| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_004302 | 15,047 | 1 | . | A | 21.8% | 101.5 / 21.2 | 55 | intergenic (+140/‑7) | r1tp26/r1tp27 | HNH endonuclease/Structural protein |
| Reads supporting (aligned to +/- strand): ref base . (41/2); new base A (12/0); total (53/2) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.58e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CCTCCCTCTGGGTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAAGAGC > NC_004302/14977‑15112 | gaatttactGGGTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑aaaa > 1:10701821/8‑75 (MQ=255)cctccctcTGGGTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑aaaa > 1:10472066/1‑75 (MQ=255) gcccttgtGGGTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑aaaaa > 1:4871012/8‑75 (MQ=255) gaccgagggTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAAt > 1:16794651/7‑75 (MQ=255) ctgcgtGGGTCAGCTAGTACTTCACGCCGTCACTGTACA‑TTTTATCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAAt > 1:111936/6‑75 (MQ=255) cctacttgTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAAtt > 1:15041127/8‑75 (MQ=255) aagaatggTCAGCTCGTACTTCACGCCGTCACTGTACATTTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAAt > 1:14157867/7‑75 (MQ=255) taatacgTCAGCTCGTACTTCACGCCGTCACTGTACATTTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAAtt > 1:2979758/7‑75 (MQ=255) gaggaggTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAAtat > 1:6503828/6‑73 (MQ=255) tagaggtaGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGAc > 1:300996/8‑75 (MQ=255) tgtagtggCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACt > 1:467989/8‑75 (MQ=255) ttgaaaGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTg > 1:13079017/6‑75 (MQ=255) gaataGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTgg > 1:7610460/5‑74 (MQ=255) gTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGaa > 1:6800047/1‑75 (MQ=255) gaaattCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGaaa > 1:11023616/6‑75 (MQ=255) gCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTCaaatga < 1:920369/75‑4 (MQ=255) ttaagaCGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGCA‑AAAAAATTGACTGAAAAAGGTAtt > 1:1313114/6‑75 (MQ=255) ttaagaCGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGCA‑AAAAAATTGACTGAAAAAGGTAtt > 1:1813265/6‑75 (MQ=255) tcgacACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTg > 1:16392395/5‑75 (MQ=255) ggtaccgcACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATAc > 1:2045748/8‑75 (MQ=255) tgcagTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGCAAAAAAAATTGACTGAAAAAGGTATTGGATa > 1:6849576/5‑75 (MQ=255) ttattggtGTAGA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCt > 1:12784227/8‑75 (MQ=255) gaggatatGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTg > 1:608593/8‑75 (MQ=255) tgtggtGTATA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTgag > 1:12789671/6‑75 (MQ=255) taagttGTATA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGACACCTgag > 1:12040934/6‑75 (MQ=255) ggtacaatACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTgag > 1:13437301/8‑75 (MQ=255) ctagggatACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTgag > 1:6443402/8‑75 (MQ=255) ccagttGTATA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTgag > 1:1909820/6‑75 (MQ=255) agtggtGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTgag > 1:13570567/6‑75 (MQ=255) ggaCTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTgaga > 1:7413561/3‑75 (MQ=255) ggaCTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTgaga > 1:15357038/3‑75 (MQ=255) tctgaCA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGAttt > 1:15229746/5‑75 (MQ=255) gata‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAg > 1:7492976/4‑75 (MQ=255) tatttttttCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGc > 1:6087109/4‑75 (MQ=255) cA‑TTTTTTCTCACGCGAC‑‑TTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGAttctgatta < 1:9019615/75‑8 (MQ=255) caaatttCTCACGCGAC‑TTTAGAAAGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCt > 1:12912342/5‑75 (MQ=255) cggtaagcgcgAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTg > 1:14436685/8‑75 (MQ=255) gcgtcACGCGAC‑TTTAGAAAGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTg > 1:378651/4‑75 (MQ=255) gcaacACGCGACTTTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTAtact > 1:16981170/5‑72 (MQ=255) gaaataCGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGt > 1:9236479/6‑75 (MQ=255) gaaataCGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGt > 1:9216420/6‑75 (MQ=255) gaaataCGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGt > 1:10845890/6‑75 (MQ=255) cctaggcgAC‑TTTAGAAAGGAGC‑‑AAAAAATTGTCTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTc > 1:10979751/6‑75 (MQ=255) tatgggatAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATaaa > 1:1409767/8‑75 (MQ=255) taagatatAGAGAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATaaa > 1:1254526/8‑75 (MQ=255) gtggccaaaGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGaa > 1:9004561/7‑75 (MQ=255) gatttgAAAGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGa > 1:3682977/6‑75 (MQ=255) agagaGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGaa > 1:12923517/5‑75 (MQ=255) tttatgaaGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGaa > 1:11542842/7‑75 (MQ=255) tttatgaaGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGaa > 1:11522956/7‑75 (MQ=255) ctgtgtgaGGAGA‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAag > 1:5283823/8‑75 (MQ=255) aatAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAag > 1:4913845/3‑75 (MQ=255) tagtgggggAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAag > 1:15481473/8‑75 (MQ=255) ggactaaGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAag > 1:8081734/6‑75 (MQ=255) ggactaaGGAGCA‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAag > 1:16508745/6‑75 (MQ=255) tgaagaagAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAagag > 1:12205933/8‑75 (MQ=255) agtacgggagg‑‑aAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAagag > 1:8093758/7‑75 (MQ=255) tgcatttaGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAAGAGc > 1:739001/8‑75 (MQ=255) tgcatttaGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAAGAGc > 1:3516038/8‑75 (MQ=255) | CCTCCCTCTGGGTCAGCTCGTACTTCACGCCGTCACTGTACA‑TTTTTTCTCACGCGAC‑TTTAGAAAGGAGC‑‑AAAAAATTGACTGAAAAAGGTATTGGATACCTGAGATTTAAGCTATCTGTTCATAAACGAAGAGC > NC_004302/14977‑15112 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |