| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,454,130 | 0 | G | A | 57.1% | 3.6 / 12.3 | 14 | E319K (GAA→AAA) | gspF | type II secretion system inner membrane protein GspF |
| Reads supporting (aligned to +/- strand): ref base G (5/1); new base A (0/8); total (5/9) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.00e-03 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-03 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCCAGCGTCTGGCAAATGCGGCAGAGAACGTTCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTT‑CCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAA > NZ_CP009273/3454068‑3454208 | cccggCGTCTGGAAAAGGGGGCAGAGAACGTTCGCCGGGGTAACAGCATTCATTTTTCGCTGAAACAACCCGCAATTTT‑CCCGCCgatga < 2:161671/86‑1 (MQ=255) ggCGTCTGGCAAAGGGGGCAGAGACCGTCCCCCGGGGTAAAAGCATTCTTCTTTCGCTGAAACAACCCGCATTTTT‑CCCGCCGATGATGc < 2:170231/89‑1 (MQ=255) cgCGTCTGGCAAATGCGGAAGAAACCGTCCCCCGGGGAAACACCTTTCTTTTTTCGCGGAAACAACCCGAATTTTT‑CCCGCCGATGATGc < 1:339414/89‑1 (MQ=255) cgCGTCGGGAAAAGGCGGCAGAAACCGTCCCCCGGGGAAAAAGAATTC‑TTTTTCGGAGAAAAAAACCCGAATTTTCCCCGCCGATGATGc < 1:233631/89‑1 (MQ=255) gtGGAAAAGGGGGCAGAGAACGTTCCCCGGGGAAACACCATTCTTCTTTCGCGGAAACAACCCCCATTTTC‑CCCGCCGATGATTCTCTAc < 2:275182/89‑1 (MQ=255) cTGGAAAATGCGGCAGAGACCGTTCGCCGGGGAAACAGCTTTCATTTTTCGCTGAAAAAACCCGCATTTTT‑CCCGCCGATGATGCTCTAc < 2:405815/90‑1 (MQ=255) aaaTGCGGCAGAGAACGTTCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTT‑CCCGCCGATGATGCTCTACAtggt > 2:470261/1‑90 (MQ=255) gCAGAGAACGTTCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTT‑CCCGCCGATGATGCTCTACATGGTGGCctct > 1:106395/1‑90 (MQ=255) gCAGAGAACGTTCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTT‑CCCGCCGATGATGCTCTACATGGTGGCctct > 1:248635/1‑90 (MQ=255) cAGAGACCGTTCGCCGGGGTAACAGCATTCATCTTTCGCTGGAACAACCCGAAATTTC‑CCCGCCGATGATGCTCTACATGGTGGCCTCTg < 2:248635/90‑1 (MQ=255) gggTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTT‑CCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCa > 1:225347/1‑90 (MQ=255) aGCATTCATTTTTCGCGGAAAAAAACCGAATTTTC‑CCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTAGGc < 1:129921/90‑1 (MQ=255) aTTCATCTTTCGCTGGAACAAACCGCAATTTT‑CCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGcaca > 2:255759/1‑90 (MQ=255) ttttttCGCTGAAAAAACCCCCATTTTT‑CCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTaa < 2:100127/87‑1 (MQ=255) | GCCAGCGTCTGGCAAATGCGGCAGAGAACGTTCGCCAGGGTAACAGCATTCATCTTTCGCTGGAACAAACCGCAATTTT‑CCCGCCGATGATGCTCTACATGGTGGCCTCTGGCGAAAAAAGCGGGCAGCTCGGCACATTAA > NZ_CP009273/3454068‑3454208 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |