| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,058 | 0 | T | C | 61.1% | 20.1 / 33.2 | 36 | D38G (GAT→GGT) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base T (10/4); new base C (0/22); total (10/26) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.94e-06 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.58e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAT > NZ_CP009273/3658969‑3659143 | cctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCAt < 2:214507/90‑1 (MQ=255) aGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCa > 2:565687/1‑90 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa > 2:351940/1‑90 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 1:565687/90‑1 (MQ=255) aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa > 2:389317/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:240057/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc > 1:700279/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc > 1:147006/1‑90 (MQ=255) aatGAAAGCGTGTCCCTTGACACGAATAAAAAATTTT‑CAACACACTTATCTCCTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCg < 2:195961/90‑1 (MQ=255) tctCCCTTGACACAAATAAAAAATTTT‑CAACCCCCTTATCTACTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAAt < 1:389317/88‑1 (MQ=255) cccTTGACCCAAAAAAAAAATTTA‑AAACACCTTTACCTCCGCAATTTTGGCTTCCTCCCGCAAAACCCAGGGCACCGCCATTAAAATAGc < 2:410952/90‑1 (MQ=255) cccTTGACACAAATAAAAATTTTT‑CAACACACTTATCTCCTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGc < 2:483988/90‑1 (MQ=255) cccTTGACACAAAAAAAAATTTTT‑CAACCCATTTATCTCCTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGc < 2:653237/90‑1 (MQ=255) cTTGACAAAAATAAAAATTTTC‑CAACACTCTTTTCTACCCGATTTTGGCTTCCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGa < 2:599291/90‑1 (MQ=255) acacAAAAACAAATTTTT‑CAACCCATTTATCTCCTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATAtt < 2:390476/90‑1 (MQ=255) cacaAATAAAAATTTTT‑AAACACACTTATCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc < 2:147006/90‑1 (MQ=255) caaaTAAAAATTTTT‑CAACACCCTTATCTCCTCGATTTTGGCTTGCACCCGCAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCAc < 2:67993/88‑1 (MQ=255) cGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAc > 2:134017/1‑90 (MQ=255) aaTACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCa > 2:574409/1‑90 (MQ=255) taaaaatTTTT‑CAACACTTTTTTCTACTCAATTTTGGCTTCCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 2:804402/87‑1 (MQ=255) taaaaaTTTTCCACCCCACTTTTCTCCTCAATTTTGGCTTCCCCCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:134017/88‑1 (MQ=255) taaaaaTTTTCCAACCCACTTTTCTACTCGATTTTGGCTTCCACCCCAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 2:723336/88‑1 (MQ=255) t‑CAACCCTCTTTCCTCCTCGATTTTGGCTTGCACCCAAAAAACCCGGCTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:490629/90‑1 (MQ=255) t‑CAACCCACTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:342034/90‑1 (MQ=255) t‑CAACACCTTTTTCTACTCAATTTTGGCTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:255854/90‑1 (MQ=255) t‑CAACACATTTATCTACTAAATTTTGGCTTGCACCCGAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:41912/90‑1 (MQ=255) t‑CAACACACTTATCTCCTCGATTTTGGCTTGCACCCGAAAAACCCGGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:713078/90‑1 (MQ=255) ccatttATCTACTAAATTTTGGTTTCCACCAGAAAAACCGGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:491659/86‑1 (MQ=255) acatTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:172944/90‑1 (MQ=255) acacTTATCTACTCAATTTTGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:118433/90‑1 (MQ=255) cctttATCTACTCAATTTTGGCTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata < 2:585642/87‑1 (MQ=255) tctcCTCAATTTTGGCTTCCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTa < 2:348337/90‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:642079/1‑90 (MQ=255) cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt > 2:333640/1‑90 (MQ=255) tGGCTTGCACCCGAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:235516/90‑1 (MQ=255) tGGCTTCCACCCAAAAAACCCGGTTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:345461/90‑1 (MQ=255) tGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAt < 2:47256/90‑1 (MQ=255) | CCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAT > NZ_CP009273/3658969‑3659143 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |