| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,058 | 0 | T | C | 52.4% | 90.0 / 126.6 | 86 | D38G (GAT→GGT) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base T (30/10); new base C (0/44); total (30/56) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.57e-14 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.68e-16 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658970‑3659144 | ctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATc < 1:1604704/90‑1 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaa < 2:304614/90‑1 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaa < 1:2066262/90‑1 (MQ=255) aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaaaa > 2:1473598/1‑90 (MQ=255) aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaaaa > 2:1021748/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaaaaa > 2:1020169/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaaaaa > 2:1004229/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaaaaa > 1:1529748/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaaaaa > 2:1872097/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCaaaaa > 1:1620867/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAAc > 1:1769771/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAAc > 1:1731003/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAAc > 1:53869/1‑90 (MQ=255) gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAAcc < 1:1743942/90‑1 (MQ=255) ggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑a < 2:1235274/90‑1 (MQ=255) aatGAAAGCGTTTCCCTTGCCAAAAATAAAAAATTTTC‑AACACCCTTATCTACCCAAATTT‑GGCTTCCACCCGAAAAAACC‑GGGTCCCCg < 2:1769771/90‑1 (MQ=255) aatAAAAGCGTGCCCCTTAACACAAAAAAAAAATTTTC‑AACACACTTATCTCCTCAATTTT‑GGCTTGCACCCGAAAAAACC‑AGGTCACCg < 2:749602/90‑1 (MQ=255) gAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCa > 2:2241980/1‑90 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCAtt > 2:1104870/1‑90 (MQ=255) aaGCGTGCCCCTTGACACAAATAAAAAATTTTC‑AACCCACTTATCTACTCAAATTT‑GGCTTGCACCCGAAAAACCC‑AGGTCACCGCCAtt < 2:53869/90‑1 (MQ=255) gCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTaa > 2:2206401/1‑90 (MQ=255) cGTGTCCTTTCACACGAATAAAAATTTTCC‑AACACCCTTATCAACAGGATTTG‑GGCTTCCCCCCAAAAAAACC‑AGGTCACCGCCATTaaa < 2:2258203/90‑1 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTaaaa > 1:1953694/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTaaaa > 1:2253825/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTaaaa > 1:510250/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTaaaa > 1:791367/1‑90 (MQ=255) tttCCCTTAACACGAATAAAAATTTTCC‑AACCCTTTTATCTACTCAATTTT‑GGCTTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAAt < 1:2206401/88‑1 (MQ=255) tgccccTTGACACAAATAAAAATTTTTC‑AACCCACTTATCTCCTCGATTTT‑GGCTTGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAAt < 1:210362/87‑1 (MQ=255) gtCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATa > 2:945032/1‑90 (MQ=255) gtCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATa > 2:61847/1‑90 (MQ=255) cccTTGACACAAAAAAAAAATTTTC‑AACCCCCTTATCTACTCGATTTT‑GGCTTGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGc < 2:183754/90‑1 (MQ=255) cccTTGACACAAAAAAAAAATTTAC‑AACCCCTTTATCTACTCGAATTT‑GGCTTGCACCCAAAAAAACC‑AGGCCACCGCCATTAAAATAGc < 2:510250/90‑1 (MQ=255) cTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCAATTAAAATAGCGa < 1:1645082/90‑1 (MQ=255) cTTGACACGAATAAAAAATTTTC‑AACCCACTTATCTACTCGATTTT‑GGCTTGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGa < 1:111983/90‑1 (MQ=255) cTTGACAAAAATAAAAAATTTTC‑AACCCTTTTATCTCCTCAATTTT‑GGCTTGCACCCCAAAAACCC‑AGGTCACCGCCATTAAAATAGCGa < 1:1872097/90‑1 (MQ=255) cTTGACAAAAAAAAAAATTTTTC‑AACCCCTTTATCTCCTCAATTTT‑GGCTTCCACCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGa < 2:450038/90‑1 (MQ=255) cacaAATAAAAATTTTTC‑AACACATTTTTCTCCTCAATTTT‑GGCTTGCATCCCAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTc < 1:1185767/90‑1 (MQ=255) cacaAATAAAAATTTTTC‑AACACATTTATCTACCCGATTTT‑GGCTTGCACCCAAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTc < 1:1314401/90‑1 (MQ=255) cacaAATAAAAATTTTCC‑AACACTTTTTTCTACTCAATTTT‑GGCTTGCACCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTc < 2:942134/90‑1 (MQ=255) cacaAATAAAAAATTTTC‑AACCCCCTTATCTACTCGATTTT‑GGCTTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTc < 1:61847/90‑1 (MQ=255) cacaAATAAAAAATTTCC‑AACACACTTATCTACTCAAATTT‑GGCTTCCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTc < 1:2119308/90‑1 (MQ=255) cacaAATAAAAAATTTAC‑AACACACTTATCTACTCGAATTT‑GGCTTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTc < 1:475992/90‑1 (MQ=255) gAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCAcc > 2:600110/1‑90 (MQ=255) gAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCAcc > 1:168871/1‑90 (MQ=255) gAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCAcc > 1:450038/1‑90 (MQ=255) aaTACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATc > 1:1547456/1‑47 (MQ=255) aaTACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATc < 2:1547456/47‑1 (MQ=255) aaTAAAAAATTTAC‑AACACACTTATCTCCCCGAATTT‑GGCTTGCACCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCa < 1:1072982/90‑1 (MQ=255) aaaaaaaaTTTTCAAACACCTTTATCT‑CCCAAATTTGGGCTTCCACCCAAAAAAACC‑GGGTCACCGCCATTAAAATAGCGATATTCACCa < 2:696151/86‑1 (MQ=255) aTACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCAt > 1:1313265/1‑90 (MQ=255) aaaaaatTTTTC‑AACCCCCTTATCTACCCGTTTTT‑GGCTTGCACCCAAAAAAACC‑GGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:2194557/87‑1 (MQ=255) aaaaaatTTTTC‑AACACACTTATCTACTCAATTTT‑GGCTTGCATCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:1104870/87‑1 (MQ=255) aaCAAAATTTCC‑ACCCACCTTATATCCTCAAATTG‑GCCTTGCCCCCGAAAAAACC‑AGGGCACCGCCATTAAAATAGCGATATTCACCAtt < 1:2211357/89‑1 (MQ=255) aaaaatTTTTC‑ACCCCCCTTATCTCCTCAATTTT‑GGTTTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTa < 1:1021748/88‑1 (MQ=255) aaaTTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAAcc > 2:1758430/1‑90 (MQ=255) atttttC‑AACACCTTTATCTCCTAAATTTT‑GGCTTGCACCCGAAAAAACC‑GGGACCCCGCCATTAAAATAGCGATATTCACCATTAACCa < 2:2147878/88‑1 (MQ=255) attttcC‑AACACATTTATCTACTCAATTTT‑GGCTTGCACCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 1:2091576/88‑1 (MQ=255) aTTTCC‑AACACATTTTTCTCCTCAAATTT‑GGCTTCCACCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCAt < 1:1689437/90‑1 (MQ=255) ttttC‑AACCCTTTTTTCTCCTAAATTTT‑GGCTTCCACCCAAAAAAACC‑AGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATg < 2:712288/90‑1 (MQ=255) tC‑AACACTTTTATCTCCTCAATTTT‑GGTTTGCACCCAAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:1473598/90‑1 (MQ=255) tC‑AACACACTTATCTACTCAATTTT‑GGCTTCCACCCAAAAAAACC‑AGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:1622417/90‑1 (MQ=255) cc‑AACCCTCTTATCTACTCAATTTT‑GGCTTCCACCCGAAAAACCC‑AGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:1020169/89‑1 (MQ=255) ac‑AACACATTTATCTACTCAATTTT‑GGCTTCCACCCAAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:831115/89‑1 (MQ=255) caaaCACCTTTATCTACAAGAATTT‑GGTTTGCATCCAAAAAACCC‑AGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:2209104/88‑1 (MQ=255) aaCACTTTTATCTACTCAATTTT‑GGCTTCCACCCAAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag < 2:2183918/90‑1 (MQ=255) cccacTTATCTCCTC‑AATTT‑GGGTTTCCACCCAAAAAACCAAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 2:174764/88‑1 (MQ=255) cacccTTATCTCCTCGATTTT‑GGCTTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:600110/90‑1 (MQ=255) cacatTTATCTCCTCGATTTT‑GGTTTGCACCCGAAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:196756/90‑1 (MQ=255) cacatTTATCTACTCTATTTT‑GTCTTGCACCCACAAAACCC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:2180028/90‑1 (MQ=255) cacatTTATCTACTCAATTTT‑GGCTTGCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:557091/90‑1 (MQ=255) ccctttATCTCCCCAATTTT‑GGTTTGCACCCAAAAAAACC‑GGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:2101397/86‑1 (MQ=255) ccctttATCTACTAAAATTT‑GGCTTCCACCCAAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCCTGGTGAGAat < 2:2010101/86‑1 (MQ=255) ccccTTACCTACTCGAATTG‑GGCTCGCCCCCAAAAAACCG‑AGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:1211634/87‑1 (MQ=255) acctttATCTCCTCAATTTT‑GGTTTCCACCCGAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:945032/86‑1 (MQ=255) acatTTATCTACCCAATTTT‑GGCTTGCAACCAAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:1528881/90‑1 (MQ=255) aTCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttt > 2:440448/1‑90 (MQ=255) cTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTAt > 2:358837/1‑90 (MQ=255) cGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt > 1:824956/1‑90 (MQ=255) t‑GGCTTGCACCCAAAAAAACC‑GGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:1368489/90‑1 (MQ=255) t‑GGCTTGCACCCAAAAAAACC‑AGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:732089/90‑1 (MQ=255) t‑GGCTTCCACCCAAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:1941960/90‑1 (MQ=255) t‑GGCTTCCACCCAAAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:867935/90‑1 (MQ=255) t‑GGCTTACACCCAAAAAACCC‑AGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:2287735/90‑1 (MQ=255) tgctttGCACCCAAAAAACCC‑AGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:2006045/86‑1 (MQ=255) gCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt > 2:128622/1‑90 (MQ=255) gCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt > 2:1627073/1‑90 (MQ=255) | CTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTC‑AACACACTTATCTACTCGAATTT‑GGCTTGCATCCGCAAAAACC‑AGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658970‑3659144 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |