| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP009273 | 1,466,527 | G→T | 8.9% | pseudogene (1754/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 1,466,527 | 0 | G | T | 8.9% | 137.7 / 3.2 | 45 | pseudogene (1754/3497 nt) | ydbA | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| Reads supporting (aligned to +/- strand): ref base G (21/20); new base T (2/2); total (23/22) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.41e-01 | |||||||||||
GTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGATGCGGTAATCGAAAACAACGGCACCATCAATATCTTCGCCAATGACTCGTTTGCATTTAGCGTACTGGGTACAGTAGGTCATGTGGTTAACAACGGCACGGTGGTGATTGCCGATGGG > CP009273/1466257‑1466788 | gTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAATCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCATTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAAAATGACGGCATCATGAACa > 1:440696/1‑275 (MQ=255) ccgtttcccaataaCATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTGTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCt < 2:138120/261‑1 (MQ=255) cGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCAACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCgg > 1:138121/1‑267 (MQ=255) gTCACATGAACATCAGGAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTAACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCNCGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGAAGGCATCATGAAAATCAGAGGCACCGGTGCTGTGGCt > 1:621488/1‑275 (MQ=255) ccACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACTATTGATGTTTCTGCGTAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGACTGACGGCATCATGAACATCAGCGGCACCGGTGCt < 1:515432/244‑1 (MQ=255) aGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAAcgcccctgacacgtat > 1:196217/1‑261 (MQ=255) ttAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGc > 1:142612/1‑275 (MQ=255) gggCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGATAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAACGGCACTGGTGCTGTGGATAAGGAAGATGATAAGAACGAGCCGATGGTTAACAATTGCACCATccagg > 2:805242/1‑271 (MQ=255) aaCGATTGATGTTTCTGCGTAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCACAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAAcgc > 1:675528/1‑216 (MQ=255) tttGATGTTTCTGCGAAGTCACTGGTAGTCAACGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAg < 2:675522/215‑1 (MQ=255) aaGTCACTGGTGNGCAGCGCTAATAATGCCGGTGATCAGAATGCCTTATTCTTGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCCACGTTATTGCCAAGAATGACGGCATCATGAACATCAGCGGCACCGGTGATGTGGCTATGGAAGGTGATAAGAAAGAGCAGCTGGTTAACAATGGCACCATCAGCCACGGTACCGCAGTCACTACTGACACGGGTATGATCGGTATGCAACTc < 2:621482/273‑1 (MQ=255) aGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCCCGGTACCGCAGGCACTACTAACACGGGTATGAACGGAATGCAAATCGAt > 1:50011/1‑275 (MQ=255) cTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTAt > 1:133158/1‑160 (MQ=255) taatcaagatagagATAAGAATGANATCTTCTGGAACACGGATAACGGGGTCATCAACTACGATCACGACAGCTCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGa < 2:544786/260‑1 (MQ=255) taatGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGt > 2:633793/1‑145 (MQ=255) taatGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGaa < 2:133157/160‑1 (MQ=255) gCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCtg < 1:633799/145‑1 (MQ=255) ggCGATCAGAATGCCTTCTTCTGGAACCAGGATATCGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATNGCACCATCNACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCAcgg > 1:544789/1‑259 (MQ=255) cGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGtt > 2:293816/1‑175 (MQ=255) aTCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCgg > 2:216135/1‑133 (MQ=255) cAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACa < 1:293819/175‑1 (MQ=255) gAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCt < 1:216138/133‑1 (MQ=255) gATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGATACGGTAATCGAAAACAACGGCACCATCAATACCTTCGCCaa > 1:145677/1‑275 (MQ=255) catcaACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGATa > 2:213954/1‑185 (MQ=255) aaCTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGATATGAt < 1:213957/185‑1 (MQ=255) tCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGTGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATAGCACCATCAACCTCGGTACCGCATGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGATGCGGTAATCGAAAACAACGGCACCATCAATATCTTCGCCAATGACTCGTCTGCATTTAGc < 1:805249/275‑1 (MQ=255) tCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTa > 2:580345/1‑177 (MQ=255) cGATCACGACAGCGCCAGTGCCGTGACAGTCACCGACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCactact > 1:545632/1‑166 (MQ=255) tCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTTCCGCAGGCACTACTGACACGGGTATGAt < 1:580348/177‑1 (MQ=255) cACGACAGCGCCAGTGCCGTGAAAGTCACCCCCAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGaca < 2:545629/166‑1 (MQ=255) gTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCgg > 2:625432/1‑70 (MQ=255) cGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCt < 1:625438/70‑1 (MQ=255) cGTGAAAGTCACCCACAGCAACTATATTGCCCAGAATTACGGCATCATGAACATCAGCGGCACCGGTGATGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGATGCGGTAATCGAAAACAACGGCACCATCAATATCTTCGCCAATGACTCGTTTGCATTTAGCGTACTGGGTACAGTAGGTCAtg < 1:219345/275‑1 (MQ=255) aGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGATGCGGTAATCGAAAACAACGGCACCATCAATATCTTCGCCAAt < 1:292808/229‑1 (MQ=255) cAACTTTATTGCCCAGAATGACGGCATCATTAACATCAGCGGCACCGGTGCtg > 2:219215/1‑53 (MQ=255) tttATTGCCCAGAATGACGGCATCATTAACATCAGCGGCACCGGTGCTGTGGc < 1:219218/53‑1 (MQ=255) ttGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCt > 2:735161/1‑50 (MQ=255) ccAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATgg < 1:735167/50‑1 (MQ=255) cAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCAcgg > 2:774127/1‑157 (MQ=255) aTGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGa < 1:774133/157‑1 (MQ=255) aTGACGGCAGCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACNATCAACCTNGGTACCGCAGGCTCTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGATGCGGTAATCGAAAACAACGGCACCATCAATATCTTCGCCAATGACTCGTTTGCATTTAGCGTACTGGGTACAGTAGGTCATGCGGTTAACAACGGCACGGTGGTGATTGCCGATggg < 1:540460/275‑1 (MQ=255) cGGCATCATTAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCactact > 1:480043/1‑106 (MQ=255) cGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCactact > 1:730003/1‑106 (MQ=255) atcatTAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTTCTGaca < 2:480040/106‑1 (MQ=255) atcatGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGaca < 2:729997/106‑1 (MQ=255) | GTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCTGGAACCAGGATAACGGGGTCATCAACTTCGATCACGACAGCGCCAGTGCCGTGAAAGTCACCCACAGCAACTTTATTGCCCAGAATGACGGCATCATGAACATCAGCGGCACCGGTGCTGTGGCTATGGAAGGTGATAAGAACGCGCAGCTGGTTAACAATGGCACCATCAACCTCGGTACCGCAGGCACTACTGACACGGGTATGATCGGTATGCAACTCGATGCCAACGCCACGGCGGATGCGGTAATCGAAAACAACGGCACCATCAATATCTTCGCCAATGACTCGTTTGCATTTAGCGTACTGGGTACAGTAGGTCATGTGGTTAACAACGGCACGGTGGTGATTGCCGATGGG > CP009273/1466257‑1466788 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |