| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 4,594,167 | 0 | C | T | 63.8% | ‑0.7 / 51.2 | 48 | S64F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| Reads supporting (aligned to +/- strand): ref base C (1/16); new base T (30/0); total (31/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.13e-11 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.76e-10 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGC > NZ_CP009273/4594078‑4594254 | cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATtttttctttttc < 2:518668/90‑1 (MQ=255)cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATtttttctttttc < 2:28371/90‑1 (MQ=255) cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTg < 2:565016/90‑1 (MQ=255) tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGcc > 2:152623/1‑90 (MQ=255) ataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTTCTTTTTTTTTTTTTTGCCa > 2:395856/1‑90 (MQ=255) cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTgaga > 2:872359/1‑90 (MQ=255) cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTgaga > 1:362253/1‑90 (MQ=255) cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATtagg > 1:631285/1‑89 (MQ=255) cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGGCCTTTTTTTTTTTTTTTCCATgaga > 1:867036/1‑90 (MQ=255) ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCCTTTTTTTTTTTTTTGCCCTgaggag > 2:274783/1‑90 (MQ=255) ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATtttttctttttc < 2:531556/78‑1 (MQ=255) tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAgcgc > 2:47033/1‑90 (MQ=255) tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAgcgc > 2:213311/1‑90 (MQ=255) ctatccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc < 2:25442/86‑1 (MQ=255) ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCa > 2:821767/1‑90 (MQ=255) ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCa > 1:769027/1‑90 (MQ=255) ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAgcgcg > 2:582379/1‑89 (MQ=255) ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGGCCTTTTTTTTTTTTTTTCCCTGAGAAGGGAgcgcg > 1:516648/1‑89 (MQ=255) aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCCTTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCagg > 1:658621/1‑89 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga < 1:687220/90‑1 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCagagag > 2:647309/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCagggag > 1:760521/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGCcgagag > 1:300382/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCagagag > 1:20776/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCagagag > 2:668668/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCagagag > 2:244598/1‑90 (MQ=255) tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGGGGGCAGAGAggg > 2:432634/1‑90 (MQ=255) ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCAGAGAGGGGtt > 1:176328/1‑90 (MQ=255) ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGtt > 2:695378/1‑90 (MQ=255) gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGTTAtt > 2:255518/1‑89 (MQ=255) tCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCt < 1:194709/90‑1 (MQ=255) tCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCt < 2:211899/90‑1 (MQ=255) cATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGGGGGGTTAtttt > 1:203646/1‑90 (MQ=255) tttCCGGATGCCCTGTCGCGGCACTCGTTTTCGGGGGGCCTTTTTTTCTTTTTGGCCAATGA‑CAGTGGACGCCGGGAGGGATTATCTTGc < 1:615402/90‑1 (MQ=255) cAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGGGCGCAGAGAGGGGTTATCTTGCctt > 2:733693/1‑89 (MQ=255) tGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCagaga > 2:677704/1‑69 (MQ=255) tGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga < 1:677704/69‑1 (MQ=255) ccATGTCGCGGATCTCGTTTGC‑GGCGGTCGTTTTTTTTTTTTTTGGCCTGAGAAGGGAGGGCAGAGGGGGATTATCTTGCCTGACTGTAc > 2:512413/1‑90 (MQ=255) ccATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAAc < 1:626182/90‑1 (MQ=255) cATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt < 1:17849/90‑1 (MQ=255) gcgGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTTCCCTGTGAAGTGAGCGCAGAGAGGGGTTATTTTGCCTGACTGAACTGGCGAt > 1:612434/1‑90 (MQ=255) gcgGATCTCGTTTGC‑GGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTTTTTTTCCTGACTGAACTGGCggt > 1:68260/1‑88 (MQ=255) gcgGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTTTTCCATGAGAAGGGAGGGCAGAGAGGGGGTTTTTTTCCTTCCTGAACTGGCggt > 1:843108/1‑88 (MQ=255) tctcGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGt < 1:47033/90‑1 (MQ=255) ctcGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGtt < 2:760521/90‑1 (MQ=255) tcGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGttt < 1:395856/90‑1 (MQ=255) gcggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAcc < 1:821767/90‑1 (MQ=255) cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc < 1:695378/90‑1 (MQ=255) ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg < 1:668668/90‑1 (MQ=255) gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg < 2:612434/90‑1 (MQ=255) aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt < 1:225349/90‑1 (MQ=255) ttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTAtt > 1:769012/1‑90 (MQ=255) ttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTAtt > 1:54050/1‑90 (MQ=255) ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc < 1:838747/90‑1 (MQ=255) ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc < 2:408654/90‑1 (MQ=255) ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc < 2:54050/90‑1 (MQ=255) ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc < 2:519042/90‑1 (MQ=255) | CCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGC‑GGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGC > NZ_CP009273/4594078‑4594254 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |