| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 61.1% | 12.2 / 57.5 | 36 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (13/1); new base A (0/22); total (13/23) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.06e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.70e-08 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAT > NZ_CP009273/3658973‑3659151 | gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGc > 2:695223/1‑90 (MQ=255) aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCaaaa > 2:183588/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCaaaaa > 2:123017/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAAc > 2:598191/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAAc > 2:513501/1‑90 (MQ=255) taatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCAcc > 2:357168/1‑90 (MQ=255) taatGAAAGCGTGCCCTTTGACACAAATAAAAAATTTTCAACACCCTTAT‑CTACTCGAATTT‑GGCTTGCATCCGAAAAAACCAGGTCAcc < 1:182498/90‑1 (MQ=255) cGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaa > 2:125035/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 1:169772/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 2:541044/1‑90 (MQ=255) cctttGACACAAATAAAAATTTTTCAACCCTTTTAT‑CTACTCAATTTT‑GGCTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGc < 2:502528/87‑1 (MQ=255) cccTTGACACAAAAAAAAAATTTTCAACCCCTTTATCCTTCTC‑AATTT‑GGCCTCCACCCCAAAAAACCAGGTCCCCGCCATTAAAATAGc < 1:598191/90‑1 (MQ=255) cccTTGACACAAAAAAAAAATTTTCAACCCCCTTAT‑CTACTCGAATTT‑GGCTTCCATCCAAAAAAACCAGGTCACCGCCATTAAAATAGc < 1:125035/90‑1 (MQ=255) cTTGACACAAATAAAAATTTTCCAACACATTTAT‑CTACTCGATTTT‑GGTTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGa < 2:564726/90‑1 (MQ=255) cacaAATACAAAATTTTCAACCCACTTAT‑CTACTAAATTTT‑GGCTTCCACCCAAAAAACCCAGGCCCCCGCCATTAAAATAGCGATATTc < 1:614024/90‑1 (MQ=255) cacaAAAACAAAATTTTCACCCCCCTTAT‑CAAC‑CAAATTTGGGTTTCCCCCCGAAAAACCCAGGCCCCCGCCATTAAAATAGCGATATTc < 1:675063/90‑1 (MQ=255) cGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAAcc < 2:457884/59‑1 (MQ=255) cGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAAcc > 1:457884/1‑59 (MQ=255) aaaaTAAAAATTTTTAAACACACTTAT‑CTACTCGATTTT‑GGCTGCCACCCGAAAAACCCGGGCCACCGCCATTAAAATAGCGATATTCAc < 2:654955/88‑1 (MQ=255) cAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTaa > 2:675063/1‑90 (MQ=255) aaTTTCCAACACCCTTAT‑CTACTAAATTTT‑GGTTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 1:513501/90‑1 (MQ=255) ttccAACACACTTAT‑CTACTCAATTTT‑GCTTTCCATCCAAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg < 1:357168/87‑1 (MQ=255) tccAACACCTTTAT‑CTACTCAATTTT‑GGCTCCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGt < 1:675475/88‑1 (MQ=255) taaaaCACATTTCT‑CTCCTAAATTTT‑GGCTTCCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt < 1:105479/87‑1 (MQ=255) taaaCCCATTTAT‑CTACTCGAATTT‑GGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:6437/88‑1 (MQ=255) tCAACCCATTTAT‑CTACTCGAATTT‑GGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:110876/90‑1 (MQ=255) tCAACACATTTAT‑CTCCTCAAATTT‑GGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:117231/90‑1 (MQ=255) ccAACCCACTTAT‑CTACTAAATTTT‑GTCTTCCATCCAAAAAAACCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:553863/89‑1 (MQ=255) cTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:153097/1‑90 (MQ=255) cGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATAAACCATGGTGAGAATATATTTATGTCtt > 1:615949/1‑90 (MQ=255) aaTTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc > 1:209557/1‑90 (MQ=255) t‑GGTTTGCACCCAAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:358440/90‑1 (MQ=255) t‑GGCTTGCACCCGAAAAACCCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:97471/90‑1 (MQ=255) t‑GGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:655743/90‑1 (MQ=255) t‑GGCTTGCACCCCAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:455089/90‑1 (MQ=255) t‑GGCTTCCACCCAAAAAACCCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:183588/90‑1 (MQ=255) t‑GGCTTCCACCCAAAAAACCCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:488679/90‑1 (MQ=255) cAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAt < 2:435774/90‑1 (MQ=255) | GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTAT‑CTACTCGAATTT‑GGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAT > NZ_CP009273/3658973‑3659151 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |