0/1:6.06919:8:6,2:6:224:2:79:-5.08939,0,-18.108']\n",
"['chr19', '620315', '.', 'A', 'C', '3.3417E-4', '.', 'AB=0.2;ABP=10.8276;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=1.53846;EPP=7.35324;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=9.4857;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=748;RO=21;RPL=1;RPP=3.0103;RPPR=8.07707;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=5.59539;SRR=8;TYPE=snp;technology.ILLUMINA=1;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3156T>G|||||3156|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3204A>C|||||3204|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2327T>G|||||2327|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1564T>G|||||1564|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2513T>G|||||2513|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1570T>G|||||1569|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3841A>C|||||3156|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1285T>G|||||1285|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2220T>G|||||2220|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3146T>G|||||3146|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4410T>G|||||4410|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/20|c.2763+50T>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:64.6902:7:7,0:7:243:0:0:0,-2.10721,-22.204', '0/0:61.6799:6:6,0:6:222:0:0:0,-1.80618,-20.3339', '0/1:0.000329745:10:8,2:8:283:2:38:-0.599489,0,-22.7972']\n",
"['chr19', '620381', '.', 'T', 'G', '5.01393E-4', '.', 'AB=0.1875;ABP=16.582;AC=2;AF=0.333333;AN=6;AO=4;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=11.6962;EPPR=7.63648;GTI=1;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=9.27648;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=693;RO=23;RPL=3;RPP=5.18177;RPPR=3.10471;RPR=1;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=9;SRP=5.3706;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=G|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|3SPA:A_827-A_916:ENST00000588649|protein_coding|11/21|c.2747A>C||||||,G|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|4BOC:A_827-A_916:ENST00000588649|protein_coding|11/21|c.2747A>C||||||,G|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/21|c.2747A>C|p.His916Pro|2832/3829|2747/3693|916/1230||,G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3222A>C|||||3222|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3138T>G|||||3138|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2393A>C|||||2393|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1630A>C|||||1630|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2579A>C|||||2579|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1636A>C|||||1635|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3907T>G|||||3222|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1219A>C|||||1219|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2154A>C|||||2154|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3080A>C|||||3080|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4344A>C|||||4344|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/1:9.44043e-05:9:7,2:7:232:2:30:-0.140693,0,-18.4911', '0/1:0.000406473:7:6,1:6:174:1:29:-0.792446,0,-13.8312', '0/0:69.3256:11:10,1:10:287:1:12:0,-2.11134,-24.8964']\n",
"['chr19', '620414', '.', 'A', 'C', '6.37073E-6', '.', 'AB=0;ABP=0;AC=0;AF=0;AN=6;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=1.5;EPP=9.52472;EPPR=10.0459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=13.6058;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=676;RO=25;RPL=2;RPP=3.73412;RPPR=3.09716;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=8;SRP=10.0459;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/21|c.2714T>G|p.Val905Gly|2799/3829|2714/3693|905/1230||,C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3255T>G|||||3255|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3105A>C|||||3105|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2426T>G|||||2426|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1663T>G|||||1663|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2612T>G|||||2612|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1669T>G|||||1668|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3940A>C|||||3255|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1186T>G|||||1186|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2121T>G|||||2121|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3047T>G|||||3047|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4311T>G|||||4311|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:59.0893:10:8,2:8:197:2:21:0,-1.01531,-15.9734', '0/0:67.8571:7:7,0:7:208:0:0:0,-2.10721,-19.0035', '0/0:71.561:11:10,1:10:271:1:11:0,-2.21133,-23.5461']\n",
"['chr19', '620429', '.', 'T', 'C', '2.46975E-5', '.', 'AB=0;ABP=0;AC=0;AF=0;AN=6;AO=4;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=11.6962;EPPR=9.32731;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=12.7169;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=54;QR=654;RO=22;RPL=3;RPP=5.18177;RPPR=3.40511;RPR=1;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=5;SRP=17.2236;SRR=17;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/21|c.2699A>G|p.Glu900Gly|2784/3829|2699/3693|900/1230||,C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3270A>G|||||3270|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3090T>C|||||3090|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2441A>G|||||2441|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1678A>G|||||1678|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2627A>G|||||2627|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1684A>G|||||1683|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3955T>C|||||3270|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1171A>G|||||1171|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2106A>G|||||2106|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3032A>G|||||3032|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4296A>G|||||4296|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:62.6975:9:8,1:8:206:1:12:0,-1.50928,-17.5903', '0/0:56.6769:7:6,1:6:192:1:12:0,-0.907216,-16.3901', '0/0:55.2286:10:8,2:8:256:2:30:0,-0.160332,-20.4918']\n",
"['chr19', '620454', '.', 'A', 'C', '4.25049E-5', '.', 'AB=0.222222;ABP=9.04217;AC=1;AF=0.166667;AN=6;AO=3;CIGAR=1X;DP=24;DPB=24;DPRA=1.21429;EPP=9.52472;EPPR=11.386;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=11.7097;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=43;QR=730;RO=21;RPL=3;RPP=9.52472;RPPR=3.94093;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=5;SRP=15.5221;SRR=16;TYPE=snp;technology.ILLUMINA=1;ANN=C|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|3SPA:A_729-A_892:ENST00000588649|protein_coding|11/21|c.2674T>G||||||,C|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|3SPA:A_819-A_892:ENST00000588649|protein_coding|11/21|c.2674T>G||||||,C|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|4BOC:A_729-A_892:ENST00000588649|protein_coding|11/21|c.2674T>G||||||,C|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|4BOC:A_819-A_892:ENST00000588649|protein_coding|11/21|c.2674T>G||||||,C|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/21|c.2674T>G|p.Trp892Gly|2759/3829|2674/3693|892/1230||,C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3295T>G|||||3295|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3065A>C|||||3065|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2466T>G|||||2466|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1703T>G|||||1703|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2652T>G|||||2652|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1709T>G|||||1708|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3980A>C|||||3295|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1146T>G|||||1146|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2081T>G|||||2081|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3007T>G|||||3007|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4271T>G|||||4271|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:59.0885:8:7,1:7:213:1:12:0,-1.20825,-18.2624', '0/0:64.6899:7:7,0:7:255:0:0:0,-2.10721,-23.2976', '0/1:3.56726e-05:9:7,2:7:262:2:31:-0.235692,0,-21.2264']\n",
"['chr19', '620459', '.', 'T', 'C', '4.96425E-5', '.', 'AB=0.285714;ABP=5.80219;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=0.875;EPP=7.35324;EPPR=11.386;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=11.4171;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=648;RO=21;RPL=0;RPP=7.35324;RPPR=3.1137;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=7;SRP=8.07707;SRR=14;TYPE=snp;technology.ILLUMINA=1;ANN=C|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|11/21|c.2669A>G|p.Glu890Gly|2754/3829|2669/3693|890/1230||,C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3300A>G|||||3300|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-3060T>C|||||3060|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2471A>G|||||2471|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1708A>G|||||1708|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2657A>G|||||2657|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1714A>G|||||1713|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*3985T>C|||||3300|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*1141A>G|||||1141|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*2076A>G|||||2076|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*3002A>G|||||3002|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*4266A>G|||||4266|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:64.6899:7:7,0:7:158:0:0:0,-2.10721,-14.4402', '0/1:4.77987e-05:7:5,2:5:194:2:26:-0.362773,0,-15.7252', '0/0:70.7105:9:9,0:9:296:0:0:0,-2.70927,-26.9543']\n",
"['chr19', '620728', '.', 'A', 'G', '0.0198511', '.', 'AB=0.428571;ABP=3.32051;AC=2;AF=0.333333;AN=6;AO=3;CIGAR=1X;DP=8;DPB=8;DPRA=3.5;EPP=9.52472;EPPR=3.44459;GTI=1;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=5.52895;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=136;RO=5;RPL=0;RPP=9.52472;RPPR=3.44459;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3569T>C|||||3569|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2791A>G|||||2791|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2740T>C|||||2740|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-1977T>C|||||1977|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-2926T>C|||||2926|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-1983T>C|||||1982|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4254A>G|||||3569|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*872T>C|||||872|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1807T>C|||||1807|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2733T>C|||||2733|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3997T>C|||||3997|,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/20|c.2641-241T>C||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/1:0.0171975:3:2,1:2:51:1:25:-1.59677,0,-3.93864', '0/1:0.000904826:4:2,2:2:45:2:28:-1.45586,0,-3.07005', '0/0:33.9788:1:1,0:1:40:0:0:0,-0.30103,-3.99568']\n",
"['chr19', '620807', '.', 'G', 'A', '41.4442', '.', 'AB=0.6;ABP=3.44459;AC=2;AF=0.333333;AN=6;AO=3;CIGAR=1X;DP=6;DPB=6;DPRA=2.5;EPP=9.52472;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=0.52212;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=80;RO=3;RPL=2;RPP=3.73412;RPPR=9.52472;RPR=1;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=A|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3648C>T|||||3648|,A|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2712G>A|||||2712|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-2819C>T|||||2819|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2056C>T|||||2056|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3005C>T|||||3005|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2062C>T|||||2061|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4333G>A|||||3648|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*793C>T|||||793|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1728C>T|||||1728|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2654C>T|||||2654|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3918C>T|||||3918|,A|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/20|c.2640+251C>T||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/1:5.1796:3:1,2:1:14:2:79:-6.59454,0,-0.4969', '0/1:6.36461:2:1,1:1:39:1:40:-3.39362,0,-3.2945', '0/0:3.13964:1:1,0:1:27:0:0:0,-0.30103,-2.69978']\n",
"['chr19', '620926', '.', 'GGGCGCCAGGGGAGGGGGAGGGGAGGAGGAAGACGGGCAGGGGGCGCGGGGGCGCCGGGGGAG', 'G', '0.005508', '.', 'AB=0;ABP=0;AC=2;AF=0.333333;AN=6;AO=2;CIGAR=1M62D1M;DP=5;DPB=3.0625;DPRA=1.33333;EPP=7.35324;EPPR=9.52472;GTI=0;LEN=62;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=7.45472;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=114;RO=3;RPL=0;RPP=7.35324;RPPR=9.52472;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=del;technology.ILLUMINA=1;Split', 'primitives;ANN=G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3829_-3768delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||3768|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2592_-2531delGGCGCCAGGGGAGGGGGAGGGGAGGAGGAAGACGGGCAGGGGGCGCGGGGGCGCCGGGGGAG|||||2592|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3000_-2939delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||2939|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2237_-2176delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||2176|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3186_-3125delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||3125|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2243_-2182delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||2181|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4453_*4514delGGCGCCAGGGGAGGGGGAGGGGAGGAGGAAGACGGGCAGGGGGCGCGGGGGCGCCGGGGGAG|||||3768|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*612_*673delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||673|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1547_*1608delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||1608|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2473_*2534delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||2534|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3737_*3798delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC|||||3798|,G|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/20|c.2640+70_2640+131delCTCCCCCGGCGCCCCCGCGCCCCCTGCCCGTCTTCCTCCTCCCCTCCCCCTCCCCTGGCGCC||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0|0:32.3807:1:1,0:1:39:0:0:0,-0.30103,-3.89656', '0|0:35.3909:2:2,0:2:75:0:0:0,-0.60206,-7.1201', '1|1:0.00013179:2:0,2:0:0:2:26:-2.46998,-0.60206,0']\n",
"['chr19', '620999', '.', 'CGCCGGGGGAGGGCGCGGGGGT', 'C', '86.6194', '.', 'AB=0.5;ABP=3.0103;AC=3;AF=0.5;AN=6;AO=3;CIGAR=1M21D1M;DP=11;DPB=8.17391;DPRA=0;EPP=9.52472;EPPR=7.35324;GTI=1;LEN=21;MEANALT=2;MQM=60;MQMR=60;NS=3;NUMALT=2;ODDS=1.32176;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=87;QR=77;RO=2;RPL=0;RPP=9.52472;RPPR=7.35324;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=2;SRP=7.35324;SRR=0;TYPE=del;technology.ILLUMINA=1;Split', 'primitives;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3861_-3841delACCCCCGCGCCCTCCCCCGGC|||||3841|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2519_-2499delGCCGGGGGAGGGCGCGGGGGT|||||2519|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3032_-3012delACCCCCGCGCCCTCCCCCGGC|||||3012|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2269_-2249delACCCCCGCGCCCTCCCCCGGC|||||2249|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3218_-3198delACCCCCGCGCCCTCCCCCGGC|||||3198|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2275_-2255delACCCCCGCGCCCTCCCCCGGC|||||2254|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4526_*4546delGCCGGGGGAGGGCGCGGGGGT|||||3841|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*580_*600delACCCCCGCGCCCTCCCCCGGC|||||600|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1515_*1535delACCCCCGCGCCCTCCCCCGGC|||||1535|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2441_*2461delACCCCCGCGCCCTCCCCCGGC|||||2461|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3705_*3725delACCCCCGCGCCCTCCCCCGGC|||||3725|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/20|c.2640+38_2640+58delACCCCCGCGCCCTCCCCCGGC||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '1|1:0.971645:1:0,0,1:0:0:0,1:0,34:-3.39891,-3.39891,-3.39891,-0.30103,-0.30103,0', '0|1:16.9454:4:0,1,2:0:0:1,2:40,53:-7.61723,-4.27472,-3.97369,-3.44487,0,-2.84281', '0|0:25.3149:6:2,3,0:2:77:3,0:104,0:-8.03444,0,-5.60909,-8.6365,-6.51218,-14.9922']\n",
"['chr19', '621020', '.', 'T', 'C', '86.6194', '.', 'AB=0.4;ABP=3.87889;AC=2;AF=0.333333;AN=6;AO=4;CIGAR=21M1X1M;DP=11;DPB=8.17391;DPRA=5;EPP=3.0103;EPPR=7.35324;GTI=1;LEN=1;MEANALT=2.5;MQM=60;MQMR=60;NS=3;NUMALT=2;ODDS=1.32176;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=144;QR=77;RO=2;RPL=2;RPP=3.0103;RPPR=7.35324;RPR=2;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=2;SRP=7.35324;SRR=0;TYPE=snp;technology.ILLUMINA=1;Split', 'primitives;ANN=C|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3861A>G|||||3861|,C|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2499T>C|||||2499|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3032A>G|||||3032|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2269A>G|||||2269|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3218A>G|||||3218|,C|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2275A>G|||||2274|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4546T>C|||||3861|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*580A>G|||||580|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1515A>G|||||1515|,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2441A>G|||||2441|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3705A>G|||||3705|,C|intron_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/20|c.2640+38A>G||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0|0:0.971645:1:0,0,1:0:0:0,1:0,34:-3.39891,-3.39891,-3.39891,-0.30103,-0.30103,0', '1|0:16.9454:4:0,1,2:0:0:1,2:40,53:-7.61723,-4.27472,-3.97369,-3.44487,0,-2.84281', '0|1:25.3149:6:2,3,0:2:77:3,0:104,0:-8.03444,0,-5.60909,-8.6365,-6.51218,-14.9922']\n",
"['chr19', '621063', '.', 'A', 'G', '10.9276', '.', 'AB=0.333333;ABP=4.45795;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=1;EPP=7.35324;EPPR=11.6962;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=2.43082;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=532;RO=16;RPL=1;RPP=3.0103;RPPR=7.89611;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=9;SRP=3.55317;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/21|c.2635T>C|p.Leu879Leu|2720/3829|2635/3693|879/1230||,G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3904T>C|||||3904|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2456A>G|||||2456|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3075T>C|||||3075|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2312T>C|||||2312|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3261T>C|||||3261|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2318T>C|||||2317|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4589A>G|||||3904|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*537T>C|||||537|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1472T>C|||||1472|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2398T>C|||||2398|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3662T>C|||||3662|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:29.8557:3:3,0:3:116:0:0:0,-0.90309,-10.8174', '0/1:10.9276:6:4,2:4:139:2:78:-5.59729,0,-11.0424', '0/0:47.9175:9:9,0:9:277:0:0:0,-2.70927,-25.2191']\n",
"['chr19', '621070', '.', 'G', 'A', '0.58651', '.', 'AB=0.333333;ABP=4.45795;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=1;EPP=7.35324;EPPR=11.6962;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=1.93393;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=595;RO=16;RPL=1;RPP=3.0103;RPPR=7.89611;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=9;SRP=3.55317;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=A|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|4BOC:A_876-A_906:ENST00000588649|protein_coding|10/21|c.2628C>T||||||,A|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/21|c.2628C>T|p.Asp876Asp|2713/3829|2628/3693|876/1230||,A|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-3911C>T|||||3911|,A|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2449G>A|||||2449|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3082C>T|||||3082|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2319C>T|||||2319|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3268C>T|||||3268|,A|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2325C>T|||||2324|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4596G>A|||||3911|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*530C>T|||||530|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1465C>T|||||1465|,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2391C>T|||||2391|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3655C>T|||||3655|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:49.2761:3:3,0:3:119:0:0:0,-0.90309,-11.0954', '0/1:0.58645:6:4,2:4:142:2:58:-3.70171,0,-11.3209', '0/0:67.3379:9:9,0:9:334:0:0:0,-2.70927,-30.4089']\n",
"['chr19', '621278', '.', 'T', 'G', '5.33025E-4', '.', 'AB=0;ABP=0;AC=0;AF=0;AN=6;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=3.2;EPP=7.35324;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=3;NUMALT=1;ODDS=9.60644;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=307;RO=11;RPL=1;RPP=3.0103;RPPR=3.20771;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=4.78696;SRR=7;TYPE=snp;technology.ILLUMINA=1;ANN=G|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/21|c.2420A>C|p.Tyr807Ser|2505/3829|2420/3693|807/1230||,G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-4119A>C|||||4119|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-2241T>G|||||2241|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3290A>C|||||3290|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2527A>C|||||2527|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3476A>C|||||3476|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2533A>C|||||2532|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*4804T>G|||||4119|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*322A>C|||||322|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*1257A>C|||||1257|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*2183A>C|||||2183|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3447A>C|||||3447|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:44.7311:3:3,0:3:80:0:0:0,-0.90309,-7.46441', '0/0:41.7208:2:2,0:2:79:0:0:0,-0.60206,-7.49763', '0/0:46.616:8:6,2:6:148:2:23:0,-0.223251,-11.3747']\n",
"['chr19', '621595', '.', 'T', 'G', '7.18569E-4', '.', 'AB=0.4;ABP=3.44459;AC=1;AF=0.166667;AN=6;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=1.66667;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.1111;NS=3;NUMALT=1;ODDS=9.5877;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=25;QR=316;RO=9;RPL=2;RPP=7.35324;RPPR=14.8328;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=3.25157;SRR=4;TYPE=snp;technology.ILLUMINA=1;ANN=G|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|3SPA:A_701-A_1136:ENST00000588649|protein_coding|10/21|c.2103A>C||||||,G|structural_interaction_variant|HIGH|POLRMT|ENSG00000099821|interaction|4BOC:A_701-A_1136:ENST00000588649|protein_coding|10/21|c.2103A>C||||||,G|missense_variant|MODERATE|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/21|c.2103A>C|p.Gln701His|2188/3829|2103/3693|701/1230||,G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-4436A>C|||||4436|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-1924T>G|||||1924|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3607A>C|||||3607|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2844A>C|||||2844|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3793A>C|||||3793|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2850A>C|||||2849|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*5121T>G|||||4436|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron||n.*5A>C|||||5|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*940A>C|||||940|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*1866A>C|||||1866|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3130A>C|||||3130|', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '0/0:43.1476:3:3,0:3:111:0:0:0,-0.90309,-10.3536', '0/1:0.000297744:5:3,2:3:86:2:25:-0.869836,0,-6.51545', '0/0:43.1476:3:3,0:3:119:0:0:0,-0.90309,-11.0922']\n",
"['chr19', '621712', '.', 'A', 'G', '424.361', '.', 'AB=0.428571;ABP=3.32051;AC=5;AF=0.833333;AN=6;AO=14;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=59.2857;MQMR=60;NS=3;NUMALT=1;ODDS=5.64974;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=544;QR=148;RO=4;RPL=6;RPP=3.63072;RPPR=3.0103;RPR=8;RUN=1;SAF=7;SAP=3.0103;SAR=7;SRF=2;SRP=3.0103;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=G|synonymous_variant|LOW|POLRMT|ENSG00000099821|transcript|ENST00000588649|protein_coding|10/21|c.1986T>C|p.Ala662Ala|2071/3829|1986/3693|662/1230||,G|upstream_gene_variant|MODIFIER|AC005559.2|ENSG00000266939|transcript|ENST00000591847|antisense||n.-4553T>C|||||4553|,G|upstream_gene_variant|MODIFIER|LLNLR-299G3.1|ENSG00000272448|transcript|ENST00000607288|antisense||n.-1807A>G|||||1807|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000592633|retained_intron||n.-3724T>C|||||3724|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000587057|retained_intron||n.-2961T>C|||||2961|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000589961|retained_intron||n.-3910T>C|||||3910|,G|upstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590336|protein_coding||c.-2967T>C|||||2966|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|HCN2|ENSG00000099822|transcript|ENST00000251287|protein_coding||c.*5238A>G|||||4553|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590709|retained_intron||n.*823T>C|||||823|,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000590573|protein_coding||c.*1749T>C|||||1749|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000588630|retained_intron||n.*3013T>C|||||3013|,G|non_coding_transcript_exon_variant|MODIFIER|POLRMT|ENSG00000099821|transcript|ENST00000586384|retained_intron|6/6|n.1214T>C||||||', 'GT:GQ:DP:AD:RO:QR:AO:QA:GL', '1/1:33.5846:7:0,7:0:0:7:272:-24.8465,-2.10721,0', '1/1:24.5537:4:0,4:0:0:4:156:-14.4095,-1.20412,0', '0/1:68.6139:7:4,3:4:148:3:116:-8.70733,0,-11.572']\n",
"37\n"
]
}
],
"source": [
"with open(fn) as f:\n",
" c = 0\n",
" for l in f:\n",
" if l[0] == '#':\n",
" continue\n",
" c +=1\n",
" \n",
" print (l.split())\n",
" \n",
"print (c)"
]
},
{
"cell_type": "code",
"execution_count": 151,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[{'chromosome': 'chr19', 'position': 617614}, {'chromosome': 'chr19', 'position': 617804}, {'chromosome': 'chr19', 'position': 617959}, {'chromosome': 'chr19', 'position': 618159}, {'chromosome': 'chr19', 'position': 618428}, {'chromosome': 'chr19', 'position': 618851}, {'chromosome': 'chr19', 'position': 618854}, {'chromosome': 'chr19', 'position': 618911}, {'chromosome': 'chr19', 'position': 619021}, {'chromosome': 'chr19', 'position': 619139}, {'chromosome': 'chr19', 'position': 619408}, {'chromosome': 'chr19', 'position': 619574}, {'chromosome': 'chr19', 'position': 619772}, {'chromosome': 'chr19', 'position': 619913}, {'chromosome': 'chr19', 'position': 620004}, {'chromosome': 'chr19', 'position': 620045}, {'chromosome': 'chr19', 'position': 620201}, {'chromosome': 'chr19', 'position': 620210}, {'chromosome': 'chr19', 'position': 620214}, {'chromosome': 'chr19', 'position': 620228}, {'chromosome': 'chr19', 'position': 620299}, {'chromosome': 'chr19', 'position': 620315}, {'chromosome': 'chr19', 'position': 620381}, {'chromosome': 'chr19', 'position': 620414}, {'chromosome': 'chr19', 'position': 620429}, {'chromosome': 'chr19', 'position': 620454}, {'chromosome': 'chr19', 'position': 620459}, {'chromosome': 'chr19', 'position': 620728}, {'chromosome': 'chr19', 'position': 620807}, {'chromosome': 'chr19', 'position': 620926}, {'chromosome': 'chr19', 'position': 620999}, {'chromosome': 'chr19', 'position': 621020}, {'chromosome': 'chr19', 'position': 621063}, {'chromosome': 'chr19', 'position': 621070}, {'chromosome': 'chr19', 'position': 621278}, {'chromosome': 'chr19', 'position': 621595}, {'chromosome': 'chr19', 'position': 621712}]\n"
]
}
],
"source": [
"d = []\n",
"with open(fn) as f:\n",
" c = 0\n",
" for l in f:\n",
" if l[0] == '#':\n",
" continue\n",
" c +=1\n",
" \n",
" ls = l.split()\n",
" d.append({'chromosome': ls[0], 'position': int(ls[1])})\n",
" \n",
"print (d)"
]
},
{
"cell_type": "code",
"execution_count": 155,
"metadata": {},
"outputs": [],
"source": [
"with open('test.txt', 'w') as f:\n",
" f.write(str(d))"
]
},
{
"cell_type": "code",
"execution_count": 156,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'[1, 2, 3, 4]'"
]
},
"execution_count": 156,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"a = [1,2,3,4]\n",
"str(a)"
]
},
{
"cell_type": "code",
"execution_count": 157,
"metadata": {},
"outputs": [],
"source": [
"with open('test.txt') as f:\n",
" data = f.read()"
]
},
{
"cell_type": "code",
"execution_count": 159,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"str"
]
},
"execution_count": 159,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"type(data)"
]
},
{
"cell_type": "code",
"execution_count": 163,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['M', 'I', 'T', 'S', 'O', 'S']"
]
},
"execution_count": 163,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list('MITSOS')"
]
},
{
"cell_type": "code",
"execution_count": 164,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"4"
]
},
"execution_count": 164,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"eval('4')"
]
},
{
"cell_type": "code",
"execution_count": 166,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[1, 2, 3]"
]
},
"execution_count": 166,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"eval('[1,2,3]')"
]
},
{
"cell_type": "code",
"execution_count": 167,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[{'chromosome': 'chr19', 'position': 617614},\n",
" {'chromosome': 'chr19', 'position': 617804},\n",
" {'chromosome': 'chr19', 'position': 617959},\n",
" {'chromosome': 'chr19', 'position': 618159},\n",
" {'chromosome': 'chr19', 'position': 618428},\n",
" {'chromosome': 'chr19', 'position': 618851},\n",
" {'chromosome': 'chr19', 'position': 618854},\n",
" {'chromosome': 'chr19', 'position': 618911},\n",
" {'chromosome': 'chr19', 'position': 619021},\n",
" {'chromosome': 'chr19', 'position': 619139},\n",
" {'chromosome': 'chr19', 'position': 619408},\n",
" {'chromosome': 'chr19', 'position': 619574},\n",
" {'chromosome': 'chr19', 'position': 619772},\n",
" {'chromosome': 'chr19', 'position': 619913},\n",
" {'chromosome': 'chr19', 'position': 620004},\n",
" {'chromosome': 'chr19', 'position': 620045},\n",
" {'chromosome': 'chr19', 'position': 620201},\n",
" {'chromosome': 'chr19', 'position': 620210},\n",
" {'chromosome': 'chr19', 'position': 620214},\n",
" {'chromosome': 'chr19', 'position': 620228},\n",
" {'chromosome': 'chr19', 'position': 620299},\n",
" {'chromosome': 'chr19', 'position': 620315},\n",
" {'chromosome': 'chr19', 'position': 620381},\n",
" {'chromosome': 'chr19', 'position': 620414},\n",
" {'chromosome': 'chr19', 'position': 620429},\n",
" {'chromosome': 'chr19', 'position': 620454},\n",
" {'chromosome': 'chr19', 'position': 620459},\n",
" {'chromosome': 'chr19', 'position': 620728},\n",
" {'chromosome': 'chr19', 'position': 620807},\n",
" {'chromosome': 'chr19', 'position': 620926},\n",
" {'chromosome': 'chr19', 'position': 620999},\n",
" {'chromosome': 'chr19', 'position': 621020},\n",
" {'chromosome': 'chr19', 'position': 621063},\n",
" {'chromosome': 'chr19', 'position': 621070},\n",
" {'chromosome': 'chr19', 'position': 621278},\n",
" {'chromosome': 'chr19', 'position': 621595},\n",
" {'chromosome': 'chr19', 'position': 621712}]"
]
},
"execution_count": 167,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"eval(data)"
]
},
{
"cell_type": "code",
"execution_count": 168,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[{'chromosome': 'chr19', 'position': 617614},\n",
" {'chromosome': 'chr19', 'position': 617804},\n",
" {'chromosome': 'chr19', 'position': 617959},\n",
" {'chromosome': 'chr19', 'position': 618159},\n",
" {'chromosome': 'chr19', 'position': 618428},\n",
" {'chromosome': 'chr19', 'position': 618851},\n",
" {'chromosome': 'chr19', 'position': 618854},\n",
" {'chromosome': 'chr19', 'position': 618911},\n",
" {'chromosome': 'chr19', 'position': 619021},\n",
" {'chromosome': 'chr19', 'position': 619139},\n",
" {'chromosome': 'chr19', 'position': 619408},\n",
" {'chromosome': 'chr19', 'position': 619574},\n",
" {'chromosome': 'chr19', 'position': 619772},\n",
" {'chromosome': 'chr19', 'position': 619913},\n",
" {'chromosome': 'chr19', 'position': 620004},\n",
" {'chromosome': 'chr19', 'position': 620045},\n",
" {'chromosome': 'chr19', 'position': 620201},\n",
" {'chromosome': 'chr19', 'position': 620210},\n",
" {'chromosome': 'chr19', 'position': 620214},\n",
" {'chromosome': 'chr19', 'position': 620228},\n",
" {'chromosome': 'chr19', 'position': 620299},\n",
" {'chromosome': 'chr19', 'position': 620315},\n",
" {'chromosome': 'chr19', 'position': 620381},\n",
" {'chromosome': 'chr19', 'position': 620414},\n",
" {'chromosome': 'chr19', 'position': 620429},\n",
" {'chromosome': 'chr19', 'position': 620454},\n",
" {'chromosome': 'chr19', 'position': 620459},\n",
" {'chromosome': 'chr19', 'position': 620728},\n",
" {'chromosome': 'chr19', 'position': 620807},\n",
" {'chromosome': 'chr19', 'position': 620926},\n",
" {'chromosome': 'chr19', 'position': 620999},\n",
" {'chromosome': 'chr19', 'position': 621020},\n",
" {'chromosome': 'chr19', 'position': 621063},\n",
" {'chromosome': 'chr19', 'position': 621070},\n",
" {'chromosome': 'chr19', 'position': 621278},\n",
" {'chromosome': 'chr19', 'position': 621595},\n",
" {'chromosome': 'chr19', 'position': 621712}]"
]
},
"execution_count": 168,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"content = [{'chromosome': 'chr19', 'position': 617614}, {'chromosome': 'chr19', 'position': 617804}, {'chromosome': 'chr19', 'position': 617959}, {'chromosome': 'chr19', 'position': 618159}, {'chromosome': 'chr19', 'position': 618428}, {'chromosome': 'chr19', 'position': 618851}, {'chromosome': 'chr19', 'position': 618854}, {'chromosome': 'chr19', 'position': 618911}, {'chromosome': 'chr19', 'position': 619021}, {'chromosome': 'chr19', 'position': 619139}, {'chromosome': 'chr19', 'position': 619408}, {'chromosome': 'chr19', 'position': 619574}, {'chromosome': 'chr19', 'position': 619772}, {'chromosome': 'chr19', 'position': 619913}, {'chromosome': 'chr19', 'position': 620004}, {'chromosome': 'chr19', 'position': 620045}, {'chromosome': 'chr19', 'position': 620201}, {'chromosome': 'chr19', 'position': 620210}, {'chromosome': 'chr19', 'position': 620214}, {'chromosome': 'chr19', 'position': 620228}, {'chromosome': 'chr19', 'position': 620299}, {'chromosome': 'chr19', 'position': 620315}, {'chromosome': 'chr19', 'position': 620381}, {'chromosome': 'chr19', 'position': 620414}, {'chromosome': 'chr19', 'position': 620429}, {'chromosome': 'chr19', 'position': 620454}, {'chromosome': 'chr19', 'position': 620459}, {'chromosome': 'chr19', 'position': 620728}, {'chromosome': 'chr19', 'position': 620807}, {'chromosome': 'chr19', 'position': 620926}, {'chromosome': 'chr19', 'position': 620999}, {'chromosome': 'chr19', 'position': 621020}, {'chromosome': 'chr19', 'position': 621063}, {'chromosome': 'chr19', 'position': 621070}, {'chromosome': 'chr19', 'position': 621278}, {'chromosome': 'chr19', 'position': 621595}, {'chromosome': 'chr19', 'position': 621712}]"
]
},
{
"cell_type": "code",
"execution_count": 169,
"metadata": {},
"outputs": [],
"source": [
"a = '[4,5,6]'"
]
},
{
"cell_type": "code",
"execution_count": 170,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"str"
]
},
"execution_count": 170,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"type(a)"
]
},
{
"cell_type": "code",
"execution_count": 171,
"metadata": {},
"outputs": [],
"source": [
"b = eval(a)"
]
},
{
"cell_type": "code",
"execution_count": 172,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"list"
]
},
"execution_count": 172,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"type(b)"
]
},
{
"cell_type": "code",
"execution_count": 173,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[4, 5, 6]"
]
},
"execution_count": 173,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"b"
]
},
{
"cell_type": "code",
"execution_count": 175,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'mitsos' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-175-8fd924ce1576>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0meval\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'mitsos'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m<string>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mNameError\u001b[0m: name 'mitsos' is not defined"
]
}
],
"source": [
"eval('mitsos')"
]
},
{
"cell_type": "code",
"execution_count": 174,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'mitsos' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-174-952f5670bad6>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmitsos\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mNameError\u001b[0m: name 'mitsos' is not defined"
]
}
],
"source": [
"mitsos"
]
},
{
"cell_type": "code",
"execution_count": 176,
"metadata": {},
"outputs": [],
"source": [
"mitsos = 'kwstas'"
]
},
{
"cell_type": "code",
"execution_count": 177,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'kwstas'"
]
},
"execution_count": 177,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"eval('mitsos')"
]
},
{
"cell_type": "code",
"execution_count": 178,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'kwstas'"
]
},
"execution_count": 178,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mitsos"
]
},
{
"cell_type": "code",
"execution_count": 180,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'kwstas' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-180-23b485a5ef3a>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0meval\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmitsos\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m<string>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mNameError\u001b[0m: name 'kwstas' is not defined"
]
}
],
"source": [
"eval(mitsos)"
]
},
{
"cell_type": "code",
"execution_count": 181,
"metadata": {},
"outputs": [],
"source": [
"a = '[lambda x: x+1, lambda x:x+2]'"
]
},
{
"cell_type": "code",
"execution_count": 184,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"8"
]
},
"execution_count": 184,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"eval(a)[1](6)"
]
},
{
"cell_type": "code",
"execution_count": 186,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'hello' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-186-fdba9b461628>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0meval\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'hello'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m<string>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mNameError\u001b[0m: name 'hello' is not defined"
]
}
],
"source": [
"eval('hello')"
]
},
{
"cell_type": "code",
"execution_count": 185,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'hello' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-185-f572d396fae9>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mhello\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mNameError\u001b[0m: name 'hello' is not defined"
]
}
],
"source": [
"hello"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# DO NOT EVER USE EVAL!!!!!"
]
},
{
"cell_type": "code",
"execution_count": 188,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 188,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import os; os.system('ls -l')"
]
},
{
"cell_type": "code",
"execution_count": 190,
"metadata": {},
"outputs": [],
"source": [
"#with open('file.txt') as f:\n",
"# eval(f.read())\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# SERIALIZATION / DESIRIALIZATION"
]
},
{
"cell_type": "code",
"execution_count": 192,
"metadata": {},
"outputs": [],
"source": [
"import pickle"
]
},
{
"cell_type": "code",
"execution_count": 196,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[{'chromosome': 'chr19', 'position': 617614},\n",
" {'chromosome': 'chr19', 'position': 617804},\n",
" {'chromosome': 'chr19', 'position': 617959},\n",
" {'chromosome': 'chr19', 'position': 618159},\n",
" {'chromosome': 'chr19', 'position': 618428},\n",
" {'chromosome': 'chr19', 'position': 618851},\n",
" {'chromosome': 'chr19', 'position': 618854},\n",
" {'chromosome': 'chr19', 'position': 618911},\n",
" {'chromosome': 'chr19', 'position': 619021},\n",
" {'chromosome': 'chr19', 'position': 619139},\n",
" {'chromosome': 'chr19', 'position': 619408},\n",
" {'chromosome': 'chr19', 'position': 619574},\n",
" {'chromosome': 'chr19', 'position': 619772},\n",
" {'chromosome': 'chr19', 'position': 619913},\n",
" {'chromosome': 'chr19', 'position': 620004},\n",
" {'chromosome': 'chr19', 'position': 620045},\n",
" {'chromosome': 'chr19', 'position': 620201},\n",
" {'chromosome': 'chr19', 'position': 620210},\n",
" {'chromosome': 'chr19', 'position': 620214},\n",
" {'chromosome': 'chr19', 'position': 620228},\n",
" {'chromosome': 'chr19', 'position': 620299},\n",
" {'chromosome': 'chr19', 'position': 620315},\n",
" {'chromosome': 'chr19', 'position': 620381},\n",
" {'chromosome': 'chr19', 'position': 620414},\n",
" {'chromosome': 'chr19', 'position': 620429},\n",
" {'chromosome': 'chr19', 'position': 620454},\n",
" {'chromosome': 'chr19', 'position': 620459},\n",
" {'chromosome': 'chr19', 'position': 620728},\n",
" {'chromosome': 'chr19', 'position': 620807},\n",
" {'chromosome': 'chr19', 'position': 620926},\n",
" {'chromosome': 'chr19', 'position': 620999},\n",
" {'chromosome': 'chr19', 'position': 621020},\n",
" {'chromosome': 'chr19', 'position': 621063},\n",
" {'chromosome': 'chr19', 'position': 621070},\n",
" {'chromosome': 'chr19', 'position': 621278},\n",
" {'chromosome': 'chr19', 'position': 621595},\n",
" {'chromosome': 'chr19', 'position': 621712}]"
]
},
"execution_count": 196,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"d"
]
},
{
"cell_type": "code",
"execution_count": 198,
"metadata": {},
"outputs": [],
"source": [
"p_dump = pickle.dumps(d) # Serialize"
]
},
{
"cell_type": "code",
"execution_count": 199,
"metadata": {},
"outputs": [],
"source": [
"p_deserial = pickle.loads(p_dump) # Deserialize"
]
},
{
"cell_type": "code",
"execution_count": 200,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[{'chromosome': 'chr19', 'position': 617614},\n",
" {'chromosome': 'chr19', 'position': 617804},\n",
" {'chromosome': 'chr19', 'position': 617959},\n",
" {'chromosome': 'chr19', 'position': 618159},\n",
" {'chromosome': 'chr19', 'position': 618428},\n",
" {'chromosome': 'chr19', 'position': 618851},\n",
" {'chromosome': 'chr19', 'position': 618854},\n",
" {'chromosome': 'chr19', 'position': 618911},\n",
" {'chromosome': 'chr19', 'position': 619021},\n",
" {'chromosome': 'chr19', 'position': 619139},\n",
" {'chromosome': 'chr19', 'position': 619408},\n",
" {'chromosome': 'chr19', 'position': 619574},\n",
" {'chromosome': 'chr19', 'position': 619772},\n",
" {'chromosome': 'chr19', 'position': 619913},\n",
" {'chromosome': 'chr19', 'position': 620004},\n",
" {'chromosome': 'chr19', 'position': 620045},\n",
" {'chromosome': 'chr19', 'position': 620201},\n",
" {'chromosome': 'chr19', 'position': 620210},\n",
" {'chromosome': 'chr19', 'position': 620214},\n",
" {'chromosome': 'chr19', 'position': 620228},\n",
" {'chromosome': 'chr19', 'position': 620299},\n",
" {'chromosome': 'chr19', 'position': 620315},\n",
" {'chromosome': 'chr19', 'position': 620381},\n",
" {'chromosome': 'chr19', 'position': 620414},\n",
" {'chromosome': 'chr19', 'position': 620429},\n",
" {'chromosome': 'chr19', 'position': 620454},\n",
" {'chromosome': 'chr19', 'position': 620459},\n",
" {'chromosome': 'chr19', 'position': 620728},\n",
" {'chromosome': 'chr19', 'position': 620807},\n",
" {'chromosome': 'chr19', 'position': 620926},\n",
" {'chromosome': 'chr19', 'position': 620999},\n",
" {'chromosome': 'chr19', 'position': 621020},\n",
" {'chromosome': 'chr19', 'position': 621063},\n",
" {'chromosome': 'chr19', 'position': 621070},\n",
" {'chromosome': 'chr19', 'position': 621278},\n",
" {'chromosome': 'chr19', 'position': 621595},\n",
" {'chromosome': 'chr19', 'position': 621712}]"
]
},
"execution_count": 200,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"p_deserial"
]
},
{
"cell_type": "code",
"execution_count": 202,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 202,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"p_deserial == d"
]
},
{
"cell_type": "code",
"execution_count": 203,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[{'chromosome': 'chr19', 'position': 617614},\n",
" {'chromosome': 'chr19', 'position': 617804},\n",
" {'chromosome': 'chr19', 'position': 617959},\n",
" {'chromosome': 'chr19', 'position': 618159},\n",
" {'chromosome': 'chr19', 'position': 618428},\n",
" {'chromosome': 'chr19', 'position': 618851},\n",
" {'chromosome': 'chr19', 'position': 618854},\n",
" {'chromosome': 'chr19', 'position': 618911},\n",
" {'chromosome': 'chr19', 'position': 619021},\n",
" {'chromosome': 'chr19', 'position': 619139},\n",
" {'chromosome': 'chr19', 'position': 619408},\n",
" {'chromosome': 'chr19', 'position': 619574},\n",
" {'chromosome': 'chr19', 'position': 619772},\n",
" {'chromosome': 'chr19', 'position': 619913},\n",
" {'chromosome': 'chr19', 'position': 620004},\n",
" {'chromosome': 'chr19', 'position': 620045},\n",
" {'chromosome': 'chr19', 'position': 620201},\n",
" {'chromosome': 'chr19', 'position': 620210},\n",
" {'chromosome': 'chr19', 'position': 620214},\n",
" {'chromosome': 'chr19', 'position': 620228},\n",
" {'chromosome': 'chr19', 'position': 620299},\n",
" {'chromosome': 'chr19', 'position': 620315},\n",
" {'chromosome': 'chr19', 'position': 620381},\n",
" {'chromosome': 'chr19', 'position': 620414},\n",
" {'chromosome': 'chr19', 'position': 620429},\n",
" {'chromosome': 'chr19', 'position': 620454},\n",
" {'chromosome': 'chr19', 'position': 620459},\n",
" {'chromosome': 'chr19', 'position': 620728},\n",
" {'chromosome': 'chr19', 'position': 620807},\n",
" {'chromosome': 'chr19', 'position': 620926},\n",
" {'chromosome': 'chr19', 'position': 620999},\n",
" {'chromosome': 'chr19', 'position': 621020},\n",
" {'chromosome': 'chr19', 'position': 621063},\n",
" {'chromosome': 'chr19', 'position': 621070},\n",
" {'chromosome': 'chr19', 'position': 621278},\n",
" {'chromosome': 'chr19', 'position': 621595},\n",
" {'chromosome': 'chr19', 'position': 621712}]"
]
},
"execution_count": 203,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pickle.loads(p_dump)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# DO NOT EVER USE PICKLE (just kidding)"
]
},
{
"cell_type": "code",
"execution_count": 204,
"metadata": {},
"outputs": [],
"source": [
"import json"
]
},
{
"cell_type": "code",
"execution_count": 206,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'[{\"chromosome\": \"chr19\", \"position\": 617614}, {\"chromosome\": \"chr19\", \"position\": 617804}, {\"chromosome\": \"chr19\", \"position\": 617959}, {\"chromosome\": \"chr19\", \"position\": 618159}, {\"chromosome\": \"chr19\", \"position\": 618428}, {\"chromosome\": \"chr19\", \"position\": 618851}, {\"chromosome\": \"chr19\", \"position\": 618854}, {\"chromosome\": \"chr19\", \"position\": 618911}, {\"chromosome\": \"chr19\", \"position\": 619021}, {\"chromosome\": \"chr19\", \"position\": 619139}, {\"chromosome\": \"chr19\", \"position\": 619408}, {\"chromosome\": \"chr19\", \"position\": 619574}, {\"chromosome\": \"chr19\", \"position\": 619772}, {\"chromosome\": \"chr19\", \"position\": 619913}, {\"chromosome\": \"chr19\", \"position\": 620004}, {\"chromosome\": \"chr19\", \"position\": 620045}, {\"chromosome\": \"chr19\", \"position\": 620201}, {\"chromosome\": \"chr19\", \"position\": 620210}, {\"chromosome\": \"chr19\", \"position\": 620214}, {\"chromosome\": \"chr19\", \"position\": 620228}, {\"chromosome\": \"chr19\", \"position\": 620299}, {\"chromosome\": \"chr19\", \"position\": 620315}, {\"chromosome\": \"chr19\", \"position\": 620381}, {\"chromosome\": \"chr19\", \"position\": 620414}, {\"chromosome\": \"chr19\", \"position\": 620429}, {\"chromosome\": \"chr19\", \"position\": 620454}, {\"chromosome\": \"chr19\", \"position\": 620459}, {\"chromosome\": \"chr19\", \"position\": 620728}, {\"chromosome\": \"chr19\", \"position\": 620807}, {\"chromosome\": \"chr19\", \"position\": 620926}, {\"chromosome\": \"chr19\", \"position\": 620999}, {\"chromosome\": \"chr19\", \"position\": 621020}, {\"chromosome\": \"chr19\", \"position\": 621063}, {\"chromosome\": \"chr19\", \"position\": 621070}, {\"chromosome\": \"chr19\", \"position\": 621278}, {\"chromosome\": \"chr19\", \"position\": 621595}, {\"chromosome\": \"chr19\", \"position\": 621712}]'"
]
},
"execution_count": 206,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"json.dumps(d)"
]
},
{
"cell_type": "code",
"execution_count": 209,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 617614\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 617804\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 617959\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 618159\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 618428\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 618851\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 618854\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 618911\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 619021\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 619139\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 619408\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 619574\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 619772\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 619913\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620004\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620045\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620201\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620210\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620214\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620228\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620299\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620315\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620381\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620414\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620429\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620454\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620459\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620728\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620807\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620926\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 620999\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 621020\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 621063\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 621070\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 621278\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 621595\n",
" },\n",
" {\n",
" \"chromosome\": \"chr19\",\n",
" \"position\": 621712\n",
" }\n",
"]\n"
]
}
],
"source": [
"print (json.dumps(d, indent=4))"
]
},
{
"cell_type": "code",
"execution_count": 210,
"metadata": {},
"outputs": [],
"source": [
"j_ser = json.dumps(d, indent=4)"
]
},
{
"cell_type": "code",
"execution_count": 211,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"str"
]
},
"execution_count": 211,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"type(j_ser)"
]
},
{
"cell_type": "code",
"execution_count": 216,
"metadata": {},
"outputs": [],
"source": [
"a = [1,2,3]"
]
},
{
"cell_type": "code",
"execution_count": 217,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[1, 2, 3]\n"
]
}
],
"source": [
"print (json.dumps(a))"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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