| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,124,799 | 0 | T | C | 60.0% | 3.5 / 13.8 | 15 | pseudogene (969/1065 nt) | yghQ | lipopolysaccharide biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base T (6/0); new base C (0/9); total (6/9) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.00e-04 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.47e-04 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAA > NZ_CP009273/3124718‑3124882 | ttCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTccgcccgc > 2:14047/1‑90 (MQ=255) ccTTACCCCCAACCCCCAGCAAAATGGGCGGCTTCCCGACGATCACCCCCGCGAGCCCCCCCAGAATACCGATCCCGCCCGCCAGTAAAc < 1:41334/89‑1 (MQ=255) cTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAAcc > 2:628600/1‑90 (MQ=255) ccaaaaCCCCAGAAAAAGGGGGGGCTGGCCAACAACCACCCCCGCGAGCCCCACAAAAATCCCGATCCCCCCCGCCAGTAAACCGGACtt < 1:613941/87‑1 (MQ=255) cacCAGCAAAAGGGGCGGCTCGCCGACAATCACCCCCGCGACCCCCACAAAAATCCCGTTCCCGCCCGCCAGTAAACCGGACTTCACAcc < 1:318734/90‑1 (MQ=255) aGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTaac > 1:314822/1‑90 (MQ=255) aggggCGGCTTCCCGACAACCACCCCCGCGAGCCCCACCAAAACCCCGTTCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:191368/86‑1 (MQ=255) aggggCGGCTGGCCGACAACCACCCCCGCGACCCCCACAAAAATCCCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:266749/86‑1 (MQ=255) aggggCGGCTGGCCAACGACCACCCCCGCGGCCCCCACAAAAACCCCGTCCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 2:216211/86‑1 (MQ=255) aggggCGGCTCGCCGACAACCACCCCCGCGAGCCCCACCAAAATCCCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc < 1:152254/86‑1 (MQ=255) aTGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCAc > 2:318734/1‑90 (MQ=255) cgccccacaaAAATACCGACCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATc < 1:317841/86‑1 (MQ=255) aCCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTaaaa > 2:368310/1‑90 (MQ=255) gATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATc > 2:484857/1‑73 (MQ=255) gATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATc < 1:484857/73‑1 (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 < 18 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |