| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 56.5% | 16.5 / 85.1 | 69 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| Reads supporting (aligned to +/- strand): ref base C (4/26); new base T (39/0); total (43/26) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.90e-15 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.50e-12 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTCCGCGTACCCGGCGTTTAG > NZ_CP009273/4594076‑4594247 | aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATtttttttttt > 2:138380/1‑90 (MQ=255) cccTTATAAGCTCCATACCTATACCAGTCAGGAGTTATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATtttttctttttc < 2:1252885/90‑1 (MQ=255) cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATtttttctttttc < 1:138380/90‑1 (MQ=255) cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTg < 1:758476/90‑1 (MQ=255) tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGG‑CCTTTTTTTTTTTTTTGcc > 2:1038832/1‑90 (MQ=255) gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCCTgag > 2:1018201/1‑90 (MQ=255) cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATgaga > 2:1014923/1‑90 (MQ=255) tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTGCCATGAGaa > 2:964982/1‑90 (MQ=255) tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGaa < 1:1018201/90‑1 (MQ=255) tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGaa < 1:1338974/90‑1 (MQ=255) cagaTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGaa < 1:1107884/87‑1 (MQ=255) ccATATATATACCAGTCAGGAGTCATTTCAGGACGCCATGCCGCGGATCTCGTTTGCGGCGAT‑CATTTTTTCTTTTTCCGCCATGAGAAg < 1:649231/90‑1 (MQ=255) ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CCTTTTTTTTTTTTTTTCCATGAGAAg > 2:265738/1‑90 (MQ=255) cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGt < 1:629256/90‑1 (MQ=255) aCCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAg < 1:702893/90‑1 (MQ=255) ccTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAgc < 2:801830/90‑1 (MQ=255) tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGTGAgcgc > 2:1338974/1‑90 (MQ=255) tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc < 2:1115414/90‑1 (MQ=255) ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCa > 2:1166898/1‑90 (MQ=255) taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag < 1:1415725/90‑1 (MQ=255) taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag < 1:858627/90‑1 (MQ=255) aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCaga > 2:116730/1‑90 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CAttttttttttttt > 1:1652858/1‑65 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATtttttctttttc < 2:1652858/66‑1 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGGGGGCGCcgagg > 1:366736/1‑89 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga < 2:567927/90‑1 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga < 2:4179/90‑1 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga < 1:128281/90‑1 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga < 1:964614/90‑1 (MQ=255) cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGG‑TATTTTTTTTTTTTTTGGCCTTAGAAGGGGGCGCagggg > 2:1107884/1‑87 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGGTCTCGTTTGCGGCGGT‑CCTTTTTTTTTTTTTTGCCACGGGAAGGGAGAGCctagag > 1:1296429/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTTCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGGGCGCcgagag > 1:687341/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTTCCCTG‑GAAGTGAGCGCagcgag > 1:1125096/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CAtttttttttttt > 1:723396/1‑64 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATtttttcttttt < 2:723396/64‑1 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCagagag > 1:1497331/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCagagag > 2:859911/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGGGGGGGCagagag > 2:702893/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCagagag > 2:80431/1‑90 (MQ=255) aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGG‑CATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCcgaggg > 1:673306/1‑88 (MQ=255) gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATTAGAAGGGAGCGCAGAGAgg > 2:740337/1‑90 (MQ=255) gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCAGAGAgg > 2:860148/1‑90 (MQ=255) gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAATGAGCGCAGAGAgg > 1:1246154/1‑90 (MQ=255) gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAgg > 2:1415725/1‑90 (MQ=255) gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAgg > 2:1244233/1‑90 (MQ=255) tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGTCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAggg > 2:1666968/1‑90 (MQ=255) tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCCTGAGAAGAGAGCGCAGAGAggg > 1:1319535/1‑90 (MQ=255) tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCCTGAGAAAGGAGCGCAGAGAggg > 1:738802/1‑90 (MQ=255) tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAggg > 2:1674282/1‑90 (MQ=255) cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CTGTTTTTTTTTTTTTGCCATGGGAAGGGAGGGCAGAGAgggg > 2:735107/1‑89 (MQ=255) cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAgggg > 2:632664/1‑89 (MQ=255) ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CAttttttttttttttt > 1:1679689/1‑59 (MQ=255) ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTg < 2:1679689/62‑1 (MQ=255) ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGG‑CATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAGGGGtt > 1:218963/1‑90 (MQ=255) gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGG‑CATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAGGGGTTAtt > 1:687533/1‑89 (MQ=255) tCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCt < 1:1014923/90‑1 (MQ=255) cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGG‑CATTTTTTTTTTTTTTTCCATGAGGAGGGAGGGCAGAGAGGGGTTATCtt > 1:1032233/1‑90 (MQ=255) tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc < 1:818593/90‑1 (MQ=255) ttCAGGATGCCATGTTGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGcc < 2:979517/90‑1 (MQ=255) ttCAGGATGCCATGTCGCGGATCTCGTTTGCGGTGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGcc < 2:1367845/90‑1 (MQ=255) tGCCATGTCGCGGATCTCGTTTGCGGCGGG‑CATTTTTTTTTTTTCTTCCATGAAAAGGGAGGGCAGAGGGGGGTTATCTTGCctgactga > 2:360211/1‑90 (MQ=255) ccATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTGCCCTGAGGAGGGGGGGCGGGGGGGGAGTATTTTGTCTGACTTAAc > 1:524239/1‑90 (MQ=255) cATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt < 2:1032233/90‑1 (MQ=255) cATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt < 1:13862/90‑1 (MQ=255) ggATCTCGTTTGCGGCGGT‑GATTTTTTTTTTTTTTTCCATGTGGAGTGAGCGCAGAGGGGGAATATTTTTTCTTGCTGCGCTGGC‑Gactt > 1:1149377/1‑87 (MQ=255) ggATCTCGTTTGCGGCGGT‑CATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCAGAGAGGGGTTATTTTGCCTGACTGAACTGGC‑GGTTa > 1:1567664/1‑90 (MQ=255) ggATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTTTGCCATGAGAAGGGAGGGCAGAGAGGGGTTTTCTTGCCTGTCTGAACTGGC‑GATTa > 1:608516/1‑90 (MQ=255) gATCTCGTTTGCGGCGGG‑CATTTTTTTTTTTTCTGCCATGAGAAGGGAGGGCAGAGAGGGGTTATCTTTCCTGACTGAAATGGC‑GATTaa > 2:1613088/1‑90 (MQ=255) tcGTTTGCGGCGGT‑CATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGGTTTTTTTCCTGACTGAACTGGC‑GATTAAAttt > 1:1148548/1‑90 (MQ=255) gTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTcc < 2:1489461/90‑1 (MQ=255) gcggcgGT‑CATTTTTTTTTTTTCTGCCATGTGAAGGGGGCGCCGAGAGGGGTTTTTTTTCCCGACTGAAATGGC‑GATTAAATTTTcgccg > 2:1617518/1‑88 (MQ=255) gcggcgGT‑CATTTTTTCTTTTTTTTCCCTGAGAAGAGAGCGCGGAGAGGGGGTATCTTTCCTGACTTAACTTGCGGATAAAATTTcccgg > 1:15541/1‑87 (MQ=255) cggT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTCCGCGTAccc < 1:1674282/90‑1 (MQ=255) ggT‑CATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGGAGGGAGGGATTATCTTGCCTTTCTGAACTGGC‑GGTTAAGTTTCCGCGTACCCg > 1:1423939/1‑90 (MQ=255) ggT‑CATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTCCGCGTACCCg > 2:1454063/1‑90 (MQ=255) t‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTCCGCGTACCCGGc < 2:708907/90‑1 (MQ=255) t‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTCCGCGTACCCGGc < 1:1244233/90‑1 (MQ=255) tttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTCCGCGTACCCGGCGTTTAg > 2:1304966/1‑90 (MQ=255) | AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGT‑CATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGC‑GATTAAGTTTCCGCGTACCCGGCGTTTAG > NZ_CP009273/4594076‑4594247 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |