| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 51.6% | 78.0 / 129.7 | 62 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (24/6); new base A (0/32); total (24/38) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.12e-12 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.71e-12 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658973‑3659144 | gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc < 1:33046/90‑1 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa > 2:774287/1‑90 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:1697612/90‑1 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 1:992933/90‑1 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 2:1182352/90‑1 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:998641/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 1:1230078/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 1:265765/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 1:1535672/1‑90 (MQ=255) cGGGAGAAATAACGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc > 2:1913172/1‑90 (MQ=255) ggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCa < 2:692079/90‑1 (MQ=255) aatGAAAGCGTGTCCCTTGACACAAAAAAAAATTTTTCAACCCCCTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCg < 2:1535672/90‑1 (MQ=255) aatAAAAGCGTGCCCTTTGACACAAAAAAAAAATTTTCAACACATTTATCTACTCAATTTTGGCTTGCACCCAAAAAAACCAGGCCACCg < 2:393543/90‑1 (MQ=255) tGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc > 1:552372/1‑90 (MQ=255) aggCGTGTCCTTTGACACAAATAAAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCAtt < 1:687048/88‑1 (MQ=255) aaGCGTGTCCCTTAACACAAAAAAAAAATTTTCAACCCACTTATCTCCTCAAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCAtt < 1:1469355/90‑1 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 1:1899467/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 2:1805723/1‑90 (MQ=255) gtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 2:1120447/1‑90 (MQ=255) gtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 2:1872375/1‑90 (MQ=255) cctttGAAAAGAAAAAAAATTTTCCAACCCTTTTATCTACTCGAATTTGGTTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGc < 1:1103037/87‑1 (MQ=255) cccTTCCCACAAAAAAAAAATTTCCAACCCCTTTATCTCCCCAATTTTGGCTTCCACCCCAAAAACCCAGGTCACCGCCATTAAAATAGc < 1:1212312/90‑1 (MQ=255) tGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGata > 2:1684569/1‑90 (MQ=255) cccaaaTAAAAATTTTTCAACACCCTTATCTACCCAAATTTGGCTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 1:136379/86‑1 (MQ=255) cccaaaTAAAAATTTTCCAACCCCTTTTTCTTTTTGATTTTGGCTGGCACCCCAAAAACCCAGGCCGCCGCCATTAAAATAGCGATATTc < 1:1057732/86‑1 (MQ=255) cacaAATAAAAATTTTTCAACCCCCTTTTCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc < 1:1264861/90‑1 (MQ=255) cacaAATAAAAATTTTTCAACCCCCTTACCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc < 1:792458/90‑1 (MQ=255) cacaAATAAAAATTTTTCAACACATTTATCTACCCGATTTTGGCTTGCCCCCGAAAAACCCAGGCCCCCGCCATTAAAATAGCGATATTc < 1:1872375/90‑1 (MQ=255) cacaAATAAAAATTTTCCAACCCACTTATCTCCTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 1:560506/90‑1 (MQ=255) cacaAATAAAAAATTTTCAACCCCTTTTTCTACTCGATTTTGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 2:377778/90‑1 (MQ=255) cacaAATAAAAAATTTTCAACACCTTTATCTCCTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc < 1:473305/90‑1 (MQ=255) cacaAATAAAAAATTTCCAACACCTTTATTTCCTCAATTTTGGCTTGCCCCCGAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTc < 2:1443760/90‑1 (MQ=255) aaaaaatTTTTCAACCCACTTTTCTCCTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:1220353/87‑1 (MQ=255) aaaTTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAAcc > 1:87481/1‑90 (MQ=255) ttCAACACATTTATCTACTCAATTTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt < 2:552372/90‑1 (MQ=255) taaaCACCCTTATCTCCTCGAATTTGGCTTGCATCCGAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:52259/88‑1 (MQ=255) tCAACCCACTTATCTACTCAATTTTGGCTTCCACCCGAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:998641/90‑1 (MQ=255) tCAACACATTTATCTCCTCGAATTTGGTTTGCACCCACAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCAAGGTg < 1:119868/90‑1 (MQ=255) tCAACACACTTATCTACTCAATTTTGGCTTGCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:1363508/90‑1 (MQ=255) caaaCCCATTTATCTCCTCAATTTTGGTTTCCACCAAAAAAAACCGGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:1203391/88‑1 (MQ=255) cAACACACTTATCTACTCAATTTTGGTTTCCACCCAAAAAAACCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga < 2:1811709/90‑1 (MQ=255) cacacTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:485540/90‑1 (MQ=255) ccatttATCTCCTCGATTTTGGCTTCCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:521844/86‑1 (MQ=255) acatTTATTTACTCAATTTTGGCTTGCACCCGAAAAAACGGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:732710/90‑1 (MQ=255) cacTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata > 1:294244/1‑90 (MQ=255) cacTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata > 2:926854/1‑90 (MQ=255) tACTCAATTTTGGCTTCCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATg < 1:1587529/90‑1 (MQ=255) cTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc < 1:1119440/90‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc < 1:392797/40‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc > 2:392797/1‑40 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTCTGTc > 2:1471692/1‑90 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 2:144730/1‑90 (MQ=255) cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATGTTCACCATTAACCATGGTGAGAATATATTTATGTCtt > 2:764399/1‑90 (MQ=255) aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc > 1:1498449/1‑90 (MQ=255) aTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg > 2:1578294/1‑69 (MQ=255) aTTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:1578294/69‑1 (MQ=255) tcgCTTCCACCCGAAAAAACCAGGCCGCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:977258/88‑1 (MQ=255) tGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:460705/90‑1 (MQ=255) tGGCTTCCACCCAAAAAAACCGGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:393006/90‑1 (MQ=255) ggCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg > 2:1811231/1‑90 (MQ=255) gCTTGCATCAAAAAAACCGGGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGc < 2:1693377/90‑1 (MQ=255) gCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt > 2:1707896/1‑90 (MQ=255) gCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt > 1:978512/1‑90 (MQ=255) | GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATT > NZ_CP009273/3658973‑3659144 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |