| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,058 | 0 | T | C | 55.6% | 16.5 / 25.4 | 27 | D38G (GAT→GGT) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base T (8/4); new base C (0/15); total (8/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.23e-04 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.53e-04 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658973‑3659138 | gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc > 1:460588/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:552627/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 1:543612/1‑90 (MQ=255) aaaTAATAAAGGCGTGTCCCTTGACACAAATAAAAAATTTTCAACCCCCTTATCTCCTCGATTTTGGCTTGCATCCGAAAAAACCAGGTc < 2:84048/90‑1 (MQ=255) aatAAAAGCGTGTCCCTTGCCCCAAAAAAAAAATTTTCAACCCACTTATCTACTCAATTTTGGCTTGCACCCACAAAACCCAGGTCACCg < 2:403146/90‑1 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 2:621052/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCa < 2:540372/73‑1 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCa > 1:540372/1‑73 (MQ=255) gtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa > 2:5474/1‑90 (MQ=255) cctttGACACAAATAAAAAATTTTCAACACACTTATCTCCTCGATTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGc < 1:5682/87‑1 (MQ=255) cccTTGACACGAATACAAAATTTTCAACACCTTTATCTCCTCGAATTTGGCTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGc < 1:215922/90‑1 (MQ=255) cTTGACACAAATACAAAATTTTCAACACCCTTATCTACTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGa < 1:191632/90‑1 (MQ=255) cacaAATAAAAATTTTCCACCACATTTTTCTCCTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 1:44273/90‑1 (MQ=255) aaTACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCa > 2:291367/1‑90 (MQ=255) aaaaaatTTTTCAACCCATTTTTCTCCTCGATTTTGGTTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:551941/87‑1 (MQ=255) tttCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg > 2:544604/1‑90 (MQ=255) ttCAACACTCTTATCTACTCGATTTTGGCTTCCACCCAAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt < 1:440602/90‑1 (MQ=255) tCAACACCTTTATCTACTCGAATTTGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:291367/90‑1 (MQ=255) tCAACACCCTTATCTACTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:5474/90‑1 (MQ=255) ccAACACATTTATCTACTAAATTTTGGTTTCCACCCAAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:499788/89‑1 (MQ=255) ccacTTTTCTCCTCAATTTTGGCTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:196903/89‑1 (MQ=255) cacTTATCTACTCAATTTTGGTTTCCACCCAAAAAACCCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata < 2:207792/90‑1 (MQ=255) tCTACTGGATTTGGGCTTGCACCCGAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTa < 1:621052/90‑1 (MQ=255) tGGTTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:365226/90‑1 (MQ=255) tGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:172918/90‑1 (MQ=255) tGGCTTCCACCCAAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:413536/90‑1 (MQ=255) tGGCTCGCACCCAAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:518228/90‑1 (MQ=255) | GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658973‑3659138 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |