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ArcA ChIP peaks comparison to Park et al.
Raw
gistfile1.txt
{
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},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"ArcA ChIP peak comparison tables for Fig. S5"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from trnlib.omeORM import *\n",
"from pandas import *\n",
"\n",
"from numpy import array\n",
"from sqlalchemy import func\n",
"\n",
"from IPython.core.display import HTML\n",
"\n",
"ome = Session()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "heading",
"level": 3,
"metadata": {},
"source": [
"Read in table S1 from Park et al."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"most_peaks = read_table('arcA_ChIP_seq_only.txt', index_col='gene')"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"HTML(most_peaks.sort().to_html())"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Replicate 1 position</th>\n",
" <th>Replicate 1 enrichment</th>\n",
" <th>Replicate 2 position</th>\n",
" <th>Replicate 2 enrichment</th>\n",
" <th>Location of ArcA box</th>\n",
" <th>Strand</th>\n",
" <th>Ri (bits)</th>\n",
" </tr>\n",
" <tr>\n",
" <th>gene</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>CO343</th>\n",
" <td> 1407214</td>\n",
" <td> 4.6</td>\n",
" <td> 1407252</td>\n",
" <td> 4.0</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>acnB</th>\n",
" <td> 131400</td>\n",
" <td> 3.8</td>\n",
" <td> 131463</td>\n",
" <td> 3.7</td>\n",
" <td> 131465</td>\n",
" <td> +</td>\n",
" <td> 17.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>acs</th>\n",
" <td> 4285384</td>\n",
" <td> 11.9</td>\n",
" <td> 4285404</td>\n",
" <td> 11.8</td>\n",
" <td> 4285418</td>\n",
" <td> +</td>\n",
" <td> 18.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>aldA</th>\n",
" <td> 1486187</td>\n",
" <td> 7.8</td>\n",
" <td> 1486202</td>\n",
" <td> 5.6</td>\n",
" <td> 1486221</td>\n",
" <td> -</td>\n",
" <td> 10.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>appY</th>\n",
" <td> 582513</td>\n",
" <td> 3.8</td>\n",
" <td> 582538</td>\n",
" <td> 3.9</td>\n",
" <td> 582518</td>\n",
" <td> +</td>\n",
" <td> 15.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>argT</th>\n",
" <td> 2425894</td>\n",
" <td> 6.6</td>\n",
" <td> 2425921</td>\n",
" <td> 6.3</td>\n",
" <td> 2425934</td>\n",
" <td> +</td>\n",
" <td> 13.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>astC</th>\n",
" <td> 1830008</td>\n",
" <td> 15.4</td>\n",
" <td> 1830017</td>\n",
" <td> 13.6</td>\n",
" <td> 1830032</td>\n",
" <td> +</td>\n",
" <td> 19.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>atpI</th>\n",
" <td> 3920795</td>\n",
" <td> 3.2</td>\n",
" <td> 3920826</td>\n",
" <td> 3.3</td>\n",
" <td> 3920874</td>\n",
" <td> -</td>\n",
" <td> 13.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>avtA</th>\n",
" <td> 3737499</td>\n",
" <td> 2.4</td>\n",
" <td> 3737631</td>\n",
" <td> 3.2</td>\n",
" <td> 3737679</td>\n",
" <td> +</td>\n",
" <td> 13.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>betT/betI</th>\n",
" <td> 328597</td>\n",
" <td> 4.5</td>\n",
" <td> 328632</td>\n",
" <td> 6.3</td>\n",
" <td> 328630</td>\n",
" <td> +</td>\n",
" <td> 14.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>bssR/rimO</th>\n",
" <td> 877347</td>\n",
" <td> 2.5</td>\n",
" <td> 877383</td>\n",
" <td> 2.8</td>\n",
" <td> 877374</td>\n",
" <td> +</td>\n",
" <td> 10.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cadB</th>\n",
" <td> 4358301</td>\n",
" <td> 5.3</td>\n",
" <td> 4358333</td>\n",
" <td> 4.6</td>\n",
" <td> 4358302</td>\n",
" <td> +</td>\n",
" <td> 15.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>caiT</th>\n",
" <td> 41949</td>\n",
" <td> 8.6</td>\n",
" <td> 41981</td>\n",
" <td> 6.9</td>\n",
" <td> 41980</td>\n",
" <td> +</td>\n",
" <td> 17.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cirA</th>\n",
" <td> 2244973</td>\n",
" <td> 3.0</td>\n",
" <td> 2244987</td>\n",
" <td> 3.0</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>csgB</th>\n",
" <td> 1103086</td>\n",
" <td> 2.6</td>\n",
" <td> 1103088</td>\n",
" <td> 2.6</td>\n",
" <td> 1103096</td>\n",
" <td> -</td>\n",
" <td> 13.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>csgD</th>\n",
" <td> 1102574</td>\n",
" <td> 2.7</td>\n",
" <td> 1102613</td>\n",
" <td> 3.4</td>\n",
" <td> 1102593</td>\n",
" <td> +</td>\n",
" <td> 10.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>csiD</th>\n",
" <td> 2786818</td>\n",
" <td> 6.1</td>\n",
" <td> 2786839</td>\n",
" <td> 7.6</td>\n",
" <td> 2786863</td>\n",
" <td> +</td>\n",
" <td> 19.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cspA1</th>\n",
" <td> 3717947</td>\n",
" <td> 4.8</td>\n",
" <td> 3717921</td>\n",
" <td> 5.2</td>\n",
" <td> 3717865</td>\n",
" <td> +</td>\n",
" <td> 13.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>csrD_intragenic</th>\n",
" <td> 3399820</td>\n",
" <td> 6.8</td>\n",
" <td> 3399827</td>\n",
" <td> 5.7</td>\n",
" <td> 3399851</td>\n",
" <td> -</td>\n",
" <td> 15.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cycA</th>\n",
" <td> 4427654</td>\n",
" <td> 7.8</td>\n",
" <td> 4427673</td>\n",
" <td> 6.4</td>\n",
" <td> 4427748</td>\n",
" <td> -</td>\n",
" <td> 18.9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cydA1</th>\n",
" <td> 770043</td>\n",
" <td> 8.4</td>\n",
" <td> 770066</td>\n",
" <td> 8.9</td>\n",
" <td> 770094</td>\n",
" <td> +</td>\n",
" <td> 19.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cydA2</th>\n",
" <td> 770253</td>\n",
" <td> 5.8</td>\n",
" <td> 770271</td>\n",
" <td> 6.2</td>\n",
" <td> 770277</td>\n",
" <td> -</td>\n",
" <td> 12.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cydA3</th>\n",
" <td> 770462</td>\n",
" <td> 3.1</td>\n",
" <td> 770494</td>\n",
" <td> 3.7</td>\n",
" <td> 770543</td>\n",
" <td> -</td>\n",
" <td> 15.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cydD</th>\n",
" <td> 930264</td>\n",
" <td> 27.6</td>\n",
" <td> 930288</td>\n",
" <td> 27.6</td>\n",
" <td> 930292</td>\n",
" <td> +</td>\n",
" <td> 20.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cyoA1</th>\n",
" <td> 450852</td>\n",
" <td> 9.1</td>\n",
" <td> 450857</td>\n",
" <td> 6.8</td>\n",
" <td> 450898</td>\n",
" <td> +</td>\n",
" <td> 13.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cyoA2</th>\n",
" <td> 450990</td>\n",
" <td> 11.5</td>\n",
" <td> 451010</td>\n",
" <td> 14.4</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>cyoA3</th>\n",
" <td> 451069</td>\n",
" <td> 19.7</td>\n",
" <td> 451088</td>\n",
" <td> 16.5</td>\n",
" <td> 451094</td>\n",
" <td> -</td>\n",
" <td> 18.9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dctA</th>\n",
" <td> 3681512</td>\n",
" <td> 4.5</td>\n",
" <td> 3681557</td>\n",
" <td> 4.0</td>\n",
" <td> 3681576</td>\n",
" <td> +</td>\n",
" <td> 13.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dcuA</th>\n",
" <td> 4364813</td>\n",
" <td> 18.7</td>\n",
" <td> 4364810</td>\n",
" <td> 21.1</td>\n",
" <td> 4364837</td>\n",
" <td> +</td>\n",
" <td> 17.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dcuB</th>\n",
" <td> 4346931</td>\n",
" <td> 4.7</td>\n",
" <td> 4346943</td>\n",
" <td> 5.8</td>\n",
" <td> 4347011</td>\n",
" <td> +</td>\n",
" <td> 13.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ddpX</th>\n",
" <td> 1561199</td>\n",
" <td> 3.7</td>\n",
" <td> 1561200</td>\n",
" <td> 3.9</td>\n",
" <td> 1561217</td>\n",
" <td> -</td>\n",
" <td> 16.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>dhaR/dhaK</th>\n",
" <td> 1250169</td>\n",
" <td> 9.0</td>\n",
" <td> 1250183</td>\n",
" <td> 14.4</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>exuT/uxaC</th>\n",
" <td> 3242801</td>\n",
" <td> 3.4</td>\n",
" <td> 3242819</td>\n",
" <td> 3.4</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fadB</th>\n",
" <td> 4029013</td>\n",
" <td> 5.3</td>\n",
" <td> 4029043</td>\n",
" <td> 5.0</td>\n",
" <td> 4029059</td>\n",
" <td> +</td>\n",
" <td> 12.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fadD</th>\n",
" <td> 1887807</td>\n",
" <td> 14.3</td>\n",
" <td> 1887816</td>\n",
" <td> 13.6</td>\n",
" <td> 1887844</td>\n",
" <td> -</td>\n",
" <td> 17.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fadE</th>\n",
" <td> 243344</td>\n",
" <td> 2.8</td>\n",
" <td> 243375</td>\n",
" <td> 4.4</td>\n",
" <td> 243400</td>\n",
" <td> -</td>\n",
" <td> 18.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fadH</th>\n",
" <td> 3229633</td>\n",
" <td> 3.4</td>\n",
" <td> 3229636</td>\n",
" <td> 2.4</td>\n",
" <td> 3229670</td>\n",
" <td> -</td>\n",
" <td> 19.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fadI</th>\n",
" <td> 2458502</td>\n",
" <td> 9.1</td>\n",
" <td> 2458529</td>\n",
" <td> 11.2</td>\n",
" <td> 2458556</td>\n",
" <td> -</td>\n",
" <td> 18.9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fadL</th>\n",
" <td> 2459101</td>\n",
" <td> 3.6</td>\n",
" <td> 2459138</td>\n",
" <td> 4.1</td>\n",
" <td> 2459195</td>\n",
" <td> -</td>\n",
" <td> 11.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>feaB/feaR</th>\n",
" <td> 1445316</td>\n",
" <td> 3.9</td>\n",
" <td> 1445299</td>\n",
" <td> 2.1</td>\n",
" <td> 1445343</td>\n",
" <td> +</td>\n",
" <td> 13.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>feoA</th>\n",
" <td> 3537845</td>\n",
" <td> 4.2</td>\n",
" <td> 3537882</td>\n",
" <td> 3.3</td>\n",
" <td> 3537905</td>\n",
" <td> -</td>\n",
" <td> 17.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fiu</th>\n",
" <td> 840921</td>\n",
" <td> 14.8</td>\n",
" <td> 840928</td>\n",
" <td> 9.9</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fnrS</th>\n",
" <td> 1407082</td>\n",
" <td> 4.6</td>\n",
" <td> 1407110</td>\n",
" <td> 5.0</td>\n",
" <td> 1407023</td>\n",
" <td> +</td>\n",
" <td> 9.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>focA1</th>\n",
" <td> 953477</td>\n",
" <td> 2.2</td>\n",
" <td> 953615</td>\n",
" <td> 2.9</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>focA2</th>\n",
" <td> 953962</td>\n",
" <td> 4.1</td>\n",
" <td> 953967</td>\n",
" <td> 3.8</td>\n",
" <td> 953988</td>\n",
" <td> -</td>\n",
" <td> 16.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fumA</th>\n",
" <td> 1686433</td>\n",
" <td> 4.4</td>\n",
" <td> 1686468</td>\n",
" <td> 5.7</td>\n",
" <td> 1686496</td>\n",
" <td> -</td>\n",
" <td> 16.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>fumC</th>\n",
" <td> 1684662</td>\n",
" <td> 8.0</td>\n",
" <td> 1684681</td>\n",
" <td> 8.7</td>\n",
" <td> 1684699</td>\n",
" <td> -</td>\n",
" <td> 16.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gadE</th>\n",
" <td> 3656148</td>\n",
" <td> 2.5</td>\n",
" <td> 3656141</td>\n",
" <td> 3.3</td>\n",
" <td> 3656188</td>\n",
" <td> -</td>\n",
" <td> 12.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gadX</th>\n",
" <td> 3664058</td>\n",
" <td> 7.6</td>\n",
" <td> 3664072</td>\n",
" <td> 7.3</td>\n",
" <td> 3664074</td>\n",
" <td> -</td>\n",
" <td> 15.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gapA</th>\n",
" <td> 1860780</td>\n",
" <td> 2.8</td>\n",
" <td> 1860752</td>\n",
" <td> 2.3</td>\n",
" <td> 1860771</td>\n",
" <td> -</td>\n",
" <td> 10.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gcd</th>\n",
" <td> 141230</td>\n",
" <td> 7.6</td>\n",
" <td> 141251</td>\n",
" <td> 8.0</td>\n",
" <td> 141262</td>\n",
" <td> -</td>\n",
" <td> 12.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gcvB/gcvA</th>\n",
" <td> 2940582</td>\n",
" <td> 13.6</td>\n",
" <td> 2940613</td>\n",
" <td> 12.9</td>\n",
" <td> 2940632</td>\n",
" <td> -</td>\n",
" <td> 13.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>glcC/glcD</th>\n",
" <td> 3126158</td>\n",
" <td> 12.9</td>\n",
" <td> 3126179</td>\n",
" <td> 9.1</td>\n",
" <td> 3126191</td>\n",
" <td> +</td>\n",
" <td> 17.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>glpD/glpE</th>\n",
" <td> 3559932</td>\n",
" <td> 3.7</td>\n",
" <td> 3559956</td>\n",
" <td> 5.8</td>\n",
" <td> 3559947</td>\n",
" <td> +</td>\n",
" <td> 15.9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gltA</th>\n",
" <td> 753985</td>\n",
" <td> 7.5</td>\n",
" <td> 754015</td>\n",
" <td> 8.8</td>\n",
" <td> 754030</td>\n",
" <td> +</td>\n",
" <td> 15.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>hcaE/hcaR</th>\n",
" <td> 2666920</td>\n",
" <td> 3.2</td>\n",
" <td> 2666984</td>\n",
" <td> 3.2</td>\n",
" <td> 2666984</td>\n",
" <td> -</td>\n",
" <td> 15.9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>hyaA</th>\n",
" <td> 1031271</td>\n",
" <td> 3.6</td>\n",
" <td> 1031264</td>\n",
" <td> 2.1</td>\n",
" <td> 1031206</td>\n",
" <td> -</td>\n",
" <td> 13.9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>icd</th>\n",
" <td> 1194217</td>\n",
" <td> 5.7</td>\n",
" <td> 1194224</td>\n",
" <td> 6.8</td>\n",
" <td> 1194249</td>\n",
" <td> -</td>\n",
" <td> 18.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>intF</th>\n",
" <td> 296397</td>\n",
" <td> 5.0</td>\n",
" <td> 296437</td>\n",
" <td> 6.3</td>\n",
" <td> 296426</td>\n",
" <td> -</td>\n",
" <td> 15.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>intF_intergenic</th>\n",
" <td> 295252</td>\n",
" <td> 2.8</td>\n",
" <td> 295257</td>\n",
" <td> 2.1</td>\n",
" <td> 295293</td>\n",
" <td> -</td>\n",
" <td> 18.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>intergenic</th>\n",
" <td> 1620836</td>\n",
" <td> 2.8</td>\n",
" <td> 1620824</td>\n",
" <td> 2.0</td>\n",
" <td> 1620802</td>\n",
" <td> +</td>\n",
" <td> 11.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>intergenic</th>\n",
" <td> 1640360</td>\n",
" <td> 3.9</td>\n",
" <td> 1640373</td>\n",
" <td> 4.4</td>\n",
" <td> 1640421</td>\n",
" <td> -</td>\n",
" <td> 12.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>intergenic</th>\n",
" <td> 2563347</td>\n",
" <td> 3.0</td>\n",
" <td> 2563326</td>\n",
" <td> 3.9</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>kgtP1</th>\n",
" <td> 2723801</td>\n",
" <td> 7.8</td>\n",
" <td> 2723815</td>\n",
" <td> 7.5</td>\n",
" <td> 2723830</td>\n",
" <td> +</td>\n",
" <td> 12.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>kgtP2</th>\n",
" <td> 2724010</td>\n",
" <td> 5.7</td>\n",
" <td> 2723996</td>\n",
" <td> 3.5</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>lldP</th>\n",
" <td> 3775233</td>\n",
" <td> 10.9</td>\n",
" <td> 3775232</td>\n",
" <td> 13.2</td>\n",
" <td> 3775302</td>\n",
" <td> -</td>\n",
" <td> 17.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>lon</th>\n",
" <td> 457929</td>\n",
" <td> 3.5</td>\n",
" <td> 457923</td>\n",
" <td> 4.8</td>\n",
" <td> 457950</td>\n",
" <td> -</td>\n",
" <td> 10.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>lpd</th>\n",
" <td> 127646</td>\n",
" <td> 3.4</td>\n",
" <td> 127683</td>\n",
" <td> 3.8</td>\n",
" <td> 127682</td>\n",
" <td> +</td>\n",
" <td> 21.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mdh</th>\n",
" <td> 3382502</td>\n",
" <td> 3.7</td>\n",
" <td> 3382529</td>\n",
" <td> 3.8</td>\n",
" <td> 3382553</td>\n",
" <td> -</td>\n",
" <td> 17.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mdtL</th>\n",
" <td> 3889503</td>\n",
" <td> 2.5</td>\n",
" <td> 3889536</td>\n",
" <td> 2.9</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mglB</th>\n",
" <td> 2238549</td>\n",
" <td> 20.6</td>\n",
" <td> 2238577</td>\n",
" <td> 18.3</td>\n",
" <td> 2238613</td>\n",
" <td> +</td>\n",
" <td> 15.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mhpA/mhpR</th>\n",
" <td> 367720</td>\n",
" <td> 18.9</td>\n",
" <td> 367746</td>\n",
" <td> 19.3</td>\n",
" <td> 367772</td>\n",
" <td> -</td>\n",
" <td> 20.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mqo</th>\n",
" <td> 2304831</td>\n",
" <td> 5.3</td>\n",
" <td> 2304821</td>\n",
" <td> 5.8</td>\n",
" <td> 2304850</td>\n",
" <td> -</td>\n",
" <td> 20.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>msrB</th>\n",
" <td> 1860459</td>\n",
" <td> 6.0</td>\n",
" <td> 1860472</td>\n",
" <td> 6.4</td>\n",
" <td> 1860513</td>\n",
" <td> -</td>\n",
" <td> 14.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ndh</th>\n",
" <td> 1165227</td>\n",
" <td> 11.9</td>\n",
" <td> 1165239</td>\n",
" <td> 11.0</td>\n",
" <td> 1165277</td>\n",
" <td> -</td>\n",
" <td> 18.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ndk</th>\n",
" <td> 2642953</td>\n",
" <td> 11.8</td>\n",
" <td> 2642972</td>\n",
" <td> 11.3</td>\n",
" <td> 2642995</td>\n",
" <td> -</td>\n",
" <td> 18.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nepI</th>\n",
" <td> 3839764</td>\n",
" <td> 2.8</td>\n",
" <td> 3839819</td>\n",
" <td> 2.2</td>\n",
" <td> 3839842</td>\n",
" <td> -</td>\n",
" <td> 15.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nuoA1</th>\n",
" <td> 2403217</td>\n",
" <td> 6.1</td>\n",
" <td> 2403245</td>\n",
" <td> 8.0</td>\n",
" <td> 2403298</td>\n",
" <td> -</td>\n",
" <td> 15.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nuoA2</th>\n",
" <td> 2403439</td>\n",
" <td> 4.3</td>\n",
" <td> 2403443</td>\n",
" <td> 3.0</td>\n",
" <td> 2403520</td>\n",
" <td> -</td>\n",
" <td> 10.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>nupC</th>\n",
" <td> 2511118</td>\n",
" <td> 2.6</td>\n",
" <td> 2511163</td>\n",
" <td> 1.9</td>\n",
" <td> 2511176</td>\n",
" <td> +</td>\n",
" <td> 17.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ompC</th>\n",
" <td> 2310725</td>\n",
" <td> 2.4</td>\n",
" <td> 2310766</td>\n",
" <td> 1.9</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ompW</th>\n",
" <td> 1311945</td>\n",
" <td> 3.9</td>\n",
" <td> 1311978</td>\n",
" <td> 3.1</td>\n",
" <td> 1312024</td>\n",
" <td> -</td>\n",
" <td> 14.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>oppA1</th>\n",
" <td> 1298696</td>\n",
" <td> 6.1</td>\n",
" <td> 1298685</td>\n",
" <td> 5.0</td>\n",
" <td> 1298736</td>\n",
" <td> +</td>\n",
" <td> 15.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>oppA2</th>\n",
" <td> 1298985</td>\n",
" <td> 3.2</td>\n",
" <td> 1298848</td>\n",
" <td> 2.8</td>\n",
" <td> 1298896</td>\n",
" <td> -</td>\n",
" <td> 16.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>paaA</th>\n",
" <td> 1451838</td>\n",
" <td> 4.7</td>\n",
" <td> 1451847</td>\n",
" <td> 5.1</td>\n",
" <td> 1451882</td>\n",
" <td> -</td>\n",
" <td> 14.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>pdhR</th>\n",
" <td> 121950</td>\n",
" <td> 9.6</td>\n",
" <td> 121923</td>\n",
" <td> 5.4</td>\n",
" <td> 121871</td>\n",
" <td> +</td>\n",
" <td> 15.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>phnC</th>\n",
" <td> 4323209</td>\n",
" <td> 5.2</td>\n",
" <td> 4323222</td>\n",
" <td> 4.2</td>\n",
" <td> 4323245</td>\n",
" <td> +</td>\n",
" <td> 15.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>phoH</th>\n",
" <td> 1084064</td>\n",
" <td> 7.5</td>\n",
" <td> 1084083</td>\n",
" <td> 5.8</td>\n",
" <td> 1084108</td>\n",
" <td> +</td>\n",
" <td> 16.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>potF1</th>\n",
" <td> 892675</td>\n",
" <td> 11.1</td>\n",
" <td> 892688</td>\n",
" <td> 12.3</td>\n",
" <td> 892735</td>\n",
" <td> -</td>\n",
" <td> 11.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>proP</th>\n",
" <td> 4328283</td>\n",
" <td> 3.4</td>\n",
" <td> 4328306</td>\n",
" <td> 2.6</td>\n",
" <td> 4328272</td>\n",
" <td> -</td>\n",
" <td> 10.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ptsH</th>\n",
" <td> 2531443</td>\n",
" <td> 3.3</td>\n",
" <td> 2531456</td>\n",
" <td> 2.8</td>\n",
" <td> 2531413</td>\n",
" <td> +</td>\n",
" <td> 18.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>putA</th>\n",
" <td> 1078132</td>\n",
" <td> 7.1</td>\n",
" <td> 1078166</td>\n",
" <td> 6.1</td>\n",
" <td> 1078166</td>\n",
" <td> +</td>\n",
" <td> 10.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>putP</th>\n",
" <td> 1078326</td>\n",
" <td> 4.5</td>\n",
" <td> 1078367</td>\n",
" <td> 3.5</td>\n",
" <td> 1078379</td>\n",
" <td> +</td>\n",
" <td> 15.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>puuD/puuA</th>\n",
" <td> 1359011</td>\n",
" <td> 9.8</td>\n",
" <td> 1359020</td>\n",
" <td> 8.5</td>\n",
" <td> 1359019</td>\n",
" <td> +</td>\n",
" <td> 14.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>rcsD</th>\n",
" <td> 2311224</td>\n",
" <td> 7.5</td>\n",
" <td> 2311254</td>\n",
" <td> 10.0</td>\n",
" <td> 2311279</td>\n",
" <td> -</td>\n",
" <td> 21.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>rsd</th>\n",
" <td> 4194840</td>\n",
" <td> 3.3</td>\n",
" <td> 4194871</td>\n",
" <td> 3.1</td>\n",
" <td> 4194878</td>\n",
" <td> +</td>\n",
" <td> 17.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>rstA/ydgC</th>\n",
" <td> 1680030</td>\n",
" <td> 3.9</td>\n",
" <td> 1680050</td>\n",
" <td> 4.3</td>\n",
" <td> 1680078</td>\n",
" <td> -</td>\n",
" <td> 17.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>rutR/rutA</th>\n",
" <td> 1073279</td>\n",
" <td> 36.6</td>\n",
" <td> 1073290</td>\n",
" <td> 36.0</td>\n",
" <td> 1073297</td>\n",
" <td> +</td>\n",
" <td> 19.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ryeA/pphA</th>\n",
" <td> 1920997</td>\n",
" <td> 2.4</td>\n",
" <td> 1921059</td>\n",
" <td> 2.3</td>\n",
" <td> 1921032</td>\n",
" <td> -</td>\n",
" <td> 16.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sdhC</th>\n",
" <td> 754094</td>\n",
" <td> 16.0</td>\n",
" <td> 754117</td>\n",
" <td> 13.1</td>\n",
" <td> 754146</td>\n",
" <td> +</td>\n",
" <td> 14.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>secE</th>\n",
" <td> 4175225</td>\n",
" <td> 3.2</td>\n",
" <td> 4175239</td>\n",
" <td> 3.7</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>spf1</th>\n",
" <td> 4047953</td>\n",
" <td> 6.8</td>\n",
" <td> 4047886</td>\n",
" <td> 3.4</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sstT</th>\n",
" <td> 3237784</td>\n",
" <td> 3.9</td>\n",
" <td> 3237801</td>\n",
" <td> 3.1</td>\n",
" <td> 3237787</td>\n",
" <td> +</td>\n",
" <td> 13.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sthA</th>\n",
" <td> 4158803</td>\n",
" <td> 6.2</td>\n",
" <td> 4158830</td>\n",
" <td> 6.1</td>\n",
" <td> 4158858</td>\n",
" <td> -</td>\n",
" <td> 12.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>thiC2</th>\n",
" <td> 4194328</td>\n",
" <td> 13.4</td>\n",
" <td> 4194389</td>\n",
" <td> 5.3</td>\n",
" <td> 4194329</td>\n",
" <td> +</td>\n",
" <td> 15.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>trpD</th>\n",
" <td> 1317927</td>\n",
" <td> 3.4</td>\n",
" <td> 1317949</td>\n",
" <td> 2.0</td>\n",
" <td> 1317981</td>\n",
" <td> +</td>\n",
" <td> 16.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>trxC/yfiF</th>\n",
" <td> 2716648</td>\n",
" <td> 3.6</td>\n",
" <td> 2716665</td>\n",
" <td> 3.5</td>\n",
" <td> 2716706</td>\n",
" <td> -</td>\n",
" <td> 18.9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ubiC</th>\n",
" <td> 4250399</td>\n",
" <td> 7.6</td>\n",
" <td> 4250416</td>\n",
" <td> 8.1</td>\n",
" <td> 4250427</td>\n",
" <td> +</td>\n",
" <td> 12.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ugpB</th>\n",
" <td> 3590405</td>\n",
" <td> 7.8</td>\n",
" <td> 3590427</td>\n",
" <td> 6.4</td>\n",
" <td> 3590448</td>\n",
" <td> -</td>\n",
" <td> 16.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ung/yfiD</th>\n",
" <td> 2714537</td>\n",
" <td> 3.5</td>\n",
" <td> 2714570</td>\n",
" <td> 3.2</td>\n",
" <td> 2714527</td>\n",
" <td> +</td>\n",
" <td> 10.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>uspC</th>\n",
" <td> 1977521</td>\n",
" <td> 15.5</td>\n",
" <td> 1977537</td>\n",
" <td> 18.4</td>\n",
" <td> 1977548</td>\n",
" <td> +</td>\n",
" <td> 17.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>uxaB1</th>\n",
" <td> 1608750</td>\n",
" <td> 6.0</td>\n",
" <td> 1608715</td>\n",
" <td> 4.9</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yaiZ/yaiY</th>\n",
" <td> 398660</td>\n",
" <td> 5.1</td>\n",
" <td> 398696</td>\n",
" <td> 6.2</td>\n",
" <td> 398716</td>\n",
" <td> -</td>\n",
" <td> 11.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ybaY/tesB</th>\n",
" <td> 474480</td>\n",
" <td> 3.0</td>\n",
" <td> 474519</td>\n",
" <td> 2.7</td>\n",
" <td> 474531</td>\n",
" <td> +</td>\n",
" <td> 18.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ybcV_intragenic</th>\n",
" <td> 578611</td>\n",
" <td> 4.0</td>\n",
" <td> 578634</td>\n",
" <td> 3.0</td>\n",
" <td> 578708</td>\n",
" <td> +</td>\n",
" <td> 12.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ybdJ</th>\n",
" <td> 605400</td>\n",
" <td> 3.2</td>\n",
" <td> 605428</td>\n",
" <td> 3.0</td>\n",
" <td> 605430</td>\n",
" <td> +</td>\n",
" <td> 17.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ybdN</th>\n",
" <td> 1451687</td>\n",
" <td> 3.7</td>\n",
" <td> 1451713</td>\n",
" <td> 4.4</td>\n",
" <td> 1451753</td>\n",
" <td> -</td>\n",
" <td> 15.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ybfA/kdpF</th>\n",
" <td> 728168</td>\n",
" <td> 4.4</td>\n",
" <td> 728182</td>\n",
" <td> 4.2</td>\n",
" <td> 728198</td>\n",
" <td> -</td>\n",
" <td> 15.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ybiU</th>\n",
" <td> 858305</td>\n",
" <td> 16.3</td>\n",
" <td> 858323</td>\n",
" <td> 15.4</td>\n",
" <td> 858343</td>\n",
" <td> +</td>\n",
" <td> 17.1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yceJ</th>\n",
" <td> 1118283</td>\n",
" <td> 3.3</td>\n",
" <td> 1118305</td>\n",
" <td> 2.0</td>\n",
" <td> 1118341</td>\n",
" <td> -</td>\n",
" <td> 15.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ycgV</th>\n",
" <td> 1255346</td>\n",
" <td> 2.4</td>\n",
" <td> 1255320</td>\n",
" <td> 2.1</td>\n",
" <td> 1255353</td>\n",
" <td> -</td>\n",
" <td> 19.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ycjG/tpx</th>\n",
" <td> 1386819</td>\n",
" <td> 2.6</td>\n",
" <td> 1386801</td>\n",
" <td> 2.7</td>\n",
" <td> 1386864</td>\n",
" <td> -</td>\n",
" <td> 17.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ydcJ/ydcI</th>\n",
" <td> 1493129</td>\n",
" <td> 2.7</td>\n",
" <td> 1493151</td>\n",
" <td> 3.6</td>\n",
" <td> 1493175</td>\n",
" <td> -</td>\n",
" <td> 15.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yecR/isrB_or_azuC</th>\n",
" <td> 1986029</td>\n",
" <td> 5.4</td>\n",
" <td> 1986030</td>\n",
" <td> 3.9</td>\n",
" <td> 1986099</td>\n",
" <td> +</td>\n",
" <td> 17.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yegE/udk</th>\n",
" <td> 2141127</td>\n",
" <td> 2.9</td>\n",
" <td> 2141185</td>\n",
" <td> 2.7</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yehB_intragenic</th>\n",
" <td> 2188596</td>\n",
" <td> 3.6</td>\n",
" <td> 2188623</td>\n",
" <td> 3.0</td>\n",
" <td> 2188606</td>\n",
" <td> +</td>\n",
" <td> 15.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yeiQ1</th>\n",
" <td> 2264169</td>\n",
" <td> 12.1</td>\n",
" <td> 2264107</td>\n",
" <td> 3.5</td>\n",
" <td> 2264237</td>\n",
" <td> +</td>\n",
" <td> 20.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yejG1</th>\n",
" <td> 2276269</td>\n",
" <td> 8.2</td>\n",
" <td> 2276279</td>\n",
" <td> 8.5</td>\n",
" <td> 2276322</td>\n",
" <td> -</td>\n",
" <td> 18.8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yfbM</th>\n",
" <td> 2384795</td>\n",
" <td> 4.5</td>\n",
" <td> 2384816</td>\n",
" <td> 4.5</td>\n",
" <td> 2384825</td>\n",
" <td> +</td>\n",
" <td> 14.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yffQ</th>\n",
" <td> 2561375</td>\n",
" <td> 5.9</td>\n",
" <td> 2561415</td>\n",
" <td> 6.3</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ygbE</th>\n",
" <td> 2871290</td>\n",
" <td> 2.7</td>\n",
" <td> 2871334</td>\n",
" <td> 5.3</td>\n",
" <td> 2871332</td>\n",
" <td> +</td>\n",
" <td> 15.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ygjG</th>\n",
" <td> 3217347</td>\n",
" <td> 12.5</td>\n",
" <td> 3217372</td>\n",
" <td> 12.0</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yhiS_2_intragenic</th>\n",
" <td> 3651471</td>\n",
" <td> 3.6</td>\n",
" <td> 3651471</td>\n",
" <td> 3.5</td>\n",
" <td> 3651490</td>\n",
" <td> +</td>\n",
" <td> 13.5</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yhjE</th>\n",
" <td> 3672558</td>\n",
" <td> 76.9</td>\n",
" <td> 3672585</td>\n",
" <td> 83.0</td>\n",
" <td> 3672621</td>\n",
" <td> -</td>\n",
" <td> 17.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yhjX</th>\n",
" <td> 3710211</td>\n",
" <td> 12.4</td>\n",
" <td> 3710222</td>\n",
" <td> 15.2</td>\n",
" <td> 3710228</td>\n",
" <td> +</td>\n",
" <td> 14.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yifK</th>\n",
" <td> 3978765</td>\n",
" <td> 4.9</td>\n",
" <td> 3978811</td>\n",
" <td> 4.9</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" <td> NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yigG</th>\n",
" <td> 4001166</td>\n",
" <td> 4.0</td>\n",
" <td> 4001194</td>\n",
" <td> 3.6</td>\n",
" <td> 4001224</td>\n",
" <td> -</td>\n",
" <td> 19.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yjiJ</th>\n",
" <td> 4560669</td>\n",
" <td> 2.8</td>\n",
" <td> 4560714</td>\n",
" <td> 2.8</td>\n",
" <td> 4560740</td>\n",
" <td> -</td>\n",
" <td> 20.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yjiS/yjiR</th>\n",
" <td> 4569683</td>\n",
" <td> 3.0</td>\n",
" <td> 4569668</td>\n",
" <td> 2.4</td>\n",
" <td> 4569691</td>\n",
" <td> +</td>\n",
" <td> 17.4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yjtD</th>\n",
" <td> 4638845</td>\n",
" <td> 4.1</td>\n",
" <td> 4638852</td>\n",
" <td> 4.9</td>\n",
" <td> 4638882</td>\n",
" <td> +</td>\n",
" <td> 16.6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ymgJ/ymjI</th>\n",
" <td> 1222398</td>\n",
" <td> 5.0</td>\n",
" <td> 1222442</td>\n",
" <td> 3.1</td>\n",
" <td> 1222426</td>\n",
" <td> +</td>\n",
" <td> 10.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ynaJ</th>\n",
" <td> 1395308</td>\n",
" <td> 10.8</td>\n",
" <td> 1395329</td>\n",
" <td> 13.3</td>\n",
" <td> 1395358</td>\n",
" <td> -</td>\n",
" <td> 16.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yncE/yncD</th>\n",
" <td> 1521168</td>\n",
" <td> 3.6</td>\n",
" <td> 1521200</td>\n",
" <td> 3.8</td>\n",
" <td> 1521129</td>\n",
" <td> +</td>\n",
" <td> 14.3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>yohO</th>\n",
" <td> 2213656</td>\n",
" <td> 2.5</td>\n",
" <td> 2213637</td>\n",
" <td> 1.9</td>\n",
" <td> 2213630</td>\n",
" <td> -</td>\n",
" <td> 14.2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ypdA/yfdZ</th>\n",
" <td> 2496459</td>\n",
" <td> 2.9</td>\n",
" <td> 2496499</td>\n",
" <td> 3.3</td>\n",
" <td> 2496526</td>\n",
" <td> -</td>\n",
" <td> 14.7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>ytfF</th>\n",
" <td> 4431123</td>\n",
" <td> 4.0</td>\n",
" <td> 4431150</td>\n",
" <td> 3.3</td>\n",
" <td> 4431197</td>\n",
" <td> -</td>\n",
" <td> 19.2</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 6,
"text": [
"<IPython.core.display.HTML at 0x10f5b1ed0>"
]
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ome.query(ChipPeakGene).filter_by(gene_name='caiT').all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 7,
"text": [
"[ChipPeakGene (ArcA): (Gene: caiT (b0040), Condition: C:glucose, N:NH4Cl, e:NO3, BindingSite: (+)41664-42181),\n",
" ChipPeakGene (ArcA): (Gene: caiT (b0040), Condition: C:glucose, N:NH4Cl, e:anaerobic, BindingSite: (+)41673-42043)]"
]
}
],
"prompt_number": 7
},
{
"cell_type": "heading",
"level": 3,
"metadata": {},
"source": [
"Manually curated list of discrepancies"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"kiley_discrepancies = {\n",
" 'pdhR':'very weak, insignificant peak',\\\n",
" 'gcd': 'very weak, insignificant peak',\\\n",
" 'intF_intergenic': 'variable, phage related peak',\\\n",
" 'intF': 'variable, phage related peak',\\\n",
" 'yaiZ/yaiY': 'weak peak, fell just below threshold',\\\n",
" 'lon': 'variable, potential sraA small RNA contamination',\\\n",
" 'ybcV_intragenic': 'weak, variable, phage proximal',\\\n",
" 'ybdJ': 'very weak, essentially no signal',\\\n",
" 'ybaY/tesB': 'three significant out of 12',\\\n",
" 'hyaA': 'two significant nitrate peaks',\\\n",
" 'csgD': 'two significant anaerobic peaks',\\\n",
" 'csgB': 'two significant anaerobic peaks',\\\n",
" 'ymgJ/ymjI': 'no signal',\\\n",
" 'ycgV': 'two signficant anaerobic peaks',\\\n",
" 'ompW': 'two significant anaerobic peaks',\\\n",
" 'fnrS': 'no signal',\\\n",
" 'CO343': 'phage',\\\n",
" 'ybdN': 'two significant anaerobic peaks',\\\n",
" 'ydcJ/ydcI': 'very weak, insignificant peaks',\\\n",
" 'intergenic': 'all weak and insignificant, 2563400 is phage',\\\n",
" 'ryeA/pphA': 'three weak insignificant peaks',\\\n",
" 'yegE/udk': 'no signal',\\\n",
" 'yohO': 'weak, insignificant signal, possibly small RNA contamination',\\\n",
" 'ung/yfiD': 'no signal',\\\n",
" 'yhiS_2_intragenic': 'two significant anaerobic peaks',\\\n",
" 'gadE': 'two weak peaks, one significant',\\\n",
" 'dctA': 'two significant anaerobic peaks',\\\n",
" 'mdtL': 'no signal',\\\n",
" 'yifK': 'no upstream signal',\\\n",
" 'spfl': 'weak signal, possibly small RNA contamination',\\\n",
" 'secE': 'ribosomal contamination',\\\n",
" 'proP': 'weak, insignificant nitrate peaks',\\\n",
" 'cadB': 'two significant anaerobic peaks' \n",
" }\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 1
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"len(kiley_discrepancies.keys())"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 2,
"text": [
"33"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}
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