| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 50.0% | 12.1 / 12.7 | 20 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (5/5); new base A (0/10); total (5/15) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.25e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658973‑3659138 | gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc > 1:59307/1‑90 (MQ=255)gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc > 2:114308/1‑90 (MQ=255) gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa > 2:254477/1‑90 (MQ=255) gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAcc < 2:101640/90‑1 (MQ=255) gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAcc < 2:158568/90‑1 (MQ=255) taatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCAcc > 2:221653/1‑90 (MQ=255) aatGAAAGCGTGCCCCTTGACACAAATAAAAAATTTTCAACCCCTTTATCTCCTCGATTTTGGCTTGCATCCGCAAAAACCAGGTCACCg < 1:138300/90‑1 (MQ=255) atGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGc > 1:227684/1‑90 (MQ=255) cccTTGACACAAATAAAAAATTTTCAACACCTTTATCTACTAAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGc < 1:130515/90‑1 (MQ=255) cccTTGACACAAAAAAAAATTTTTAACCACTCTTTTCTACTAAAATTGGGTTTGCACCCGCAAAACCCGGGTCACCGCCATTAAAATAGc < 1:68883/90‑1 (MQ=255) cccTTAACACAAATAAAAATTTTCCACCCCATTTATCTACTAAATTTTGGCTTCCACCCCAAAAACCCAGGTCCCCGCCATTAAAATAGc < 1:253518/90‑1 (MQ=255) ttGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa < 1:304608/60‑1 (MQ=255) ttGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa > 2:304608/1‑60 (MQ=255) cacaAATAAAAAATTTCCAACACACTTATCTCCCCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 2:5392/90‑1 (MQ=255) cacaAATAAAAAATTTACAACACCCTTATCTACTCAATTTTGGCTTCCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTc < 1:96491/90‑1 (MQ=255) cacGAATAAAAAATTTTAAACACCTTTATCTCCTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 2:59307/90‑1 (MQ=255) cacGAATAAAAAATTTACAACCCTCTTATCTACTAAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc < 1:93362/90‑1 (MQ=255) caaaaaTAAAAAATTTCCAACACCCTTATCTACTCAATTTTGGTTTCCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTc < 1:254477/86‑1 (MQ=255) tCAACACTTTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCGGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:227684/90‑1 (MQ=255) acacTTATCTACAAAATTTTGTCTTCCACCCAAAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:33194/90‑1 (MQ=255) cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt > 1:108407/1‑90 (MQ=255) tGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 2:321639/90‑1 (MQ=255) | GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658973‑3659138 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |