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@eachanjohnson
eachanjohnson committed Oct 1, 2024
2 parents 0ed9cfa + 0a037ba commit 93328da
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Showing 31 changed files with 104,326 additions and 101,037 deletions.
1 change: 0 additions & 1 deletion .github/workflows/tests.yml
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Expand Up @@ -33,5 +33,4 @@ jobs:
python setup.py install
- name: Test with PyTest
run: |
export PYTHONHASHSEED=0
pytest -v tests/test_umi_tools.py
1 change: 0 additions & 1 deletion README.rst
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Expand Up @@ -121,4 +121,3 @@ Dependencies
------------
umi_tools is dependent on `python>=3.5`, `numpy`, `pandas`, `scipy`, `cython`, `pysam`,
`future`, `regex` and `matplotlib`

2,180 changes: 1,090 additions & 1,090 deletions tests/chr19_gene_assigned_cell.tsv
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46 changes: 23 additions & 23 deletions tests/count_tab_cell.tsv
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@@ -1,24 +1,24 @@
cell gene count
b'GATCGATTCGAGGATA' ENSG00000011304.18 54
b'ATAGATAGCGATAGCG' ENSG00000011304.18 52
b'GATCGATTCGAGGATA' ENSG00000065268.10 12
b'ATAGATAGCGATAGCG' ENSG00000065268.10 10
b'ATAGATAGCGATAGCG' ENSG00000070404.9 1
b'ATAGATAGCGATAGCG' ENSG00000070423.17 7
b'GATCGATTCGAGGATA' ENSG00000070423.17 4
b'ATAGATAGCGATAGCG' ENSG00000099804.8 8
b'GATCGATTCGAGGATA' ENSG00000099804.8 8
b'GATCGATTCGAGGATA' ENSG00000099821.13 3
b'ATAGATAGCGATAGCG' ENSG00000099821.13 5
b'GATCGATTCGAGGATA' ENSG00000099864.17 1
b'ATAGATAGCGATAGCG' ENSG00000099864.17 2
b'GATCGATTCGAGGATA' ENSG00000105556.11 3
b'ATAGATAGCGATAGCG' ENSG00000105556.11 3
b'GATCGATTCGAGGATA' ENSG00000116017.10 24
b'ATAGATAGCGATAGCG' ENSG00000116017.10 26
b'GATCGATTCGAGGATA' ENSG00000172270.18 7
b'ATAGATAGCGATAGCG' ENSG00000172270.18 8
b'ATAGATAGCGATAGCG' ENSG00000175221.14 3
b'GATCGATTCGAGGATA' ENSG00000175221.14 4
b'GATCGATTCGAGGATA' ENSG00000198858.9 1
b'ATAGATAGCGATAGCG' ENSG00000267751.5 1
GATCGATTCGAGGATA ENSG00000011304.18 54
ATAGATAGCGATAGCG ENSG00000011304.18 52
GATCGATTCGAGGATA ENSG00000065268.10 12
ATAGATAGCGATAGCG ENSG00000065268.10 10
ATAGATAGCGATAGCG ENSG00000070404.9 1
ATAGATAGCGATAGCG ENSG00000070423.17 7
GATCGATTCGAGGATA ENSG00000070423.17 4
ATAGATAGCGATAGCG ENSG00000099804.8 8
GATCGATTCGAGGATA ENSG00000099804.8 8
GATCGATTCGAGGATA ENSG00000099821.13 3
ATAGATAGCGATAGCG ENSG00000099821.13 5
GATCGATTCGAGGATA ENSG00000099864.17 1
ATAGATAGCGATAGCG ENSG00000099864.17 2
GATCGATTCGAGGATA ENSG00000105556.11 3
ATAGATAGCGATAGCG ENSG00000105556.11 3
GATCGATTCGAGGATA ENSG00000116017.10 24
ATAGATAGCGATAGCG ENSG00000116017.10 26
GATCGATTCGAGGATA ENSG00000172270.18 7
ATAGATAGCGATAGCG ENSG00000172270.18 8
ATAGATAGCGATAGCG ENSG00000175221.14 3
GATCGATTCGAGGATA ENSG00000175221.14 4
GATCGATTCGAGGATA ENSG00000198858.9 1
ATAGATAGCGATAGCG ENSG00000267751.5 1
97,560 changes: 48,780 additions & 48,780 deletions tests/group_adj_py3.sam
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97,560 changes: 48,780 additions & 48,780 deletions tests/group_adj_py3.tsv
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50 changes: 25 additions & 25 deletions tests/group_cluster_py3.sam
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52 changes: 26 additions & 26 deletions tests/group_cluster_py3.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -667,8 +667,8 @@ SRR2057595.13442648_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.13549325_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.13587544_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.13626788_ATCGG chr19 3571762 NA ATCGG 186 ATCGG 188 3
SRR2057595.7273343_ATTGG chr19 3571762 NA ATTGG 1 ATCGG 188 3
SRR2057595.10958947_ATCGA chr19 3571762 NA ATCGA 1 ATCGG 188 3
SRR2057595.7273343_ATTGG chr19 3571762 NA ATTGG 1 ATCGG 188 3
SRR2057595.7803605_TCGGC chr19 3571763 NA TCGGC 2 TCGGC 2 4
SRR2057595.8458115_TCGGC chr19 3571763 NA TCGGC 2 TCGGC 2 4
SRR2057595.40212_ATTCT chr19 3576313 NA ATTCT 90 ATTCT 90 5
Expand Down Expand Up @@ -1317,9 +1317,9 @@ SRR2057595.13499597_ACAGA chr19 4078320 NA ACAGA 233 ACAGA 237 13
SRR2057595.13502818_ACAGA chr19 4078320 NA ACAGA 233 ACAGA 237 13
SRR2057595.13563255_ACAGA chr19 4078320 NA ACAGA 233 ACAGA 237 13
SRR2057595.6047279_ACAAA chr19 4078320 NA ACAAA 1 ACAGA 237 13
SRR2057595.8461380_GCAGA chr19 4078320 NA GCAGA 1 ACAGA 237 13
SRR2057595.11830696_ACATA chr19 4078320 NA ACATA 1 ACAGA 237 13
SRR2057595.12503000_ACAGC chr19 4078320 NA ACAGC 1 ACAGA 237 13
SRR2057595.11830696_ACATA chr19 4078320 NA ACATA 1 ACAGA 237 13
SRR2057595.8461380_GCAGA chr19 4078320 NA GCAGA 1 ACAGA 237 13
SRR2057595.11891309_TAACC chr19 4078320 NA TAACC 1 TAACC 1 14
SRR2057595.12261872_GGGCC chr19 4078320 NA GGGCC 1 GGGCC 1 15
SRR2057595.327916_GTACC chr19 4078324 NA GTACC 7 GTACC 7 16
Expand Down Expand Up @@ -1667,8 +1667,8 @@ SRR2057595.9452803_GTGGC chr19 4078333 NA GTGGC 3 GTGGC 3 46
SRR2057595.2846379_ACGGC chr19 4078333 NA ACGGC 3 ACGGC 3 47
SRR2057595.4116943_ACGGC chr19 4078333 NA ACGGC 3 ACGGC 3 47
SRR2057595.9653749_ACGGC chr19 4078333 NA ACGGC 3 ACGGC 3 47
SRR2057595.4627616_TAGAC chr19 4078333 NA TAGAC 1 TAGAC 2 48
SRR2057595.7183987_GAGAC chr19 4078333 NA GAGAC 1 TAGAC 2 48
SRR2057595.7183987_GAGAC chr19 4078333 NA GAGAC 1 GAGAC 2 48
SRR2057595.4627616_TAGAC chr19 4078333 NA TAGAC 1 GAGAC 2 48
SRR2057595.13080756_CTGCC chr19 4078333 NA CTGCC 1 CTGCC 1 49
SRR2057595.59150_AGCCG chr19 4078334 NA AGCCG 586 AGCCG 967 50
SRR2057595.61132_AGCCG chr19 4078334 NA AGCCG 586 AGCCG 967 50
Expand Down Expand Up @@ -2635,8 +2635,8 @@ SRR2057595.9512923_AACAG chr19 4078334 NA AACAG 378 AGCCG 967 50
SRR2057595.12027381_AACAG chr19 4078334 NA AACAG 378 AGCCG 967 50
SRR2057595.6570489_AACAG chr19 4078334 NA AACAG 378 AGCCG 967 50
SRR2057595.254072_AACCG chr19 4078334 NA AACCG 1 AGCCG 967 50
SRR2057595.12445458_AGTCG chr19 4078334 NA AGTCG 1 AGCCG 967 50
SRR2057595.13571873_AGCAG chr19 4078334 NA AGCAG 1 AGCCG 967 50
SRR2057595.12445458_AGTCG chr19 4078334 NA AGTCG 1 AGCCG 967 50
SRR2057595.11597812_ATAAA chr19 4078334 NA ATAAA 292 ATAAA 641 51
SRR2057595.10788_ATAAA chr19 4078334 NA ATAAA 292 ATAAA 641 51
SRR2057595.42646_ATAAA chr19 4078334 NA ATAAA 292 ATAAA 641 51
Expand Down Expand Up @@ -5948,14 +5948,14 @@ SRR2057595.11741654_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.12192177_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.12959733_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.13565871_CATGA chr19 4078346 NA CATGA 23 CATGA 23 85
SRR2057595.2949476_ATGAT chr19 4078346 NA ATGAT 3 ATGAT 8 86
SRR2057595.5134248_ATGAT chr19 4078346 NA ATGAT 3 ATGAT 8 86
SRR2057595.12286012_ATGAT chr19 4078346 NA ATGAT 3 ATGAT 8 86
SRR2057595.8560272_AAGAT chr19 4078346 NA AAGAT 3 ATGAT 8 86
SRR2057595.11481316_AAGAT chr19 4078346 NA AAGAT 3 ATGAT 8 86
SRR2057595.12911150_AAGAT chr19 4078346 NA AAGAT 3 ATGAT 8 86
SRR2057595.5483821_CTGAT chr19 4078346 NA CTGAT 2 ATGAT 8 86
SRR2057595.12468205_CTGAT chr19 4078346 NA CTGAT 2 ATGAT 8 86
SRR2057595.8560272_AAGAT chr19 4078346 NA AAGAT 3 AAGAT 8 86
SRR2057595.11481316_AAGAT chr19 4078346 NA AAGAT 3 AAGAT 8 86
SRR2057595.12911150_AAGAT chr19 4078346 NA AAGAT 3 AAGAT 8 86
SRR2057595.2949476_ATGAT chr19 4078346 NA ATGAT 3 AAGAT 8 86
SRR2057595.5134248_ATGAT chr19 4078346 NA ATGAT 3 AAGAT 8 86
SRR2057595.12286012_ATGAT chr19 4078346 NA ATGAT 3 AAGAT 8 86
SRR2057595.5483821_CTGAT chr19 4078346 NA CTGAT 2 AAGAT 8 86
SRR2057595.12468205_CTGAT chr19 4078346 NA CTGAT 2 AAGAT 8 86
SRR2057595.4318931_TCGAT chr19 4078346 NA TCGAT 1 TCGAT 1 87
SRR2057595.19310_TAACA chr19 4078347 NA TAACA 462 TAACA 832 88
SRR2057595.24047_TAACA chr19 4078347 NA TAACA 462 TAACA 832 88
Expand Down Expand Up @@ -9904,8 +9904,8 @@ SRR2057595.2210298_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.5394707_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.5779297_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.13496292_GTCAA chr19 4078354 NA GTCAA 554 GTCAA 556 107
SRR2057595.12229826_GTCGA chr19 4078354 NA GTCGA 1 GTCAA 556 107
SRR2057595.1408002_GCCAA chr19 4078354 NA GCCAA 1 GTCAA 556 107
SRR2057595.12229826_GTCGA chr19 4078354 NA GTCGA 1 GTCAA 556 107
SRR2057595.2688_GCATA chr19 4078354 NA GCATA 515 GCATA 515 108
SRR2057595.37339_GCATA chr19 4078354 NA GCATA 515 GCATA 515 108
SRR2057595.41440_GCATA chr19 4078354 NA GCATA 515 GCATA 515 108
Expand Down Expand Up @@ -11233,8 +11233,8 @@ SRR2057595.12896743_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.12492803_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.13007419_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.8484200_CTAGC chr19 4078359 NA CTAGC 317 CTAGC 319 116
SRR2057595.7487423_GTAGC chr19 4078359 NA GTAGC 1 CTAGC 319 116
SRR2057595.13443839_CTAAC chr19 4078359 NA CTAAC 1 CTAGC 319 116
SRR2057595.7487423_GTAGC chr19 4078359 NA GTAGC 1 CTAGC 319 116
SRR2057595.8085966_CCGAG chr19 4078360 NA CCGAG 1 CCGAG 1 117
SRR2057595.4460250_AAAAT chr19 4078360 NA AAAAT 1 AAAAT 1 118
SRR2057595.8722606_GCCGA chr19 4078361 NA GCCGA 152 GCCGA 154 119
Expand Down Expand Up @@ -13231,8 +13231,8 @@ SRR2057595.13489373_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.3566252_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.12978364_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.6463453_AACTT chr19 4078483 NA AACTT 236 AACTT 238 159
SRR2057595.2878355_AATTT chr19 4078483 NA AATTT 1 AACTT 238 159
SRR2057595.13442879_AACGT chr19 4078483 NA AACGT 1 AACTT 238 159
SRR2057595.2878355_AATTT chr19 4078483 NA AATTT 1 AACTT 238 159
SRR2057595.7790483_CTCTC chr19 4078483 NA CTCTC 1 CTCTC 1 160
SRR2057595.3284641_GGGCA chr19 4078484 NA GGGCA 1 GGGCA 1 161
SRR2057595.83632_TGGTC chr19 4078485 NA TGGTC 149 TGGTC 149 162
Expand Down Expand Up @@ -16368,8 +16368,8 @@ SRR2057595.13442648_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.13549325_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.13587544_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.13626788_ATCGG chr19 4379011 NA ATCGG 185 ATCGG 187 188
SRR2057595.7273343_ATTGG chr19 4379011 NA ATTGG 1 ATCGG 187 188
SRR2057595.10958947_ATCGA chr19 4379011 NA ATCGA 1 ATCGG 187 188
SRR2057595.7273343_ATTGG chr19 4379011 NA ATTGG 1 ATCGG 187 188
SRR2057595.7803605_TCGGC chr19 4379012 NA TCGGC 2 TCGGC 2 189
SRR2057595.8458115_TCGGC chr19 4379012 NA TCGGC 2 TCGGC 2 189
SRR2057595.479300_ACAGC chr19 4641015 NA ACAGC 8 ACAGC 8 190
Expand Down Expand Up @@ -17556,8 +17556,8 @@ SRR2057595.13479955_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.13491625_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.13499957_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.13618555_TATTC chr19 5038318 NA TATTC 479 TATTC 482 202
SRR2057595.1260332_TATAC chr19 5038318 NA TATAC 1 TATTC 482 202
SRR2057595.8460968_GATTC chr19 5038318 NA GATTC 1 TATTC 482 202
SRR2057595.1260332_TATAC chr19 5038318 NA TATAC 1 TATTC 482 202
SRR2057595.9269865_TATCC chr19 5038318 NA TATCC 1 TATTC 482 202
SRR2057595.35589_GGAGA chr19 5104716 NA GGAGA 12 GGAGA 12 203
SRR2057595.477494_GGAGA chr19 5104716 NA GGAGA 12 GGAGA 12 203
Expand Down Expand Up @@ -21725,9 +21725,9 @@ SRR2057595.13609810_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.13610242_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.13648468_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.2019660_GCCGA chr19 7390041 NA GCCGA 662 GCCGA 665 270
SRR2057595.8637529_GGCGA chr19 7390041 NA GGCGA 1 GCCGA 665 270
SRR2057595.8139214_GCTGA chr19 7390041 NA GCTGA 1 GCCGA 665 270
SRR2057595.13256411_CCCGA chr19 7390041 NA CCCGA 1 GCCGA 665 270
SRR2057595.8139214_GCTGA chr19 7390041 NA GCTGA 1 GCCGA 665 270
SRR2057595.8637529_GGCGA chr19 7390041 NA GGCGA 1 GCCGA 665 270
SRR2057595.9119459_ACGCA chr19 7507313 NA ACGCA 1 ACGCA 1 271
SRR2057595.46326_CAGTA chr19 7545895 NA CAGTA 157 CAGTA 157 272
SRR2057595.52336_CAGTA chr19 7545895 NA CAGTA 157 CAGTA 157 272
Expand Down Expand Up @@ -32781,8 +32781,8 @@ SRR2057595.13597841_TATGG chr19 13129321 NA TATGG 245 TATTG 521 391
SRR2057595.13626245_TATGG chr19 13129321 NA TATGG 245 TATTG 521 391
SRR2057595.2931220_TACGG chr19 13129321 NA TACGG 2 TATTG 521 391
SRR2057595.4971514_TACGG chr19 13129321 NA TACGG 2 TATTG 521 391
SRR2057595.2867945_CATTG chr19 13129321 NA CATTG 1 TATTG 521 391
SRR2057595.13255450_AATGG chr19 13129321 NA AATGG 1 TATTG 521 391
SRR2057595.2867945_CATTG chr19 13129321 NA CATTG 1 TATTG 521 391
SRR2057595.11618608_TAATG chr19 13129321 NA TAATG 1 TATTG 521 391
SRR2057595.116977_CGCTT chr19 13129321 NA CGCTT 254 CGCTT 254 392
SRR2057595.223450_CGCTT chr19 13129321 NA CGCTT 254 CGCTT 254 392
Expand Down Expand Up @@ -39738,8 +39738,8 @@ SRR2057595.13421676_GCTAA chr19 32596081 NA GCTAA 221 GCTAA 224 512
SRR2057595.13463857_GCTAA chr19 32596081 NA GCTAA 221 GCTAA 224 512
SRR2057595.13584467_GCTAA chr19 32596081 NA GCTAA 221 GCTAA 224 512
SRR2057595.12488286_GCAAA chr19 32596081 NA GCAAA 1 GCTAA 224 512
SRR2057595.13441427_GCTGA chr19 32596081 NA GCTGA 1 GCTAA 224 512
SRR2057595.9833878_GCCAA chr19 32596081 NA GCCAA 1 GCTAA 224 512
SRR2057595.13441427_GCTGA chr19 32596081 NA GCTGA 1 GCTAA 224 512
SRR2057595.1134582_GATGT chr19 32850823 NA GATGT 2 GATGT 2 513
SRR2057595.8708447_GATGT chr19 32850823 NA GATGT 2 GATGT 2 513
SRR2057595.965130_GACAG chr19 32981872 NA GACAG 1 GACAG 1 514
Expand Down Expand Up @@ -40219,8 +40219,8 @@ SRR2057595.13290815_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.13313064_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.13322565_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.13476968_ATACC chr19 35673172 NA ATACC 261 ATACC 263 529
SRR2057595.6413612_ATCCC chr19 35673172 NA ATCCC 1 ATACC 263 529
SRR2057595.4829989_ACACC chr19 35673172 NA ACACC 1 ATACC 263 529
SRR2057595.6413612_ATCCC chr19 35673172 NA ATCCC 1 ATACC 263 529
SRR2057595.308008_GTGGA chr19 35902269 NA GTGGA 256 GTGGA 258 530
SRR2057595.311184_GTGGA chr19 35902269 NA GTGGA 256 GTGGA 258 530
SRR2057595.360154_GTGGA chr19 35902269 NA GTGGA 256 GTGGA 258 530
Expand Down Expand Up @@ -50799,8 +50799,8 @@ SRR2057595.13594861_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.13595630_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.13601460_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.13640428_ATGAA chr19 56007799 NA ATGAA 455 ATGAA 457 659
SRR2057595.4392906_ATGAT chr19 56007799 NA ATGAT 1 ATGAA 457 659
SRR2057595.11588152_ATGAG chr19 56007799 NA ATGAG 1 ATGAA 457 659
SRR2057595.4392906_ATGAT chr19 56007799 NA ATGAT 1 ATGAA 457 659
SRR2057595.9339337_TGGAA chr19 56007800 NA TGGAA 2 TGGAA 2 660
SRR2057595.9424164_TGGAA chr19 56007800 NA TGGAA 2 TGGAA 2 660
SRR2057595.1122774_ATGAA chr19 56007800 NA ATGAA 1 ATGAA 1 661
Expand Down Expand Up @@ -54724,9 +54724,9 @@ SRR2057595.13443130_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.13576443_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.13581746_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.13623055_CTGCG chr19 61240340 NA CTGCG 237 CTGCG 240 707
SRR2057595.4284087_CTGTG chr19 61240340 NA CTGTG 1 CTGCG 240 707
SRR2057595.8361213_AAGCG chr19 61240340 NA AAGCG 1 CTGCG 240 707
SRR2057595.10713055_CAGCG chr19 61240340 NA CAGCG 1 CTGCG 240 707
SRR2057595.4284087_CTGTG chr19 61240340 NA CTGTG 1 CTGCG 240 707
SRR2057595.2364090_TGGTT chr19 61240340 NA TGGTT 3 TGGTT 3 708
SRR2057595.2489631_TGGTT chr19 61240340 NA TGGTT 3 TGGTT 3 708
SRR2057595.9327159_TGGTT chr19 61240340 NA TGGTT 3 TGGTT 3 708
Expand Down
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