| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,124,771 | 0 | A | C | 60.0% | 11.5 / 14.6 | 15 | pseudogene (997/1065 nt) | yghQ | lipopolysaccharide biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base A (4/2); new base C (0/9); total (4/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.10e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.47e-04 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGG > NZ_CP009273/3124690‑3124848 | cGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGa < 1:589239/90‑1 (MQ=255) aCCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAgcg < 2:379222/90‑1 (MQ=255) 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) | CGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACACCAGCGAAATGAGCGGCTTGCCGACGATCAACACCGCGAGCGCCACCAGAATACCGATTCCGCCCGCCAGTAAACCGGACTTCACACCTAACAACCACGGTCTGGTGG > NZ_CP009273/3124690‑3124848 |
| 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: ‑ |