| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 2,221,751 | 0 | A | C | 61.1% | 10.0 / 16.1 | 18 | pseudogene (487/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| Reads supporting (aligned to +/- strand): ref base A (5/2); new base C (0/11); total (5/13) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.45e-03 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.86e-03 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACC > NZ_CP009273/2221666‑2221839 | cAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTc < 2:533547/90‑1 (MQ=255) cGCTGCAAGCCAGCAATTGGCGGGTTTGCGCGCGGTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTACCCTCCGCCCGATTCt < 1:834283/90‑1 (MQ=255) gcAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGGAGTAACCTCCGCCCGATTCTTTCCCCAGatat > 1:898525/1‑90 (MQ=255) cgccCGTGCTTTAACCGTACCCAGGCGGGCAGTACCCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCaaa < 2:299578/90‑1 (MQ=255) tttACCCGTCCCCGGGGGGGCAGTACCCCCCCCCCGTTTCTTCCCCCAGATATCGAGATCCCAGCCCGCCGTTAAGCCAAAAGTACCGtt < 1:372662/90‑1 (MQ=255) tttACCCGTCCCCGGGGGGGCAGTACCCCCCCCCCGATTTTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGtt < 2:898525/90‑1 (MQ=255) tttACCCGTCCCCAGGCGGGCAGTACCCCCCCCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGtt < 2:64912/90‑1 (MQ=255) tttACCCGTCCCCAGGCGGGCAGTAACCCCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGtt < 2:346385/90‑1 (MQ=255) tttACCCGCCCCCGGGGGGGCAGTACCCCCCCCCCGTTTTTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGtt < 1:202516/90‑1 (MQ=255) tttACCCGCCCCCGGGGGGGAAGTACCCCCCCCCCGATTCTTCCCCAAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGtt < 1:182465/90‑1 (MQ=255) tacccGTCCCCAGGCGGGCAGTACCCCCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTgg < 2:33352/87‑1 (MQ=255) aaCCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGgt > 1:525169/1‑90 (MQ=255) aCCGTCCCCAGGCGGGCAGTACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGgtg < 2:85730/90‑1 (MQ=255) aCCGTACCCAGGCGGGCAGTACCCCCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGgtg < 2:305539/90‑1 (MQ=255) gTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTAc > 2:555990/1‑90 (MQ=255) ggCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGc > 2:425239/1‑90 (MQ=255) ggCGGGAAGTACCCCCCCCCCGTTTCTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGc < 2:1226536/90‑1 (MQ=255) gggCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCgg > 2:786621/1‑90 (MQ=255) aaCCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTAcc > 1:261148/1‑90 (MQ=255) | CAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACC > NZ_CP009273/2221666‑2221839 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |