| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,058 | 0 | T | C | 54.0% | 41.8 / 53.8 | 37 | D38G (GAT→GGT) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base T (13/4); new base C (0/20); total (13/24) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.68e-07 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.04e-08 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658975‑3659138 | gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaa < 2:196643/90‑1 (MQ=255)gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaa < 1:589274/90‑1 (MQ=255)gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaa < 2:665607/90‑1 (MQ=255)gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaa < 2:665372/90‑1 (MQ=255) cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaaa > 1:167008/1‑90 (MQ=255) aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaaaa > 1:650972/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaaaaa > 2:475702/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCaaaaa > 1:585737/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAAc > 1:815243/1‑90 (MQ=255) cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAAc > 2:755193/1‑90 (MQ=255) aaaTAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTc > 1:726060/1‑90 (MQ=255) cGTCTCCTTTGACACAAATAAAAAATTTCCAACCCATTTATCTCCTCGAA‑TTTGCCTTCCACCCGCAAAAACCA‑GGTCACCGCCATTaaa < 2:596598/90‑1 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTaaaa > 2:70793/1‑90 (MQ=255) ttccccTTAACAAAAAAAAAAAATTTCCAACCCATTTATCTACTCAAT‑TTTGGCTTGCACCCGAAAAAACCA‑GGTCACCGCCATTAAAAt < 1:254845/87‑1 (MQ=255) tCCTTTGACAAGAATAAAAATTTTTCAACCCACTTATCTACTCAAT‑TTTGGCTTCCACCCGAAAAACCCA‑GGTCCCCGCCATTAAAATAg < 1:499733/90‑1 (MQ=255) cccTTGACACAAATAAAAAATTTCAAACACCCTTATCT‑CCCGAATTTTGGCTTCCACCCCAAAAACCCG‑GGTCACCGCCATTAAAATAGc < 2:770013/90‑1 (MQ=255) cacaAATAAAAATTTTTCAACACATTTATCTCCTCGAT‑TTTGGCTTGCACCCGAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTc < 2:480433/90‑1 (MQ=255) cacaAATAAAAATTTTTCAACACACTTATCTCCTCAAA‑TTTGGCTTGCACCCGAAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTc < 2:272605/90‑1 (MQ=255) cacGAAAAAAAAATTTACAACACCTTTATCTCCTCAAT‑TTTGCCTTCCCCCCCCAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTc < 2:574447/90‑1 (MQ=255) gAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCAcc > 2:99589/1‑90 (MQ=255) taaaaatTTTTCAACACACTTATCTACTCGAA‑TTTGGCTTCCACCCGAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCAtt < 2:72787/87‑1 (MQ=255) aaaaaatTTTTAAACACACTTATCTCCTCAAA‑TTTGGCTTGCACCCAAAAAACCCA‑GGTCCCCGCCATTAAAATAGCGATATTCACCAtt < 2:611151/87‑1 (MQ=255) atttttCAACACACTTATCTACTCGAA‑TTTGGCTTGCACCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa < 2:132883/88‑1 (MQ=255) taaaCACACTTATCATCTCGAT‑TTTGGTTTGCCCCCAAAAAACCAA‑GGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:73634/88‑1 (MQ=255) tCAACCCATTTATCTCCTCAAT‑TTTGGCTTCCACCCGAAAAAACCA‑GGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:649178/90‑1 (MQ=255) tCAACACTTTTATCTACTAAAT‑TTTGGTTTCCACCCAAAAAAACGA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:755192/90‑1 (MQ=255) cAACACATTTATCTCCTCGAT‑TTTGGCTTGCACCCGAAAAAACCA‑GGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga < 2:811009/90‑1 (MQ=255) cccccTTATCTCCTCGAT‑TTTGCCTTGCCCCCCAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 2:101620/86‑1 (MQ=255) cacacTTTTCTACGAAAT‑TTTGGTTTCCACCCAAAAAAACGG‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa < 1:600768/90‑1 (MQ=255) tATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAtt > 2:88295/1‑90 (MQ=255) tCTACTCGAT‑TTTGGCTTGCACCCGAAAAAACCA‑GGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTa < 2:650973/90‑1 (MQ=255) cTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:368982/1‑90 (MQ=255) cTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 1:398580/1‑90 (MQ=255) ttGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa > 1:677874/1‑90 (MQ=255) tgctttGCACCCG‑AAAAACCAGGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:815244/86‑1 (MQ=255) tGGTTTCCACCCGAAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:21247/90‑1 (MQ=255) tGGCTTCCACCCAAAAAAACCG‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:70793/90‑1 (MQ=255) | GCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658975‑3659138 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |