| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,125,835 | 0 | A | C | 53.3% | 12.7 / 18.0 | 15 | V162G (GTA→GGA) | flgA | flagellar basal body P‑ring formation chaperone FlgA |
| Reads supporting (aligned to +/- strand): ref base A (6/1); new base C (0/8); total (6/9) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.40e-03 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.15e-03 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTGTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGTTGATTGAT > NZ_CP009273/1125757‑1125923 | ttGTTCAGCGCCTGCCCTTCTGCGTTGGCGCTAAACCCATCCCCGCGGGCGATCACATTGACGCGTTTTCCCGTTTTTCCCCGCCATGcc < 2:317078/90‑1 (MQ=255) gcccTTCTGGGTGGGCGCAAACCCCACCCCCGCTGGCGAACATTTTGACGCGTTGCCCCCCTTTTCCCCGCCATGCCTGGCGAAACTggg < 1:565/88‑1 (MQ=255) tCTGCTTGGGCCCTAACCCCAACCCCGCTGGCGAGCCCATTGCGTCGTTGCCCCGTTTTTACCCGCCATGCCTGGCGAAACTGGGTTAAc < 2:600081/90‑1 (MQ=255) tCTGCGTTGGCGCTAAACCCGCCCCCGCTGGCGATCACATTGCCGCGTTGTCCCGCTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAAc < 2:179450/90‑1 (MQ=255) gTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGAt > 1:509375/1‑90 (MQ=255) tAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGAt > 2:245851/1‑90 (MQ=255) accccATCCCCGCTGGCGATCACATTGCCGGGTTGCCCCGCTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCg < 2:278948/88‑1 (MQ=255) accccACCCCCGCGGGCGATCACTTGGCCGGTTTGCCCCGTTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCg < 1:463760/88‑1 (MQ=255) gCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATc > 1:12711/1‑90 (MQ=255) gCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATc > 1:427965/1‑90 (MQ=255) gCGATCACATGGACGCGTTGCCCCGCTTTTCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCgcgc < 2:509375/90‑1 (MQ=255) gTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATcaa > 2:366609/1‑90 (MQ=255) ttttCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGttgatt < 1:366609/90‑1 (MQ=255) ttttCCCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGttgatt < 2:270555/90‑1 (MQ=255) tACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGTtgattgat > 2:573314/1‑90 (MQ=255) | TTGTTCAGCGCCTGACCTTCTGCGTTGGCGCTAAACCCATCACCGCTGGCGATCACATTGACGCGTTGTCCCGCTTTTACCCGCCATGCCTGGCGAAACTGGGTTAACTGGATAGGTTGATCGGGTGATAGATCGCGCAGGCTAATGGCATCAACAAGTTGATTGAT > NZ_CP009273/1125757‑1125923 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |