| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 50.8% | 38.5 / 88.8 | 64 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (21/10); new base A (0/32); total (21/43) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.61e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.96e-08 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT > NZ_CP009273/3658940‑3659189 | tttATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCACCCGAAAAAACC‑AGGTCAcc < 2:346371/138‑1 (MQ=255) aaGATTTAATGCCTCCTCCTTGAGCATCGGGAAAAATAATGAAAGCGTGCCCCTTGACACAAATAAAAAATTTTCAACACTCTTATCTACTCGATTTTGGT‑TTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAg < 1:473996/139‑1 (MQ=255) aaGATTTAATCCCCCCCCCTTGAGCATCGGGAAAAAAAATAAAGGCGTGTCCCTTGACACGAATAAAAAATTTCCAACACCCTTATCTACTCGAATTTGGC‑TTGCACCCGAAAAACCC‑AGTTCACCGCCATTAAAATAg < 1:584113/139‑1 (MQ=255) tttAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGa > 1:233023/1‑138 (MQ=255) atccctcctcctTGACCATCGGGAAAAATAATAAAACCGTGCCCCTTGACACAAATACAAAATTTTCACCACACTTATCTACTCAAATTTGCC‑TTCCACCCGCAAAACCC‑AGGCCACCGCCATTAAAATAGCGATAtt < 1:644329/135‑1 (MQ=255) atccctcctcctGAAGCATCGGAAAAAAAAATGAAAGCTTGTCCCTTAACACGAAAAAAAAATTTTCAACACATTTATCTACTCAAATTTGGC‑TTCCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATAtt < 1:311917/135‑1 (MQ=255) atcccccctcctTTACCACCGGGAGAAATAATAAAGGCGTCCCCCTTAACCTGAATACAAATTTTCCAACTCCTTTCTCTCCCCGATTTTGGC‑TTCCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATAtt < 1:610495/132‑1 (MQ=255) atcccccctcctTGAGCATCGGGAAAAAAAATGAAAGCGTGTCCCTTAACACAAATACAAAATTTCCAACACACTTACCTACTCGAATTTGGT‑TTGCACCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATAtt < 2:233023/132‑1 (MQ=255) accccccctcctTGACCATCGGAAAAAAAAATAAAAGCGTGTCCTTTGACACAAATAAAAAATTTTCAACACACTTATCTACTCGATTTTGGC‑TTGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATAtt < 2:472158/132‑1 (MQ=255) aTGCCTCCTCCTTGAGCAGGGGGAAAAATAATAAAAGCGTGTCCCTTGACACGAATAAAAAATTTTAAACACATTTATCTACTCGAATTTGGC‑TTGCACCCGAAAAAACC‑AGGCCACCGCCATTAAAATAGCGATAtt < 1:247418/138‑1 (MQ=255) aTGCCTCCTCCTTGAGCACCGGGAAAAAAAATAAAGGCGTGTCCCGTGACAAGAATACAAAATTTTCAACACACTTACCTACTCGAATTTGGC‑TTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATAtt < 1:159065/138‑1 (MQ=255) aTGCCCCCTCCTGGAGCATCGGGAAAAATAATGAAGGCTTTCCCCTTGACACGAATAAAAAATTTTCAACACACTTATCTACTCAAATTTGGC‑TTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATAtt < 1:96840/138‑1 (MQ=255) ctcctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCa > 1:722293/1‑139 (MQ=255) tcctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCAt > 1:701406/1‑139 (MQ=255) cctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCAt > 1:887292/1‑138 (MQ=255) ctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTa > 2:820392/1‑139 (MQ=255) ctcctTGACCAGGGGGAGAAATAATAAAAGCGTGTCCCTTGACACAAATAAAAAATTTTCAACACTCTGTTCTACTCGAATTGGGC‑TGGCCTCCGAAAAAACA‑AGCTCCCCGCCATTAAAATAGCGATATTCACCAt < 1:820392/137‑1 (MQ=255) gcgtCGGGAAAAAAAATAAAAGCGTGCCCCTTGACACGAAAAAAAAATTTTCAACACACTTATCTACTCAATTTTGGT‑TGGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt < 2:241146/136‑1 (MQ=255) gCATCGGGAAAAATAATGAAAGCGTGTCCCTTAACACGAATACAAAATTTTCACCACACTTATCTACCCGATTTTGGC‑TTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt < 1:554757/139‑1 (MQ=255) gCATCGGAAAAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCACCCCACTTATCTACTCAATTTTGGC‑TTGCCCCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt < 1:457863/139‑1 (MQ=255) cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCa < 1:170450/88‑1 (MQ=255) cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCa > 2:170450/1‑88 (MQ=255) cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt > 1:171233/1‑138 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag > 1:706354/1‑138 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag > 1:539680/1‑138 (MQ=255) gaaaaaTAATGAAAGCGTTCCCCTTGACACAAATAAAAAATTTTCAACACACTTTTCTACTCAAATTTGGC‑TTGCATCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata < 2:487401/136‑1 (MQ=255) cGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCa > 1:380517/1‑139 (MQ=255) cGTGTCCCTTGACACAAATAAAAAATTTCCAACACACTTACCTACTCAAATTTGTC‑TTGCACCCAAAAAAACC‑AGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCa < 2:701406/139‑1 (MQ=255) cGTGCCCCTTGAAACGAATAAAAAATTTTCACCACCATTATCTCCTCGAATTTGGT‑TTGCATCCAAAAAACCC‑AGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCa < 1:687116/139‑1 (MQ=255) tgtCCCTTGACACAAATAAAAAATTTCCAACACACTTATCTACTCAAATTTGGC‑TTGCACCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa < 2:906301/139‑1 (MQ=255) ttCCCTTGACACAAAAAAAAAATTTTCAACACCCTTATCTACTAGATTTGGTC‑TTGCACCCGCAAAAACC‑AGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa < 2:388248/137‑1 (MQ=255) tCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg > 1:193363/1‑139 (MQ=255) gACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCa > 2:169442/1‑57 (MQ=255) gACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCa < 1:169442/57‑1 (MQ=255) aagAATACAAAATTTCCAACACATTTATCTACTCGATTTGGGC‑TTCCACCCGAAAAAACC‑AGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc < 1:158764/137‑1 (MQ=255) aaaaaaaaaaTTTTAAACCCTCTTACCCACCCAAATTTGGC‑TT‑CAACCCAAAAAACCGAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa < 2:758109/133‑1 (MQ=255) aaaTACAAAATTTTCAACACACTTATCTACTCAAATTTGGC‑TTGCACCCACAAAACCC‑GGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa < 1:210069/138‑1 (MQ=255) aaaTAAAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCACCCGAAAAAACC‑AGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa < 2:132196/138‑1 (MQ=255) aaaTAAAAAATTTTAAACACTCTTATCTACTCAAATTTGGT‑TGGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa < 1:341019/138‑1 (MQ=255) aaaTAAAAAATTTCCAACACATTTATCTACTCGATTTTGGC‑TTGCATCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa < 1:354920/138‑1 (MQ=255) aaTACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAt > 1:758109/1‑139 (MQ=255) aaTACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAt > 1:389796/1‑139 (MQ=255) aaaaaaatTTTTAAACACCTTTATCTACCCGATTTTGCT‑TTGCACCCCAAAAAACC‑GGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt < 2:171233/135‑1 (MQ=255) ctttaCATCACATTTATCTACACGTATTTGGT‑GTCCAACAATAACACCA‑GGGTCCCCGCCATTAAAATAGCGATATTCACCATTATCCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt < 2:637433/138‑1 (MQ=255) aTTTTCAACACACTTTTCTACTATAATTTGGT‑TTACATCCACAAAACCG‑GGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt < 2:193363/139‑1 (MQ=255) tttaCAACACACTTATCTACACAAATTTGGT‑TGGAACCCAAAAAAACG‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTa < 2:722293/139‑1 (MQ=255) tacAACCCTCTTACCTACTCAAATTGGGT‑TTGCACCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAg < 2:706354/136‑1 (MQ=255) taaaaCACACTGATCTAC‑CAAAATTGGCTTTGCACCCGAAAAACCC‑AGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAg < 2:389796/135‑1 (MQ=255) tCAACACACTTATCTCCTCAAATTTGGC‑TTGCATCCAAAAAAACC‑AGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGt < 1:564066/138‑1 (MQ=255) aaCACATTTATCTACCCGATTTTGGC‑TTGCATCC‑AAAAAACC‑AGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAtt < 1:833190/139‑1 (MQ=255) tACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa < 2:719264/99‑1 (MQ=255) tACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa > 1:719264/1‑99 (MQ=255) cacaaaTTTGTC‑TTCCACCCGAAAAAACC‑GTGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGa < 2:832375/132‑1 (MQ=255) cacGATTTTGGC‑TTGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACt < 2:627186/136‑1 (MQ=255) tcaaaTTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTccc < 1:543520/111‑1 (MQ=255) tCGAATTTGGC‑TTGCATCCGCAGAAACC‑AGGTCTCCGCCATTAAACTAGCGATATTCATCATTAACCATGGTGCGCATCTCTTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACtt > 2:902084/1‑138 (MQ=255) tCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTccc > 2:543520/1‑114 (MQ=255) tCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACtt > 1:615467/1‑138 (MQ=255) gAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGt > 2:566874/1‑130 (MQ=255) gAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGt < 1:566874/130‑1 (MQ=255) gAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTaa > 1:251877/1‑138 (MQ=255) gAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTaa > 1:713817/1‑138 (MQ=255) aaaTTTGGC‑TTGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAat < 2:887292/138‑1 (MQ=255) tc‑TTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt < 1:508599/138‑1 (MQ=255) | TTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGC‑TTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAT > NZ_CP009273/3658940‑3659189 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |