| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,124,793 | 0 | A | C | 58.8% | 13.3 / 18.8 | 17 | pseudogene (975/1065 nt) | yghQ | lipopolysaccharide biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base A (7/0); new base C (0/10); total (7/10) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.14e-05 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.65e-04 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAA > NZ_CP009273/3124718‑3124882 | ttCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTccgcccgc > 2:242150/1‑90 (MQ=255) caaaaCACCCGTGAAACGAGCGGTTCGCCGAATACCCCCCCCGCGCGCGCCACCAAAACCCCCATCCCGCCCGCCAGTAAACCGGACTTc < 1:354364/88‑1 (MQ=255) aaaCACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTcac > 1:448955/1‑90 (MQ=255) ccAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTa > 2:18441/1‑90 (MQ=255) aGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTaac > 2:153233/1‑90 (MQ=255) aggggCGGCTTGCCGACAACCACCCCCGCGAGCCCCCCAAAAATCCCGATCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:153233/86‑1 (MQ=255) aggggCGGCTGGCCGACAACCACCCCCGCGACCCCCCCAAAAACCCCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:476418/86‑1 (MQ=255) aggAGCGCCTTGCCGACGATCACCCCCGCGGCCCCCACCAAAATCCCGTTCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:13100/88‑1 (MQ=255) aTGGGCGGCTTGCCGACGACCACCCCCCCGCGCCCCACAAAAATCCCGTTCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:276446/90‑1 (MQ=255) aTGGGCGGCTTGCCGACAAACACCCCCGCGAGCCCCACCAAAATCCCGTTCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:479883/90‑1 (MQ=255) gggCGGCTCGCCGACAACCCCCCCCGCCACCCCCCCAAAAATCCCGTTCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACgg < 2:533273/88‑1 (MQ=255) gAGCGGCTTGCCGACAACCACCCCCGCGACCCCCACAAAAATCCCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACgg < 1:103225/90‑1 (MQ=255) tcccGACAATCACCCCCGCGAGCCCCCCCAAAATCCCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCtggtgg < 1:28931/88‑1 (MQ=255) ccGCGCGCCCCACAAAAATCCCGTTCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAAc < 1:71985/90‑1 (MQ=255) cgcgAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACg > 1:495337/1‑90 (MQ=255) cgcgAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACg > 2:415844/1‑90 (MQ=255) cgAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCa > 1:286192/1‑90 (MQ=255) aCCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTaaaa > 1:478151/1‑90 (MQ=255) | TTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAA > NZ_CP009273/3124718‑3124882 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |