Read alignment evidence... | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NZ_CP009273 | 1,429,978 | 0 | T | A | 32.4% | 64.4 / 13.4 | 37 | intergenic (‑102/+39) | uspF/ompN | universal stress protein UspF/porin OmpN |
Reads supporting (aligned to +/- strand): ref base T (23/2); new base A (0/12); total (23/14) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 4.91e-08 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
Rejected as consensus: Frequency below/above cutoff threshold. |
TAGGGCAGTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCTTTATCATC > NZ_CP009273/1429740‑1430193 | tagGGCAGTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGaaa > 2:304702/1‑248 (MQ=255) gTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGc > 1:586755/1‑249 (MQ=255) tGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCa > 2:610449/1‑250 (MQ=255) aaataccccTTTGAATCATAATTCTTTCCCTCTCCAACAACGGGCCAAACCCCGTGTTAATTTAATT‑TAAAACGGAAAATATCGATAGGAAAAAGATTTTTTCTTTTAAAAAACCCTCTTTTTTTATTACCCGAAAAAAGTGAAACGCAAAATGCCTTTTTTTGTGA‑AATGGGGGATTTCATTTTTTTATTTAAGAAAAAGGGGGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGAt < 2:99500/243‑1 (MQ=255) aTGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGAtt > 2:362344/1‑249 (MQ=255) aaCCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAg > 2:565972/1‑249 (MQ=255) ctctGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt > 1:527449/1‑250 (MQ=255) tctGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt > 1:50309/1‑249 (MQ=255) gCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGAt > 1:621895/1‑249 (MQ=255) aaTTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCg > 1:117303/1‑248 (MQ=255) aTTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCg > 1:258099/1‑247 (MQ=255) ttCTAAATCGA‑AAATATGAAAAGAGACAAAAATCTTTCTTTACAAAAACCCTCTTTTTTTAGTACCCGAATAAAGTTTAACGCAAGATGACTTTTTTTGTTA‑AAGGACGGAGTTCATATTTTTAATTAAGAAAAAAGGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGa < 2:273602/250‑1 (MQ=255) tGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGc > 1:217968/1‑250 (MQ=255) aaaTATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCt > 2:528649/1‑250 (MQ=255) gATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATcc > 2:249313/1‑249 (MQ=255) aaaaaaaTCGTTCTTTAAAAAAACCCTCCTTTTTTAGTACCCGAAAAAAGTGAAACGCCAGATAACTTTTTTTGTGA‑AATGACGGAGTTCATATTTTTAATTTAAAAAAAAGGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGtt < 1:212390/245‑1 (MQ=255) gTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCaa > 1:464441/1‑250 (MQ=255) aTAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACg > 2:475529/1‑248 (MQ=255) ctctttttttAGTACCCGAAAAAAGTGAAACGCAAGATGACTTTTTTTGTAA‑AAAGAAGGAGTCCACATTTTAAATTAAAAAAAAAGGAGA‑AAAAAAAAAAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAc < 2:166811/244‑1 (MQ=255) tttttAGTATCAGAAAAAGGTGTACCGCAAGATGACATTTTGTGTGA‑AAAAAGGGAATCCAAATTTTAAATAAAGA‑AAAAGGAGGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATg < 1:379571/247‑1 (MQ=255) gTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGtt > 2:579490/1‑250 (MQ=255) gCATAAAGTGTAACGCCAGATTACACTTTTTGTGT‑AATGTCGGAGATCACATTTTTAATTTAGATCAAAGGTTG‑AAGATTTAGCAGATAAAGTCCGCCATAACATCGGTAAGGAGGATTTAGAACTGTTAAACCAGGCATAAATCGACAATATCATCGGTAGAGATGCCATTGGCAGCTTAGATTCTATCATCTTCATCAAGCGGATTGCTTTTATAGTCATCGTAGGTGGACATGGTTTTATTGaatt > 2:166419/1‑247 (MQ=255) gtgtACCGCAAGAGGATATTTTTTGTGA‑AATGACGGAGTTCAAATTTATAATTAAGAAAAAAGGAGA‑AAGAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTc < 1:278947/250‑1 (MQ=255) tAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTcgcg > 2:532521/1‑250 (MQ=255) tAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTcgcg > 2:103979/1‑250 (MQ=255) aacgataGATGACTTTTTTTGTGA‑AAGGAGGGTGTAAACTTTTTAAATGAAGAAAAAAGAAAG‑AAAAATAAAAAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCgcgc < 1:208223/244‑1 (MQ=255) aaCGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCgcgc > 2:145784/1‑250 (MQ=255) caagaagactcttttGGGTAAATGAGGGATTTAAATTTTTTATTTTAAAAAAAAGGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAat < 1:509298/239‑1 (MQ=255) aagatgattttttttGTGT‑AATGACGGAGTTCATTTTTTAAATAAAAACAAAAGGAGA‑AAAAAAAAAAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAata < 1:373764/240‑1 (MQ=255) tttttGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTAtt > 1:83450/1‑250 (MQ=255) ttgggat‑AAAGACGTAATTCATATTTTAAATTAAAAAAAAAGGAAA‑AAAAAAAAAAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTAttt < 2:217968/243‑1 (MQ=255) tgtgT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAAc > 2:68459/1‑250 (MQ=255) tgtgG‑AATGAGGGATTTCCATTTTTTAATTAAGAAAAAAGGAGA‑AAAAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTaa < 1:159223/249‑1 (MQ=255) ttgaaaTGACGGAGTTCACATTTTTATTTTAGAAAAAAGGAGG‑AAGAAAAAGAAAAAAAAGACCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAAcc < 1:612624/246‑1 (MQ=255) tGACGGATTTCAAATTTTAAATTAAAATAAAAGGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCt < 1:442510/250‑1 (MQ=255) gTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCTTTatcat > 2:541718/1‑250 (MQ=255) caatttttttAATTAAGAGAAAGGAAAG‑AAAAAAAAGCAAAAAACCCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCTTTatcatc < 2:527449/244‑1 (MQ=255) | TAGGGCAGTGAAGGTATTACCGTCAGGAAATGAACCTCTGCATCATCAATCTTTGCCTCTTCCTCAACGTGGCTAATCACGCGTTGAGTTAATTCTGAATCGG‑AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGT‑AATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACATGTTTTTATTGAAATAGTAAGTCGCGCCAATATCGGCGTATTTAACCAGATCTTTATCATC > NZ_CP009273/1429740‑1430193 |
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |