| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,124,799 | 0 | T | C | 53.8% | 9.7 / 17.7 | 13 | pseudogene (969/1065 nt) | yghQ | lipopolysaccharide biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base T (6/0); new base C (0/7); total (6/7) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.83e-04 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-03 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGG‑CTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCA > NZ_CP009273/3124666‑3124896 | ccGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGG‑CTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTccgcc > 2:90814/1‑139 (MQ=255) ttccccACCTCCCAAAAACCAGGCCATGCGCTGCGAAATTCTAACCGCAAAACACCAG‑AAAATGGGGGGCCTCGCCGCCTACCACCCCCGCGCGCCCCACCAAAACACCGTTCCCCCCCGCCAGTAAACCGGACTTca < 2:561978/133‑1 (MQ=255) ccaaaaaCAGGTCATCCGCTTCGAGATACTTAACGCCAAACCCCAGCGAAAGGGGCGT‑CTTGCCGACGATCAACCCCGCGAGCCCCACCAGAATCCCGATCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCa < 1:41752/136‑1 (MQ=255) ccaaaaCCAGGCCATACGCTCCGAGATACTAAACGCCAACCCCAAGCGAAATGGGCGG‑CTTGCCGACAACCAACACCGCGGGCGCCACCAGAACACCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCa < 1:588534/136‑1 (MQ=255) ataaGGTCACCCCCTTGGAGATACTAACCGCCAAACCCCAGCAAAAGGCGGGG‑CCCGCCGACGACCCCCCCCGCGAGCCCCACCAAAATCCCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTc < 2:357548/136‑1 (MQ=255) gTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGG‑CTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCtggtg > 1:561893/1‑139 (MQ=255) gTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGG‑CTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCtggtg > 1:576211/1‑139 (MQ=255) tCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGG‑CTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGAt > 1:245631/1‑139 (MQ=255) atacaaaaccccaaccccCAGCGAAGTGCGGGG‑CTGCCCGCCGACCAACCCGGCGGCCGCCCCCAGAATCCCGATCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTaaa < 2:561893/133‑1 (MQ=255) aTACTAACCCCCAAACACAAGAAAAATGGGCGG‑CTGGCCGACGACCAACCCCGCGACCCCCACAAAAATCCCGTTCCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTaaa < 2:245631/139‑1 (MQ=255) aaCACCAGCGAAATGAGCGG‑CTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTg > 1:69661/1‑139 (MQ=255) aGCAAAATGGGCGG‑CTGCCCGCCTACAACCCCCGCGAGCCCCCCCAGAATCCCGATCCCCCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTaaa < 1:458147/139‑1 (MQ=255) tGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCa > 1:467162/1‑138 (MQ=255) | CCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGG‑CTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGGTGCGCGGATCTAAACGCATCACCTCTGGGTAAAAACTTTTACCCAGCA > NZ_CP009273/3124666‑3124896 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |