| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,105,845 | 0 | C | A | 54.5% | 2.2 / 15.4 | 11 | E188D (GAG→GAT) | gspC | type II secretion system protein GspC |
| Reads supporting (aligned to +/- strand): ref base C (3/2); new base A (3/3); total (6/5) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.40e-01 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGATTTCCTCAATCACCGCGTTGTG > NZ_CP009273/3105759‑3105931 | ggCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCctct > 2:168217/1‑90 (MQ=255) cagcagGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGAc > 1:115216/1‑90 (MQ=255) agGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTcc > 1:143117/1‑73 (MQ=255) agGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTcc < 2:143117/73‑1 (MQ=255) tgcttCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCATCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATa > 2:207290/1‑90 (MQ=255) tgcttCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCATCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATa > 2:288413/1‑90 (MQ=255) tgcttCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCATCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATa > 2:92945/1‑90 (MQ=255) tCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACgc < 1:85685/90‑1 (MQ=255) tgGTCACAGCAACAGTGGAACGTTCATCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGa < 1:207290/90‑1 (MQ=255) tgGTCACAGCAACAGTGGAACGTTCATCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGa < 1:288413/90‑1 (MQ=255) tgGTCACAGCAACAGTGGAACGTTCATCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGa < 1:92945/90‑1 (MQ=255) tgAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGATTTCCTCAATCACcgc > 1:8992/2‑90 (MQ=255) ggAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGATTTCCTCAATCACcgc > 1:230222/1‑90 (MQ=255) ttCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGATTTCCTCAATCACCGCGTtgtg < 1:168217/90‑1 (MQ=255) | GGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCCCTGATAACGCAGCATCACATGGTCGCGGTTGATTTCCTCAATCACCGCGTTGTG > NZ_CP009273/3105759‑3105931 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |