| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_004302 | 7,392 | 1 | . | A | 20.0% | 138.4 / 24.7 | 70 | coding (498/735 nt) | r1tp11 | ORF11 |
| Reads supporting (aligned to +/- strand): ref base . (56/0); new base A (14/0); total (70/0) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-02 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GTTATTCCATATTCTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACGGTTGTGGAC > NC_004302/7318‑7458 | gatcaatcATATTCTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAt > 1:14491908/8‑75 (MQ=255) ttATTCCATATTCTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑a > 1:15785680/1‑75 (MQ=255) gaaTTCCATATTCTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑a > 1:6566537/3‑75 (MQ=255) aagaaagcTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑aaaaaa > 1:6463541/8‑75 (MQ=255) cATATTCTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑aaaacta < 1:12905683/75‑4 (MQ=255) gagctCTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑aaaaaaat > 1:11289135/5‑73 (MQ=255) cctagcagAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAAtt > 1:15968279/8‑75 (MQ=255) cctagcagAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAAtt > 1:4328057/8‑75 (MQ=255) agttcaaaaTTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGa > 1:4105288/7‑75 (MQ=255) aaagggAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGTACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGa > 1:9828169/6‑75 (MQ=255) aaagggAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGCACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGa > 1:9807720/6‑75 (MQ=255) attggtgttGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTaaa > 1:13217228/8‑75 (MQ=255) atataacTTGAGTATCTAAATAAAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTaa > 1:5466979/7‑75 (MQ=255) tgctCTTAAGTATCTAAATAAAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAg > 1:9064775/4‑75 (MQ=255) gtaggtcgAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAg > 1:16094043/8‑75 (MQ=255) atttgacgAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTTAAGc > 1:4849804/8‑75 (MQ=255) atttgacgAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTTAAGc > 1:4870352/8‑75 (MQ=255) cttgatgTATCTAAAA‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATTTTTAAGC‑AAAT‑AAAAAAATGATTAAAGCaat > 1:5619193/7‑74 (MQ=255) ttgggggaTCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGa > 1:10258168/8‑75 (MQ=255) ttGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGAt > 1:11013251/1‑75 (MQ=255) taggcaTCTAAATAAAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGAt > 1:1316225/6‑75 (MQ=255) ttttgaataaaa‑aaaAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATg > 1:9470435/8‑75 (MQ=255) tcgtgccTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATg > 1:12250469/7‑75 (MQ=255) tggatggaat‑aaaAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGaa > 1:10455855/8‑75 (MQ=255) tggatggaat‑aaaAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGaa > 1:13378001/8‑75 (MQ=255) aagtggaaat‑aaaAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGaa > 1:10772591/7‑75 (MQ=255) acgtgat‑aaaAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGCAAAAT‑AAAAAATTGATTAAAGCAAGATGGAATg > 1:2427609/6‑75 (MQ=255) ccaacaaaaaaaaaC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGa > 1:2483651/8‑75 (MQ=255) cagaaaaaaaaC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAgg > 1:15969431/5‑75 (MQ=255) tccgagaC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCtat > 1:651968/7‑75 (MQ=255) tccgagaC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCtat > 1:16173674/7‑75 (MQ=255) tgtttgttGGACGAA‑GC‑TTTAG‑AATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGCAGGCTATaa > 1:14874964/8‑75 (MQ=255) gaaaaCTTGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCtata > 1:4522560/2‑75 (MQ=255) gaaaaCTTGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCtata > 1:17236859/2‑75 (MQ=255) atacttatGGACGAA‑GC‑TATAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCtat > 1:5126809/8‑75 (MQ=255) atacttatGGACGAA‑GC‑TATAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCtat > 1:495613/8‑75 (MQ=255) agtcttatGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCtata > 1:14521626/8‑75 (MQ=255) aaaacC‑TGAACGAA‑GC‑CTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCtattc > 1:14680797/1‑73 (MQ=255) tgctcatGGACGAA‑GCTTTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCtata > 1:17043514/7‑75 (MQ=255) agatatgggACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATaa > 1:5643405/8‑75 (MQ=255) caatagtgACGAA‑AC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAg > 1:13646421/8‑75 (MQ=255) caatagtgACGAA‑AC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAg > 1:12384049/8‑75 (MQ=255) agagatagACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAg > 1:13710104/8‑75 (MQ=255) ttttgagACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGc > 1:2070495/7‑75 (MQ=255) gggatcaCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCt > 1:6542783/7‑75 (MQ=255) caagggACGAATGC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGc > 1:6601282/5‑75 (MQ=255) tcaggACGAC‑GC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCt > 1:2734716/4‑75 (MQ=255) gtcgaaggAA‑GT‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTa > 1:13656001/8‑75 (MQ=255) c‑TGGACGGT‑GC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTa > 1:4204433/1‑75 (MQ=255) ttataCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTag > 1:14537198/5‑75 (MQ=255) gaaaaCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTag > 1:14302585/5‑75 (MQ=255) atGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCCATAAGcaag > 1:3193714/2‑72 (MQ=255) aatgACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTag > 1:9414654/4‑75 (MQ=255) tataCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTaca > 1:15573770/4‑73 (MQ=255) tataCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTaca > 1:11494267/4‑73 (MQ=255) tataCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTaca > 1:13985298/4‑73 (MQ=255) gggACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTag > 1:8320521/2‑75 (MQ=255) ggACGAA‑GC‑TTTAGAAATGTTGACTC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGTTaga > 1:16314274/1‑75 (MQ=255) gaaCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTAAAAGCtgaag > 1:15545710/3‑71 (MQ=255) tgtgAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATTAGCTagaga > 1:15856125/4‑73 (MQ=255) ctcaggtgC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTagaa > 1:12399497/8‑75 (MQ=255) gattttgC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTagaa > 1:8809017/7‑75 (MQ=255) atgAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTagaaga > 1:10842329/3‑75 (MQ=255) aCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATATGCTaggaa > 1:10330859/1‑72 (MQ=255) aCGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTagggaa > 1:13138458/1‑71 (MQ=255) tgtgttttAGAAATGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGAt > 1:5705019/6‑75 (MQ=255) gaaagaGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTa > 1:15010931/6‑75 (MQ=255) cttttttaTGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTaaa > 1:8899069/8‑75 (MQ=255) ttAGAAACGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTACAGGCTAGAAGATTTTaaaa > 1:5136892/1‑75 (MQ=255) ggAAATCTTG‑AGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACgg > 1:11700345/2‑75 (MQ=255) atctgtGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACg > 1:15660203/6‑75 (MQ=255) ggaTGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACgg > 1:8085040/3‑75 (MQ=255) gaTGTTGAAGT‑AA‑‑‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACGGTtgt > 1:16070292/2‑75 (MQ=255) tGTTGAAGC‑AAATAAAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACGGTtg > 1:769817/1‑75 (MQ=255) aatttaaaaaT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACGGTTGTgg > 1:5197266/8‑75 (MQ=255) tcatc‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACGGTTGTGGAc > 1:7745414/5‑75 (MQ=255) | GTTATTCCATATTCTGAAATTCTTGAGTATCTAAAT‑AAAAAAAC‑TGGACGAA‑GC‑TTTAGAAATGTTGAAGC‑AAAT‑AAAAAATTGATTAAAGCAAGATGGAATGAAGGCTATAAGCTAGAAGATTTTAAAACGGTTGTGGAC > NC_004302/7318‑7458 |
| 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: ‑ |