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exploring using pandas for QIIME mapping files
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README.md

Some exploration into how the pandas DataFrame could be a useful underlying representation for QIIME's metadata mapping files.

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pandas-v-qiime-mapping-files.ipynb
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"name": ""
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"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"First we'll pull a remote mapping file (this doesn't rely on pandas or the current QIIME mapping file support - we're just pulling a tsv version of a Google Spreadsheet). The mapping file is [here](https://docs.google.com/spreadsheet/ccc?key=0AvglGXLayhG7dDNCWnUwSHhWNmxKODZISWx6VzBqU0E#gid=0)."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!load_remote_mapping_file.py -k 0AvglGXLayhG7dDNCWnUwSHhWNmxKODZISWx6VzBqU0E -o map1.tsv"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 1
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": [
"Load a mapping file with QIIME and do some work with it."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from qiime.parse import parse_mapping_file_to_dict"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qmap, comment_lines = parse_mapping_file_to_dict(open('map1.tsv'))"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 3
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can do pretty basic stuff with this: it's a 2D dict mapping sample ids to per-sample metadata dictionaries. \n",
"\n",
"**Pro**: it's easy to use.\n",
"\n",
"**Con**: anything you want to do basically requires you to pass this dict to other functions."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qmap.keys()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 4,
"text": [
"['Stillton4R2',\n",
" 'Stillton4R3',\n",
" 'Stillton4R1',\n",
" 'HCanyon3R3',\n",
" 'HCanyon3R2',\n",
" 'HCanyon3R1',\n",
" 'HCanyon8R1',\n",
" 'HCanyon2R2',\n",
" 'HCanyon2R3',\n",
" 'HCanyon2R1',\n",
" 'HCanyon8R2',\n",
" 'Halls8R1',\n",
" 'HCanyon0R1',\n",
" 'HCanyon0R2',\n",
" 'HCanyon0R3',\n",
" 'HCanyon7R3',\n",
" 'HCanyon7R2',\n",
" 'HCanyon7R1',\n",
" 'HCanyon1R1',\n",
" 'HCanyon1R3',\n",
" 'HCanyon1R2',\n",
" 'HCanyon10R2',\n",
" 'HCanyon10R3',\n",
" 'HCanyon10R1',\n",
" 'HCanyon11R3',\n",
" 'HCanyon11R2',\n",
" 'HCanyon11R1',\n",
" 'HCanyon6R2',\n",
" 'HCanyon6R3',\n",
" 'HCanyon6R1',\n",
" 'Stillton11R1',\n",
" 'HCanyon5R3',\n",
" 'HCanyon5R2',\n",
" 'HCanyon4R1',\n",
" 'HCanyon4R2',\n",
" 'HCanyon4R3',\n",
" 'HCanyon12R1',\n",
" 'HCanyon12R2',\n",
" 'HCanyon12R3',\n",
" 'Halls9R2',\n",
" 'Halls9R1',\n",
" 'HCanyon8R3',\n",
" 'Halls8R2',\n",
" 'Stillton10R1',\n",
" 'Stillton10R2',\n",
" 'Stillton10R3',\n",
" 'Halls6R1',\n",
" 'Halls6R2',\n",
" 'Halls4R2',\n",
" 'Stillton5R2',\n",
" 'Halls4R1',\n",
" 'Halls3R1',\n",
" 'Halls3R2',\n",
" 'Halls5R2',\n",
" 'Stillton1R1',\n",
" 'Stillton2R1',\n",
" 'Stillton2R2',\n",
" 'Stillton2R3',\n",
" 'Stillton3R1',\n",
" 'Stillton3R3',\n",
" 'Stillton3R2',\n",
" 'Stillton1R2',\n",
" 'Halls5R1',\n",
" 'Halls2R1',\n",
" 'Halls2R2',\n",
" 'Halls1R2',\n",
" 'Halls1R1',\n",
" 'Halls0R2',\n",
" 'Halls0R1',\n",
" 'Stillton9R3',\n",
" 'Stillton9R2',\n",
" 'Stillton9R1',\n",
" 'Stillton7R1',\n",
" 'Halls10R1',\n",
" 'Halls10R2',\n",
" 'Stillton7R2',\n",
" 'Halls7R1',\n",
" 'Halls7R2',\n",
" 'Stillton0R2',\n",
" 'Stillton0R3',\n",
" 'Stillton0R1',\n",
" 'Stillton6R1',\n",
" 'Stillton6R2',\n",
" 'Stillton6R3',\n",
" 'HCanyon9R1',\n",
" 'HCanyon9R3',\n",
" 'HCanyon9R2',\n",
" 'Stillton7R3',\n",
" 'CrustControlR1',\n",
" 'CrustControlR2',\n",
" 'CrustControlR3',\n",
" 'Stillton8R3',\n",
" 'HCanyon5R1',\n",
" 'Stillton8R1',\n",
" 'Stillton11R3']"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qmap['Stillton4R2']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 5,
"text": [
"{'BarcodeSequence': 'GTGCAATCGACG',\n",
" 'DNA_ID_No': '29',\n",
" 'Day': '29',\n",
" 'Description': 'GlenCanyon_sc3r2',\n",
" 'Env': 'DisturbedSoil',\n",
" 'Hour': '18',\n",
" 'Lane': 'Lane4',\n",
" 'Latitude': 'N37_29.865',\n",
" 'LinkerPrimerSequence': 'CATGATCCTTCTGCAGGTTCACCTAC',\n",
" 'Longitude': 'W110_41.995',\n",
" 'Month': '9',\n",
" 'Primer_Plate': '5',\n",
" 'Replicate': '2',\n",
" 'Sample_Plate': 'GlenCanyon',\n",
" 'Sample_Type': 'Soil',\n",
" 'Site': 'Stillton4',\n",
" 'Site_Name': 'Stillton',\n",
" 'SourceSink': 'sink',\n",
" 'Type': 'DisturbedSoil',\n",
" 'TypeBasic': 'Soil',\n",
" 'Well_ID': 'e3',\n",
" 'Year': '2010',\n",
" 'bag_sample_id': 'sc3r2',\n",
" 'days_since_epoch': '14881',\n",
" 'estimated_elevation': '3663',\n",
" 'estimated_last_submerged': '2001',\n",
" 'estimated_years_since_submerged': '9',\n",
" 'estimated_years_since_submerged_for_plotting': '9',\n",
" 'gps_elevation': 'no_data',\n",
" 'gps_elevation_minus_estimated_elevation': 'NA',\n",
" 'sample_pH': '8.75',\n",
" 'site_number': '4'}"
]
}
],
"prompt_number": 5
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"So if you want to, e.g., know the latitude of ``Stillton4R2``, you'd access it as follows:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qmap['Stillton4R2']['Latitude']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 6,
"text": [
"'N37_29.865'"
]
}
],
"prompt_number": 6
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": [
"Now let's try using pandas"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"import pandas as pd"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap = pd.read_csv('map1.tsv', sep='\\t', index_col=0)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 9
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can still access data in nearly the same way..."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap['Latitude']['Stillton4R2']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 10,
"text": [
"'N37_29.865'"
]
}
],
"prompt_number": 10
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Or transpose it, or you prefer to access in QIIME's way..."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap_t = pmap.transpose()\n",
"pmap_t['Stillton4R2']['Latitude']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 11,
"text": [
"'N37_29.865'"
]
}
],
"prompt_number": 11
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap['Latitude']['Stillton4R2']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 12,
"text": [
"'N37_29.865'"
]
}
],
"prompt_number": 12
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"It's easy to explore information in the mapping file by e.g., figuring out summary stats for a numeric column:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap['sample_pH'].median()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 13,
"text": [
"9.27"
]
}
],
"prompt_number": 13
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap.plot('estimated_elevation', 'sample_pH')"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 14,
"text": [
"<matplotlib.axes.AxesSubplot at 0x109a65150>"
]
},
{
"metadata": {},
"output_type": "display_data",
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YQPG5nRviq1IFHn7Ytlhu29bekfv00yU7htIlezgRkdBVrhzcfTfceSe8/bad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\n",
"text": [
"<matplotlib.figure.Figure at 0x109a578d0>"
]
}
],
"prompt_number": 14
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap.hist('sample_pH')"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 15,
"text": [
"array([[<matplotlib.axes.AxesSubplot object at 0x109a78d50>]], dtype=object)"
]
},
{
"metadata": {},
"output_type": "display_data",
"png": 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fo8MGzKDDtnf2RP087Orq6tDnb7zxRtgZJACA2Gg1sGfNmqVx48bp8OHD6t+/v373u99p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\nJghsALAJAhsAbILABgCbILABwCb+H4fMLvj4ElOfAAAAAElFTkSuQmCC\n",
"text": [
"<matplotlib.figure.Figure at 0x109a7b750>"
]
}
],
"prompt_number": 15
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"or to count the number of non-$NA$ entries per category"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap.count()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 16,
"text": [
"BarcodeSequence 95\n",
"LinkerPrimerSequence 95\n",
"site_number 95\n",
"bag_sample_id 95\n",
"sample_pH 95\n",
"Sample_Type 95\n",
"Well_ID 95\n",
"Sample_Plate 95\n",
"Primer_Plate 95\n",
"Lane 95\n",
"Latitude 95\n",
"Longitude 95\n",
"Type 95\n",
"TypeBasic 95\n",
"Env 77\n",
"SourceSink 77\n",
"estimated_elevation 95\n",
"estimated_years_since_submerged 68\n",
"estimated_years_since_submerged_for_plotting 92\n",
"estimated_last_submerged 68\n",
"gps_elevation 95\n",
"gps_elevation_minus_estimated_elevation 66\n",
"Month 95\n",
"Day 95\n",
"Year 95\n",
"days_since_epoch 95\n",
"Hour 95\n",
"Site 95\n",
"Site_Name 95\n",
"Replicate 95\n",
"DNA_ID_No 95\n",
"Description 95\n",
"dtype: int64"
]
}
],
"prompt_number": 16
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"or clean-up, to normalize how $NA$ is represented"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap['estimated_years_since_submerged']['Stillton9R3']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 17,
"text": [
"nan"
]
}
],
"prompt_number": 17
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap['gps_elevation']['Stillton9R3']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 18,
"text": [
"'no_data'"
]
}
],
"prompt_number": 18
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap = pmap.replace('no_data',nan)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 19
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap['gps_elevation']['Stillton9R3']"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 20,
"text": [
"nan"
]
}
],
"prompt_number": 20
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"These objects also display nicely in IPython Notebook."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pmap"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>BarcodeSequence</th>\n",
" <th>LinkerPrimerSequence</th>\n",
" <th>site_number</th>\n",
" <th>bag_sample_id</th>\n",
" <th>sample_pH</th>\n",
" <th>Sample_Type</th>\n",
" <th>Well_ID</th>\n",
" <th>Sample_Plate</th>\n",
" <th>Primer_Plate</th>\n",
" <th>Lane</th>\n",
" <th>Latitude</th>\n",
" <th>Longitude</th>\n",
" <th>Type</th>\n",
" <th>TypeBasic</th>\n",
" <th>Env</th>\n",
" <th>SourceSink</th>\n",
" <th>estimated_elevation</th>\n",
" <th>estimated_years_since_submerged</th>\n",
" <th>estimated_years_since_submerged_for_plotting</th>\n",
" <th>estimated_last_submerged</th>\n",
" <th></th>\n",
" </tr>\n",
" <tr>\n",
" <th>#SampleID</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></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>Halls0R1</th>\n",
" <td> GTATATCCGCAG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> ha0r1</td>\n",
" <td> 9.17</td>\n",
" <td> Soil</td>\n",
" <td> c2</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.365</td>\n",
" <td> W110_42.550</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls0R2</th>\n",
" <td> GTCGTAGCCAGA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> ha0r2</td>\n",
" <td> 9.15</td>\n",
" <td> Soil</td>\n",
" <td> d2</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.365</td>\n",
" <td> W110_42.550</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls1R1</th>\n",
" <td> GCTGTGTAGGAC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 1</td>\n",
" <td> ha1r1</td>\n",
" <td> 9.17</td>\n",
" <td> Soil</td>\n",
" <td> a2</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.365</td>\n",
" <td> W110_42.550</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls1R2</th>\n",
" <td> GGTCGTAGCGTA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 1</td>\n",
" <td> ha1r2</td>\n",
" <td> 9.16</td>\n",
" <td> Soil</td>\n",
" <td> b2</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.365</td>\n",
" <td> W110_42.550</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon0R1</th>\n",
" <td> TAGACTGTACTC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> hc1r1</td>\n",
" <td> 9.55</td>\n",
" <td> Soil</td>\n",
" <td> g10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.106</td>\n",
" <td> W110_40.479</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon0R2</th>\n",
" <td> TAGTCGTCTAGT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> hc1r2</td>\n",
" <td> 9.44</td>\n",
" <td> Soil</td>\n",
" <td> a9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.106</td>\n",
" <td> W110_40.479</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon0R3</th>\n",
" <td> GGCTATGACATC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> hc1r3</td>\n",
" <td> 9.41</td>\n",
" <td> Soil</td>\n",
" <td> a11</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.106</td>\n",
" <td> W110_40.479</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon1R1</th>\n",
" <td> GTCTTCGTCGCT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 1</td>\n",
" <td> hc0r1</td>\n",
" <td> 9.31</td>\n",
" <td> Soil</td>\n",
" <td> d10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.106</td>\n",
" <td> W110_40.479</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon1R2</th>\n",
" <td> GTGTTGCAGCAT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 1</td>\n",
" <td> hc0r2</td>\n",
" <td> 9.26</td>\n",
" <td> Soil</td>\n",
" <td> e10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.106</td>\n",
" <td> W110_40.479</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon1R3</th>\n",
" <td> TACATCACCACA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 1</td>\n",
" <td> hc0r3</td>\n",
" <td> 9.13</td>\n",
" <td> Soil</td>\n",
" <td> f10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.106</td>\n",
" <td> W110_40.479</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton0R1</th>\n",
" <td> GTGTGCTATCAG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> sc1r1</td>\n",
" <td> 8.02</td>\n",
" <td> Soil</td>\n",
" <td> e8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.719</td>\n",
" <td> W110_42.012</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton0R2</th>\n",
" <td> TACAGATGGCTC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> sc1r2</td>\n",
" <td> 8.00</td>\n",
" <td> Soil</td>\n",
" <td> f8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.719</td>\n",
" <td> W110_42.012</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton0R3</th>\n",
" <td> TACTTACTGCAG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 0</td>\n",
" <td> sc1r3</td>\n",
" <td> 8.05</td>\n",
" <td> Soil</td>\n",
" <td> g8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.719</td>\n",
" <td> W110_42.012</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton1R1</th>\n",
" <td> GTGTCTACATTG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 1</td>\n",
" <td> sc0r1</td>\n",
" <td> 8.35</td>\n",
" <td> Soil</td>\n",
" <td> e7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.719</td>\n",
" <td> W110_42.012</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton1R2</th>\n",
" <td> TACACGATCTAC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 1</td>\n",
" <td> sc0r2</td>\n",
" <td> 8.30</td>\n",
" <td> Soil</td>\n",
" <td> f7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.719</td>\n",
" <td> W110_42.012</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> Sediment</td>\n",
" <td> source</td>\n",
" <td> 3633</td>\n",
" <td> 0</td>\n",
" <td> 0.1</td>\n",
" <td> 2010</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls2R1</th>\n",
" <td> GTCAACGCGATG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> ha2r1</td>\n",
" <td> 9.23</td>\n",
" <td> Soil</td>\n",
" <td> c7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.352</td>\n",
" <td> W110_42.547</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls2R2</th>\n",
" <td> GTCTCTCTACGC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> ha2r2</td>\n",
" <td> 9.26</td>\n",
" <td> Soil</td>\n",
" <td> d7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.352</td>\n",
" <td> W110_42.547</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon2R1</th>\n",
" <td> TAGCTGAGTCCA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> hc1r1</td>\n",
" <td> 9.55</td>\n",
" <td> Soil</td>\n",
" <td> h8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.097</td>\n",
" <td> W110_40.526</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon2R2</th>\n",
" <td> GGCGACATGTAC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> hc1r2</td>\n",
" <td> 9.44</td>\n",
" <td> Soil</td>\n",
" <td> h10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.097</td>\n",
" <td> W110_40.526</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon2R3</th>\n",
" <td> GTAGATGCTTCG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> hc1r3</td>\n",
" <td> 9.41</td>\n",
" <td> Soil</td>\n",
" <td> b9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.097</td>\n",
" <td> W110_40.526</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton2R1</th>\n",
" <td> TACTGGACGCGA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> sc1r1</td>\n",
" <td> 8.02</td>\n",
" <td> Soil</td>\n",
" <td> g7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.749</td>\n",
" <td> W110_42.018</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton2R2</th>\n",
" <td> TAGCTCGTAACT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> sc1r2</td>\n",
" <td> 8.00</td>\n",
" <td> Soil</td>\n",
" <td> h7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.749</td>\n",
" <td> W110_42.018</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton2R3</th>\n",
" <td> GGCAGTGTATCG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 2</td>\n",
" <td> sc1r3</td>\n",
" <td> 8.05</td>\n",
" <td> Soil</td>\n",
" <td> a8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.749</td>\n",
" <td> W110_42.018</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3643</td>\n",
" <td> 1</td>\n",
" <td> 1.0</td>\n",
" <td> 2009</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls3R1</th>\n",
" <td> GGATCGCAGATC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> ha3r1</td>\n",
" <td> 9.45</td>\n",
" <td> Soil</td>\n",
" <td> a7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.349</td>\n",
" <td> W110_42.545</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls3R2</th>\n",
" <td> GTAGACTGCGTG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> ha3r2</td>\n",
" <td> 9.41</td>\n",
" <td> Soil</td>\n",
" <td> b7</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.349</td>\n",
" <td> W110_42.545</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon3R1</th>\n",
" <td> GTCATATCGTAC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> hc2r1</td>\n",
" <td> 9.65</td>\n",
" <td> Soil</td>\n",
" <td> c9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.087</td>\n",
" <td> W110_40.553</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon3R2</th>\n",
" <td> GTCTGGATAGCG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> hc2r2</td>\n",
" <td> 9.71</td>\n",
" <td> Soil</td>\n",
" <td> d9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.087</td>\n",
" <td> W110_40.553</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon3R3</th>\n",
" <td> GTGTGTGTCAGG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> hc2r3</td>\n",
" <td> 9.67</td>\n",
" <td> Soil</td>\n",
" <td> e9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.087</td>\n",
" <td> W110_40.553</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton3R1</th>\n",
" <td> GTAGAGCTGTTC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> sc2r1</td>\n",
" <td> 8.13</td>\n",
" <td> Soil</td>\n",
" <td> b8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.787</td>\n",
" <td> W110_42.014</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton3R2</th>\n",
" <td> GTCACGACTATT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> sc2r2</td>\n",
" <td> 8.21</td>\n",
" <td> Soil</td>\n",
" <td> c8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.787</td>\n",
" <td> W110_42.014</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton3R3</th>\n",
" <td> GTCTGACAGTTG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 3</td>\n",
" <td> sc2r3</td>\n",
" <td> 8.44</td>\n",
" <td> Soil</td>\n",
" <td> d8</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.787</td>\n",
" <td> W110_42.014</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3653</td>\n",
" <td> 8</td>\n",
" <td> 8.0</td>\n",
" <td> 2002</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls4R1</th>\n",
" <td> TACTGCGACAGT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> ha4r1</td>\n",
" <td> 9.46</td>\n",
" <td> Soil</td>\n",
" <td> g6</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.342</td>\n",
" <td> W110_42.545</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls4R2</th>\n",
" <td> TAGCGGATCACG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> ha4r2</td>\n",
" <td> 9.49</td>\n",
" <td> Soil</td>\n",
" <td> h6</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.342</td>\n",
" <td> W110_42.545</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon4R1</th>\n",
" <td> TACAGTCTCATG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> hc3r1</td>\n",
" <td> 9.49</td>\n",
" <td> Soil</td>\n",
" <td> f9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.055</td>\n",
" <td> W110_40.607</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon4R2</th>\n",
" <td> TACTTCGCTCGC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> hc3r2</td>\n",
" <td> 9.39</td>\n",
" <td> Soil</td>\n",
" <td> g9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.055</td>\n",
" <td> W110_40.607</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon4R3</th>\n",
" <td> TAGGTATCTCAC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> hc3r3</td>\n",
" <td> 9.42</td>\n",
" <td> Soil</td>\n",
" <td> h9</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.055</td>\n",
" <td> W110_40.607</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton4R1</th>\n",
" <td> GTCGTGTGTCAA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> sc3r1</td>\n",
" <td> 8.82</td>\n",
" <td> Soil</td>\n",
" <td> d3</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.865</td>\n",
" <td> W110_41.995</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton4R2</th>\n",
" <td> GTGCAATCGACG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> sc3r2</td>\n",
" <td> 8.75</td>\n",
" <td> Soil</td>\n",
" <td> e3</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.865</td>\n",
" <td> W110_41.995</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton4R3</th>\n",
" <td> TAACAGTCGCTG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 4</td>\n",
" <td> sc3r3</td>\n",
" <td> 8.71</td>\n",
" <td> Soil</td>\n",
" <td> f3</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.865</td>\n",
" <td> W110_41.995</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3663</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls5R1</th>\n",
" <td> GTGTACCTATCA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 5</td>\n",
" <td> ha5r1</td>\n",
" <td> 9.50</td>\n",
" <td> Soil</td>\n",
" <td> e6</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.309</td>\n",
" <td> W110_42.571</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3673</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls5R2</th>\n",
" <td> TACACACATGGC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 5</td>\n",
" <td> ha5r2</td>\n",
" <td> 9.54</td>\n",
" <td> Soil</td>\n",
" <td> f6</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.309</td>\n",
" <td> W110_42.571</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3673</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon5R1</th>\n",
" <td> GGCGTACTGATG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 5</td>\n",
" <td> hc4r1</td>\n",
" <td> 9.45</td>\n",
" <td> Soil</td>\n",
" <td> a10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.035</td>\n",
" <td> W110_40.612</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3673</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon5R2</th>\n",
" <td> GTAGCAACGTCT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 5</td>\n",
" <td> hc4r2</td>\n",
" <td> 9.49</td>\n",
" <td> Soil</td>\n",
" <td> b10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.035</td>\n",
" <td> W110_40.612</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3673</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon5R3</th>\n",
" <td> GTCATTCACGAG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 5</td>\n",
" <td> hc4r3</td>\n",
" <td> 9.46</td>\n",
" <td> Soil</td>\n",
" <td> c10</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.035</td>\n",
" <td> W110_40.612</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3673</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton5R2</th>\n",
" <td> GTATCCATGCGA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 5</td>\n",
" <td> sc4r2</td>\n",
" <td> 8.85</td>\n",
" <td> Soil</td>\n",
" <td> c3</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_29.877</td>\n",
" <td> W110_42.004</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3673</td>\n",
" <td> 9</td>\n",
" <td> 9.0</td>\n",
" <td> 2001</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls6R1</th>\n",
" <td> TAGTGCTGCGTA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> ha6r1</td>\n",
" <td> 9.44</td>\n",
" <td> Soil</td>\n",
" <td> h11</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.296</td>\n",
" <td> W110_42.579</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls6R2</th>\n",
" <td> GGTATACGCAGC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> ha6r2</td>\n",
" <td> 9.42</td>\n",
" <td> Soil</td>\n",
" <td> a12</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.296</td>\n",
" <td> W110_42.579</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon6R1</th>\n",
" <td> GTAGCTGACGCA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> hc5r1</td>\n",
" <td> 9.47</td>\n",
" <td> Soil</td>\n",
" <td> b12</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.026</td>\n",
" <td> W110_40.609</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon6R2</th>\n",
" <td> GTCGACTCCTCT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> hc5r2</td>\n",
" <td> 9.50</td>\n",
" <td> Soil</td>\n",
" <td> c12</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.026</td>\n",
" <td> W110_40.609</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon6R3</th>\n",
" <td> GTGACTGCGGAT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> hc5r3</td>\n",
" <td> 9.51</td>\n",
" <td> Soil</td>\n",
" <td> d12</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.026</td>\n",
" <td> W110_40.609</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton6R1</th>\n",
" <td> TAGCACACCTAT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> sc5r1</td>\n",
" <td> 9.50</td>\n",
" <td> Soil</td>\n",
" <td> h2</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_30.066</td>\n",
" <td> W110_41.972</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton6R2</th>\n",
" <td> GCTTACATCGAG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> sc5r2</td>\n",
" <td> 9.54</td>\n",
" <td> Soil</td>\n",
" <td> a3</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_30.066</td>\n",
" <td> W110_41.972</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton6R3</th>\n",
" <td> GGTGCGTGTATG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 6</td>\n",
" <td> sc5r3</td>\n",
" <td> 9.49</td>\n",
" <td> Soil</td>\n",
" <td> b3</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_30.066</td>\n",
" <td> W110_41.972</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3683</td>\n",
" <td> 10</td>\n",
" <td> 10.0</td>\n",
" <td> 2000</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls7R1</th>\n",
" <td> GCTGTAGTATGC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 7</td>\n",
" <td> ha7r1</td>\n",
" <td> 9.06</td>\n",
" <td> Soil</td>\n",
" <td> a1</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.291</td>\n",
" <td> W110_42.592</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3693</td>\n",
" <td> 11</td>\n",
" <td> 11.0</td>\n",
" <td> 1999</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Halls7R2</th>\n",
" <td> GTTGACGACAGC</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 7</td>\n",
" <td> ha7r2</td>\n",
" <td> 9.01</td>\n",
" <td> Soil</td>\n",
" <td> f1</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_28.291</td>\n",
" <td> W110_42.592</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3693</td>\n",
" <td> 11</td>\n",
" <td> 11.0</td>\n",
" <td> 1999</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon7R1</th>\n",
" <td> GTACTCTAGACT</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 7</td>\n",
" <td> hc6r1</td>\n",
" <td> 9.34</td>\n",
" <td> Soil</td>\n",
" <td> b6</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.017</td>\n",
" <td> W110_40.602</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3693</td>\n",
" <td> 11</td>\n",
" <td> 11.0</td>\n",
" <td> 1999</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon7R2</th>\n",
" <td> GTATGTTGCTCA</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 7</td>\n",
" <td> hc6r2</td>\n",
" <td> 9.30</td>\n",
" <td> Soil</td>\n",
" <td> c6</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.017</td>\n",
" <td> W110_40.602</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3693</td>\n",
" <td> 11</td>\n",
" <td> 11.0</td>\n",
" <td> 1999</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>HCanyon7R3</th>\n",
" <td> GTCTCATGTAGG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 7</td>\n",
" <td> hc6r3</td>\n",
" <td> 9.38</td>\n",
" <td> Soil</td>\n",
" <td> d6</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_33.017</td>\n",
" <td> W110_40.602</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3693</td>\n",
" <td> 11</td>\n",
" <td> 11.0</td>\n",
" <td> 1999</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton7R1</th>\n",
" <td> GTGATAGTGCCG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 7</td>\n",
" <td> sc6r1</td>\n",
" <td> 9.29</td>\n",
" <td> Soil</td>\n",
" <td> e2</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_30.094</td>\n",
" <td> W110_41.947</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3693</td>\n",
" <td> 11</td>\n",
" <td> 11.0</td>\n",
" <td> 1999</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Stillton7R2</th>\n",
" <td> GTTGTATACTCG</td>\n",
" <td> CATGATCCTTCTGCAGGTTCACCTAC</td>\n",
" <td> 7</td>\n",
" <td> sc6r2</td>\n",
" <td> 9.38</td>\n",
" <td> Soil</td>\n",
" <td> f2</td>\n",
" <td> GlenCanyon</td>\n",
" <td> 5</td>\n",
" <td> Lane4</td>\n",
" <td> N37_30.094</td>\n",
" <td> W110_41.947</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> Soil</td>\n",
" <td> DisturbedSoil</td>\n",
" <td> sink</td>\n",
" <td> 3693</td>\n",
" <td> 11</td>\n",
" <td> 11.0</td>\n",
" <td> 1999</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th></th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>95 rows \u00d7 32 columns</p>\n",
"</div>"
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 21,
"text": [
" BarcodeSequence LinkerPrimerSequence site_number \\\n",
"#SampleID \n",
"Halls0R1 GTATATCCGCAG CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"Halls0R2 GTCGTAGCCAGA CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"Halls1R1 GCTGTGTAGGAC CATGATCCTTCTGCAGGTTCACCTAC 1 \n",
"Halls1R2 GGTCGTAGCGTA CATGATCCTTCTGCAGGTTCACCTAC 1 \n",
"HCanyon0R1 TAGACTGTACTC CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"HCanyon0R2 TAGTCGTCTAGT CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"HCanyon0R3 GGCTATGACATC CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"HCanyon1R1 GTCTTCGTCGCT CATGATCCTTCTGCAGGTTCACCTAC 1 \n",
"HCanyon1R2 GTGTTGCAGCAT CATGATCCTTCTGCAGGTTCACCTAC 1 \n",
"HCanyon1R3 TACATCACCACA CATGATCCTTCTGCAGGTTCACCTAC 1 \n",
"Stillton0R1 GTGTGCTATCAG CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"Stillton0R2 TACAGATGGCTC CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"Stillton0R3 TACTTACTGCAG CATGATCCTTCTGCAGGTTCACCTAC 0 \n",
"Stillton1R1 GTGTCTACATTG CATGATCCTTCTGCAGGTTCACCTAC 1 \n",
"Stillton1R2 TACACGATCTAC CATGATCCTTCTGCAGGTTCACCTAC 1 \n",
"Halls2R1 GTCAACGCGATG CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"Halls2R2 GTCTCTCTACGC CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"HCanyon2R1 TAGCTGAGTCCA CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"HCanyon2R2 GGCGACATGTAC CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"HCanyon2R3 GTAGATGCTTCG CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"Stillton2R1 TACTGGACGCGA CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"Stillton2R2 TAGCTCGTAACT CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"Stillton2R3 GGCAGTGTATCG CATGATCCTTCTGCAGGTTCACCTAC 2 \n",
"Halls3R1 GGATCGCAGATC CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"Halls3R2 GTAGACTGCGTG CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"HCanyon3R1 GTCATATCGTAC CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"HCanyon3R2 GTCTGGATAGCG CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"HCanyon3R3 GTGTGTGTCAGG CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"Stillton3R1 GTAGAGCTGTTC CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"Stillton3R2 GTCACGACTATT CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"Stillton3R3 GTCTGACAGTTG CATGATCCTTCTGCAGGTTCACCTAC 3 \n",
"Halls4R1 TACTGCGACAGT CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"Halls4R2 TAGCGGATCACG CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"HCanyon4R1 TACAGTCTCATG CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"HCanyon4R2 TACTTCGCTCGC CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"HCanyon4R3 TAGGTATCTCAC CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"Stillton4R1 GTCGTGTGTCAA CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"Stillton4R2 GTGCAATCGACG CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"Stillton4R3 TAACAGTCGCTG CATGATCCTTCTGCAGGTTCACCTAC 4 \n",
"Halls5R1 GTGTACCTATCA CATGATCCTTCTGCAGGTTCACCTAC 5 \n",
"Halls5R2 TACACACATGGC CATGATCCTTCTGCAGGTTCACCTAC 5 \n",
"HCanyon5R1 GGCGTACTGATG CATGATCCTTCTGCAGGTTCACCTAC 5 \n",
"HCanyon5R2 GTAGCAACGTCT CATGATCCTTCTGCAGGTTCACCTAC 5 \n",
"HCanyon5R3 GTCATTCACGAG CATGATCCTTCTGCAGGTTCACCTAC 5 \n",
"Stillton5R2 GTATCCATGCGA CATGATCCTTCTGCAGGTTCACCTAC 5 \n",
"Halls6R1 TAGTGCTGCGTA CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"Halls6R2 GGTATACGCAGC CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"HCanyon6R1 GTAGCTGACGCA CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"HCanyon6R2 GTCGACTCCTCT CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"HCanyon6R3 GTGACTGCGGAT CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"Stillton6R1 TAGCACACCTAT CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"Stillton6R2 GCTTACATCGAG CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"Stillton6R3 GGTGCGTGTATG CATGATCCTTCTGCAGGTTCACCTAC 6 \n",
"Halls7R1 GCTGTAGTATGC CATGATCCTTCTGCAGGTTCACCTAC 7 \n",
"Halls7R2 GTTGACGACAGC CATGATCCTTCTGCAGGTTCACCTAC 7 \n",
"HCanyon7R1 GTACTCTAGACT CATGATCCTTCTGCAGGTTCACCTAC 7 \n",
"HCanyon7R2 GTATGTTGCTCA CATGATCCTTCTGCAGGTTCACCTAC 7 \n",
"HCanyon7R3 GTCTCATGTAGG CATGATCCTTCTGCAGGTTCACCTAC 7 \n",
"Stillton7R1 GTGATAGTGCCG CATGATCCTTCTGCAGGTTCACCTAC 7 \n",
"Stillton7R2 GTTGTATACTCG CATGATCCTTCTGCAGGTTCACCTAC 7 \n",
" ... ... ... \n",
"\n",
" bag_sample_id sample_pH Sample_Type Well_ID Sample_Plate \\\n",
"#SampleID \n",
"Halls0R1 ha0r1 9.17 Soil c2 GlenCanyon \n",
"Halls0R2 ha0r2 9.15 Soil d2 GlenCanyon \n",
"Halls1R1 ha1r1 9.17 Soil a2 GlenCanyon \n",
"Halls1R2 ha1r2 9.16 Soil b2 GlenCanyon \n",
"HCanyon0R1 hc1r1 9.55 Soil g10 GlenCanyon \n",
"HCanyon0R2 hc1r2 9.44 Soil a9 GlenCanyon \n",
"HCanyon0R3 hc1r3 9.41 Soil a11 GlenCanyon \n",
"HCanyon1R1 hc0r1 9.31 Soil d10 GlenCanyon \n",
"HCanyon1R2 hc0r2 9.26 Soil e10 GlenCanyon \n",
"HCanyon1R3 hc0r3 9.13 Soil f10 GlenCanyon \n",
"Stillton0R1 sc1r1 8.02 Soil e8 GlenCanyon \n",
"Stillton0R2 sc1r2 8.00 Soil f8 GlenCanyon \n",
"Stillton0R3 sc1r3 8.05 Soil g8 GlenCanyon \n",
"Stillton1R1 sc0r1 8.35 Soil e7 GlenCanyon \n",
"Stillton1R2 sc0r2 8.30 Soil f7 GlenCanyon \n",
"Halls2R1 ha2r1 9.23 Soil c7 GlenCanyon \n",
"Halls2R2 ha2r2 9.26 Soil d7 GlenCanyon \n",
"HCanyon2R1 hc1r1 9.55 Soil h8 GlenCanyon \n",
"HCanyon2R2 hc1r2 9.44 Soil h10 GlenCanyon \n",
"HCanyon2R3 hc1r3 9.41 Soil b9 GlenCanyon \n",
"Stillton2R1 sc1r1 8.02 Soil g7 GlenCanyon \n",
"Stillton2R2 sc1r2 8.00 Soil h7 GlenCanyon \n",
"Stillton2R3 sc1r3 8.05 Soil a8 GlenCanyon \n",
"Halls3R1 ha3r1 9.45 Soil a7 GlenCanyon \n",
"Halls3R2 ha3r2 9.41 Soil b7 GlenCanyon \n",
"HCanyon3R1 hc2r1 9.65 Soil c9 GlenCanyon \n",
"HCanyon3R2 hc2r2 9.71 Soil d9 GlenCanyon \n",
"HCanyon3R3 hc2r3 9.67 Soil e9 GlenCanyon \n",
"Stillton3R1 sc2r1 8.13 Soil b8 GlenCanyon \n",
"Stillton3R2 sc2r2 8.21 Soil c8 GlenCanyon \n",
"Stillton3R3 sc2r3 8.44 Soil d8 GlenCanyon \n",
"Halls4R1 ha4r1 9.46 Soil g6 GlenCanyon \n",
"Halls4R2 ha4r2 9.49 Soil h6 GlenCanyon \n",
"HCanyon4R1 hc3r1 9.49 Soil f9 GlenCanyon \n",
"HCanyon4R2 hc3r2 9.39 Soil g9 GlenCanyon \n",
"HCanyon4R3 hc3r3 9.42 Soil h9 GlenCanyon \n",
"Stillton4R1 sc3r1 8.82 Soil d3 GlenCanyon \n",
"Stillton4R2 sc3r2 8.75 Soil e3 GlenCanyon \n",
"Stillton4R3 sc3r3 8.71 Soil f3 GlenCanyon \n",
"Halls5R1 ha5r1 9.50 Soil e6 GlenCanyon \n",
"Halls5R2 ha5r2 9.54 Soil f6 GlenCanyon \n",
"HCanyon5R1 hc4r1 9.45 Soil a10 GlenCanyon \n",
"HCanyon5R2 hc4r2 9.49 Soil b10 GlenCanyon \n",
"HCanyon5R3 hc4r3 9.46 Soil c10 GlenCanyon \n",
"Stillton5R2 sc4r2 8.85 Soil c3 GlenCanyon \n",
"Halls6R1 ha6r1 9.44 Soil h11 GlenCanyon \n",
"Halls6R2 ha6r2 9.42 Soil a12 GlenCanyon \n",
"HCanyon6R1 hc5r1 9.47 Soil b12 GlenCanyon \n",
"HCanyon6R2 hc5r2 9.50 Soil c12 GlenCanyon \n",
"HCanyon6R3 hc5r3 9.51 Soil d12 GlenCanyon \n",
"Stillton6R1 sc5r1 9.50 Soil h2 GlenCanyon \n",
"Stillton6R2 sc5r2 9.54 Soil a3 GlenCanyon \n",
"Stillton6R3 sc5r3 9.49 Soil b3 GlenCanyon \n",
"Halls7R1 ha7r1 9.06 Soil a1 GlenCanyon \n",
"Halls7R2 ha7r2 9.01 Soil f1 GlenCanyon \n",
"HCanyon7R1 hc6r1 9.34 Soil b6 GlenCanyon \n",
"HCanyon7R2 hc6r2 9.30 Soil c6 GlenCanyon \n",
"HCanyon7R3 hc6r3 9.38 Soil d6 GlenCanyon \n",
"Stillton7R1 sc6r1 9.29 Soil e2 GlenCanyon \n",
"Stillton7R2 sc6r2 9.38 Soil f2 GlenCanyon \n",
" ... ... ... ... ... \n",
"\n",
" Primer_Plate Lane Latitude Longitude Type \\\n",
"#SampleID \n",
"Halls0R1 5 Lane4 N37_28.365 W110_42.550 Sediment \n",
"Halls0R2 5 Lane4 N37_28.365 W110_42.550 Sediment \n",
"Halls1R1 5 Lane4 N37_28.365 W110_42.550 Sediment \n",
"Halls1R2 5 Lane4 N37_28.365 W110_42.550 Sediment \n",
"HCanyon0R1 5 Lane4 N37_33.106 W110_40.479 Sediment \n",
"HCanyon0R2 5 Lane4 N37_33.106 W110_40.479 Sediment \n",
"HCanyon0R3 5 Lane4 N37_33.106 W110_40.479 Sediment \n",
"HCanyon1R1 5 Lane4 N37_33.106 W110_40.479 Sediment \n",
"HCanyon1R2 5 Lane4 N37_33.106 W110_40.479 Sediment \n",
"HCanyon1R3 5 Lane4 N37_33.106 W110_40.479 Sediment \n",
"Stillton0R1 5 Lane4 N37_29.719 W110_42.012 Sediment \n",
"Stillton0R2 5 Lane4 N37_29.719 W110_42.012 Sediment \n",
"Stillton0R3 5 Lane4 N37_29.719 W110_42.012 Sediment \n",
"Stillton1R1 5 Lane4 N37_29.719 W110_42.012 Sediment \n",
"Stillton1R2 5 Lane4 N37_29.719 W110_42.012 Sediment \n",
"Halls2R1 5 Lane4 N37_28.352 W110_42.547 DisturbedSoil \n",
"Halls2R2 5 Lane4 N37_28.352 W110_42.547 DisturbedSoil \n",
"HCanyon2R1 5 Lane4 N37_33.097 W110_40.526 DisturbedSoil \n",
"HCanyon2R2 5 Lane4 N37_33.097 W110_40.526 DisturbedSoil \n",
"HCanyon2R3 5 Lane4 N37_33.097 W110_40.526 DisturbedSoil \n",
"Stillton2R1 5 Lane4 N37_29.749 W110_42.018 DisturbedSoil \n",
"Stillton2R2 5 Lane4 N37_29.749 W110_42.018 DisturbedSoil \n",
"Stillton2R3 5 Lane4 N37_29.749 W110_42.018 DisturbedSoil \n",
"Halls3R1 5 Lane4 N37_28.349 W110_42.545 DisturbedSoil \n",
"Halls3R2 5 Lane4 N37_28.349 W110_42.545 DisturbedSoil \n",
"HCanyon3R1 5 Lane4 N37_33.087 W110_40.553 DisturbedSoil \n",
"HCanyon3R2 5 Lane4 N37_33.087 W110_40.553 DisturbedSoil \n",
"HCanyon3R3 5 Lane4 N37_33.087 W110_40.553 DisturbedSoil \n",
"Stillton3R1 5 Lane4 N37_29.787 W110_42.014 DisturbedSoil \n",
"Stillton3R2 5 Lane4 N37_29.787 W110_42.014 DisturbedSoil \n",
"Stillton3R3 5 Lane4 N37_29.787 W110_42.014 DisturbedSoil \n",
"Halls4R1 5 Lane4 N37_28.342 W110_42.545 DisturbedSoil \n",
"Halls4R2 5 Lane4 N37_28.342 W110_42.545 DisturbedSoil \n",
"HCanyon4R1 5 Lane4 N37_33.055 W110_40.607 DisturbedSoil \n",
"HCanyon4R2 5 Lane4 N37_33.055 W110_40.607 DisturbedSoil \n",
"HCanyon4R3 5 Lane4 N37_33.055 W110_40.607 DisturbedSoil \n",
"Stillton4R1 5 Lane4 N37_29.865 W110_41.995 DisturbedSoil \n",
"Stillton4R2 5 Lane4 N37_29.865 W110_41.995 DisturbedSoil \n",
"Stillton4R3 5 Lane4 N37_29.865 W110_41.995 DisturbedSoil \n",
"Halls5R1 5 Lane4 N37_28.309 W110_42.571 DisturbedSoil \n",
"Halls5R2 5 Lane4 N37_28.309 W110_42.571 DisturbedSoil \n",
"HCanyon5R1 5 Lane4 N37_33.035 W110_40.612 DisturbedSoil \n",
"HCanyon5R2 5 Lane4 N37_33.035 W110_40.612 DisturbedSoil \n",
"HCanyon5R3 5 Lane4 N37_33.035 W110_40.612 DisturbedSoil \n",
"Stillton5R2 5 Lane4 N37_29.877 W110_42.004 DisturbedSoil \n",
"Halls6R1 5 Lane4 N37_28.296 W110_42.579 DisturbedSoil \n",
"Halls6R2 5 Lane4 N37_28.296 W110_42.579 DisturbedSoil \n",
"HCanyon6R1 5 Lane4 N37_33.026 W110_40.609 DisturbedSoil \n",
"HCanyon6R2 5 Lane4 N37_33.026 W110_40.609 DisturbedSoil \n",
"HCanyon6R3 5 Lane4 N37_33.026 W110_40.609 DisturbedSoil \n",
"Stillton6R1 5 Lane4 N37_30.066 W110_41.972 DisturbedSoil \n",
"Stillton6R2 5 Lane4 N37_30.066 W110_41.972 DisturbedSoil \n",
"Stillton6R3 5 Lane4 N37_30.066 W110_41.972 DisturbedSoil \n",
"Halls7R1 5 Lane4 N37_28.291 W110_42.592 DisturbedSoil \n",
"Halls7R2 5 Lane4 N37_28.291 W110_42.592 DisturbedSoil \n",
"HCanyon7R1 5 Lane4 N37_33.017 W110_40.602 DisturbedSoil \n",
"HCanyon7R2 5 Lane4 N37_33.017 W110_40.602 DisturbedSoil \n",
"HCanyon7R3 5 Lane4 N37_33.017 W110_40.602 DisturbedSoil \n",
"Stillton7R1 5 Lane4 N37_30.094 W110_41.947 DisturbedSoil \n",
"Stillton7R2 5 Lane4 N37_30.094 W110_41.947 DisturbedSoil \n",
" ... ... ... ... ... \n",
"\n",
" TypeBasic Env SourceSink estimated_elevation \\\n",
"#SampleID \n",
"Halls0R1 Sediment Sediment source 3633 \n",
"Halls0R2 Sediment Sediment source 3633 \n",
"Halls1R1 Sediment Sediment source 3633 \n",
"Halls1R2 Sediment Sediment source 3633 \n",
"HCanyon0R1 Sediment Sediment source 3633 \n",
"HCanyon0R2 Sediment Sediment source 3633 \n",
"HCanyon0R3 Sediment Sediment source 3633 \n",
"HCanyon1R1 Sediment Sediment source 3633 \n",
"HCanyon1R2 Sediment Sediment source 3633 \n",
"HCanyon1R3 Sediment Sediment source 3633 \n",
"Stillton0R1 Sediment Sediment source 3633 \n",
"Stillton0R2 Sediment Sediment source 3633 \n",
"Stillton0R3 Sediment Sediment source 3633 \n",
"Stillton1R1 Sediment Sediment source 3633 \n",
"Stillton1R2 Sediment Sediment source 3633 \n",
"Halls2R1 Soil DisturbedSoil sink 3643 \n",
"Halls2R2 Soil DisturbedSoil sink 3643 \n",
"HCanyon2R1 Soil DisturbedSoil sink 3643 \n",
"HCanyon2R2 Soil DisturbedSoil sink 3643 \n",
"HCanyon2R3 Soil DisturbedSoil sink 3643 \n",
"Stillton2R1 Soil DisturbedSoil sink 3643 \n",
"Stillton2R2 Soil DisturbedSoil sink 3643 \n",
"Stillton2R3 Soil DisturbedSoil sink 3643 \n",
"Halls3R1 Soil DisturbedSoil sink 3653 \n",
"Halls3R2 Soil DisturbedSoil sink 3653 \n",
"HCanyon3R1 Soil DisturbedSoil sink 3653 \n",
"HCanyon3R2 Soil DisturbedSoil sink 3653 \n",
"HCanyon3R3 Soil DisturbedSoil sink 3653 \n",
"Stillton3R1 Soil DisturbedSoil sink 3653 \n",
"Stillton3R2 Soil DisturbedSoil sink 3653 \n",
"Stillton3R3 Soil DisturbedSoil sink 3653 \n",
"Halls4R1 Soil DisturbedSoil sink 3663 \n",
"Halls4R2 Soil DisturbedSoil sink 3663 \n",
"HCanyon4R1 Soil DisturbedSoil sink 3663 \n",
"HCanyon4R2 Soil DisturbedSoil sink 3663 \n",
"HCanyon4R3 Soil DisturbedSoil sink 3663 \n",
"Stillton4R1 Soil DisturbedSoil sink 3663 \n",
"Stillton4R2 Soil DisturbedSoil sink 3663 \n",
"Stillton4R3 Soil DisturbedSoil sink 3663 \n",
"Halls5R1 Soil DisturbedSoil sink 3673 \n",
"Halls5R2 Soil DisturbedSoil sink 3673 \n",
"HCanyon5R1 Soil DisturbedSoil sink 3673 \n",
"HCanyon5R2 Soil DisturbedSoil sink 3673 \n",
"HCanyon5R3 Soil DisturbedSoil sink 3673 \n",
"Stillton5R2 Soil DisturbedSoil sink 3673 \n",
"Halls6R1 Soil DisturbedSoil sink 3683 \n",
"Halls6R2 Soil DisturbedSoil sink 3683 \n",
"HCanyon6R1 Soil DisturbedSoil sink 3683 \n",
"HCanyon6R2 Soil DisturbedSoil sink 3683 \n",
"HCanyon6R3 Soil DisturbedSoil sink 3683 \n",
"Stillton6R1 Soil DisturbedSoil sink 3683 \n",
"Stillton6R2 Soil DisturbedSoil sink 3683 \n",
"Stillton6R3 Soil DisturbedSoil sink 3683 \n",
"Halls7R1 Soil DisturbedSoil sink 3693 \n",
"Halls7R2 Soil DisturbedSoil sink 3693 \n",
"HCanyon7R1 Soil DisturbedSoil sink 3693 \n",
"HCanyon7R2 Soil DisturbedSoil sink 3693 \n",
"HCanyon7R3 Soil DisturbedSoil sink 3693 \n",
"Stillton7R1 Soil DisturbedSoil sink 3693 \n",
"Stillton7R2 Soil DisturbedSoil sink 3693 \n",
" ... ... ... ... \n",
"\n",
" estimated_years_since_submerged \\\n",
"#SampleID \n",
"Halls0R1 0 \n",
"Halls0R2 0 \n",
"Halls1R1 0 \n",
"Halls1R2 0 \n",
"HCanyon0R1 0 \n",
"HCanyon0R2 0 \n",
"HCanyon0R3 0 \n",
"HCanyon1R1 0 \n",
"HCanyon1R2 0 \n",
"HCanyon1R3 0 \n",
"Stillton0R1 0 \n",
"Stillton0R2 0 \n",
"Stillton0R3 0 \n",
"Stillton1R1 0 \n",
"Stillton1R2 0 \n",
"Halls2R1 1 \n",
"Halls2R2 1 \n",
"HCanyon2R1 1 \n",
"HCanyon2R2 1 \n",
"HCanyon2R3 1 \n",
"Stillton2R1 1 \n",
"Stillton2R2 1 \n",
"Stillton2R3 1 \n",
"Halls3R1 8 \n",
"Halls3R2 8 \n",
"HCanyon3R1 8 \n",
"HCanyon3R2 8 \n",
"HCanyon3R3 8 \n",
"Stillton3R1 8 \n",
"Stillton3R2 8 \n",
"Stillton3R3 8 \n",
"Halls4R1 9 \n",
"Halls4R2 9 \n",
"HCanyon4R1 9 \n",
"HCanyon4R2 9 \n",
"HCanyon4R3 9 \n",
"Stillton4R1 9 \n",
"Stillton4R2 9 \n",
"Stillton4R3 9 \n",
"Halls5R1 9 \n",
"Halls5R2 9 \n",
"HCanyon5R1 9 \n",
"HCanyon5R2 9 \n",
"HCanyon5R3 9 \n",
"Stillton5R2 9 \n",
"Halls6R1 10 \n",
"Halls6R2 10 \n",
"HCanyon6R1 10 \n",
"HCanyon6R2 10 \n",
"HCanyon6R3 10 \n",
"Stillton6R1 10 \n",
"Stillton6R2 10 \n",
"Stillton6R3 10 \n",
"Halls7R1 11 \n",
"Halls7R2 11 \n",
"HCanyon7R1 11 \n",
"HCanyon7R2 11 \n",
"HCanyon7R3 11 \n",
"Stillton7R1 11 \n",
"Stillton7R2 11 \n",
" ... \n",
"\n",
" estimated_years_since_submerged_for_plotting \\\n",
"#SampleID \n",
"Halls0R1 0.1 \n",
"Halls0R2 0.1 \n",
"Halls1R1 0.1 \n",
"Halls1R2 0.1 \n",
"HCanyon0R1 0.1 \n",
"HCanyon0R2 0.1 \n",
"HCanyon0R3 0.1 \n",
"HCanyon1R1 0.1 \n",
"HCanyon1R2 0.1 \n",
"HCanyon1R3 0.1 \n",
"Stillton0R1 0.1 \n",
"Stillton0R2 0.1 \n",
"Stillton0R3 0.1 \n",
"Stillton1R1 0.1 \n",
"Stillton1R2 0.1 \n",
"Halls2R1 1.0 \n",
"Halls2R2 1.0 \n",
"HCanyon2R1 1.0 \n",
"HCanyon2R2 1.0 \n",
"HCanyon2R3 1.0 \n",
"Stillton2R1 1.0 \n",
"Stillton2R2 1.0 \n",
"Stillton2R3 1.0 \n",
"Halls3R1 8.0 \n",
"Halls3R2 8.0 \n",
"HCanyon3R1 8.0 \n",
"HCanyon3R2 8.0 \n",
"HCanyon3R3 8.0 \n",
"Stillton3R1 8.0 \n",
"Stillton3R2 8.0 \n",
"Stillton3R3 8.0 \n",
"Halls4R1 9.0 \n",
"Halls4R2 9.0 \n",
"HCanyon4R1 9.0 \n",
"HCanyon4R2 9.0 \n",
"HCanyon4R3 9.0 \n",
"Stillton4R1 9.0 \n",
"Stillton4R2 9.0 \n",
"Stillton4R3 9.0 \n",
"Halls5R1 9.0 \n",
"Halls5R2 9.0 \n",
"HCanyon5R1 9.0 \n",
"HCanyon5R2 9.0 \n",
"HCanyon5R3 9.0 \n",
"Stillton5R2 9.0 \n",
"Halls6R1 10.0 \n",
"Halls6R2 10.0 \n",
"HCanyon6R1 10.0 \n",
"HCanyon6R2 10.0 \n",
"HCanyon6R3 10.0 \n",
"Stillton6R1 10.0 \n",
"Stillton6R2 10.0 \n",
"Stillton6R3 10.0 \n",
"Halls7R1 11.0 \n",
"Halls7R2 11.0 \n",
"HCanyon7R1 11.0 \n",
"HCanyon7R2 11.0 \n",
"HCanyon7R3 11.0 \n",
"Stillton7R1 11.0 \n",
"Stillton7R2 11.0 \n",
" ... \n",
"\n",
" estimated_last_submerged \n",
"#SampleID \n",
"Halls0R1 2010 ... \n",
"Halls0R2 2010 ... \n",
"Halls1R1 2010 ... \n",
"Halls1R2 2010 ... \n",
"HCanyon0R1 2010 ... \n",
"HCanyon0R2 2010 ... \n",
"HCanyon0R3 2010 ... \n",
"HCanyon1R1 2010 ... \n",
"HCanyon1R2 2010 ... \n",
"HCanyon1R3 2010 ... \n",
"Stillton0R1 2010 ... \n",
"Stillton0R2 2010 ... \n",
"Stillton0R3 2010 ... \n",
"Stillton1R1 2010 ... \n",
"Stillton1R2 2010 ... \n",
"Halls2R1 2009 ... \n",
"Halls2R2 2009 ... \n",
"HCanyon2R1 2009 ... \n",
"HCanyon2R2 2009 ... \n",
"HCanyon2R3 2009 ... \n",
"Stillton2R1 2009 ... \n",
"Stillton2R2 2009 ... \n",
"Stillton2R3 2009 ... \n",
"Halls3R1 2002 ... \n",
"Halls3R2 2002 ... \n",
"HCanyon3R1 2002 ... \n",
"HCanyon3R2 2002 ... \n",
"HCanyon3R3 2002 ... \n",
"Stillton3R1 2002 ... \n",
"Stillton3R2 2002 ... \n",
"Stillton3R3 2002 ... \n",
"Halls4R1 2001 ... \n",
"Halls4R2 2001 ... \n",
"HCanyon4R1 2001 ... \n",
"HCanyon4R2 2001 ... \n",
"HCanyon4R3 2001 ... \n",
"Stillton4R1 2001 ... \n",
"Stillton4R2 2001 ... \n",
"Stillton4R3 2001 ... \n",
"Halls5R1 2001 ... \n",
"Halls5R2 2001 ... \n",
"HCanyon5R1 2001 ... \n",
"HCanyon5R2 2001 ... \n",
"HCanyon5R3 2001 ... \n",
"Stillton5R2 2001 ... \n",
"Halls6R1 2000 ... \n",
"Halls6R2 2000 ... \n",
"HCanyon6R1 2000 ... \n",
"HCanyon6R2 2000 ... \n",
"HCanyon6R3 2000 ... \n",
"Stillton6R1 2000 ... \n",
"Stillton6R2 2000 ... \n",
"Stillton6R3 2000 ... \n",
"Halls7R1 1999 ... \n",
"Halls7R2 1999 ... \n",
"HCanyon7R1 1999 ... \n",
"HCanyon7R2 1999 ... \n",
"HCanyon7R3 1999 ... \n",
"Stillton7R1 1999 ... \n",
"Stillton7R2 1999 ... \n",
" ... \n",
"\n",
"[95 rows x 32 columns]"
]
}
],
"prompt_number": 21
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"so it'd be really nice to start using these for any functions that return tables, e.g., of statistical results. I think we could probably also inject some formatting here, so we could use this to highlight incorrectly formatted entries, etc.\n",
"\n",
"See documenation for some of the basic available functionality [here](http://pandas.pydata.org/pandas-docs/dev/generated/pandas.DataFrame.html)."
]
}
],
"metadata": {}
}
]
}
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