| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_004302 | 5,716 | 1 | . | A | 20.0% | 107.6 / 18.6 | 55 | coding (807/834 nt) | r1tp09 | ORF9 |
| Reads supporting (aligned to +/- strand): ref base . (42/2); new base A (11/0); 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 = 5.59e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CCCGACTAACAAAACTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGAACAATACCAAAA > NC_004302/5643‑5783 | ctgatttAACAAAACTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑a > 1:721692/7‑75 (MQ=255) ttgACTAACAAAACTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑at > 1:12963557/3‑74 (MQ=255) ttgACTAACAAAACTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑at > 1:12046471/3‑74 (MQ=255) ccGACTAACAAAACTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑aa > 1:2758866/1‑75 (MQ=255) gACTAACAAAACTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑aaa‑a > 1:14609224/1‑75 (MQ=255) ttataaaaaCTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑aaa‑aaa > 1:6227809/6‑75 (MQ=255) gatagttaaCTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑aga‑aaa > 1:17156105/8‑75 (MQ=255) agctcataaCTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑aaa‑aaa > 1:17204702/8‑75 (MQ=255) ataaaaaCTTGAAAACATAATTGATCCAAGCACAGAATATACTGCAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAAt > 1:2122286/4‑75 (MQ=255) ctagaaCTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGA‑AATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTa > 1:2736765/5‑75 (MQ=255) tcgttagtGAAGACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTa > 1:5615889/8‑75 (MQ=255) aaaaaCTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTa > 1:5915612/2‑75 (MQ=255) tttagggAAAACTAAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTa‑aa > 1:15351392/7‑75 (MQ=255) attatgtAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTAt > 1:2614484/7‑75 (MQ=255) atgaCTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTAt > 1:16226431/4‑75 (MQ=255) aaaaCTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTATAAGGatac < 1:5837594/75‑4 (MQ=255) ttgggtgttGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTa > 1:5010069/8‑75 (MQ=255) tctGATTCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑CAA‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAAt > 1:14168342/3‑75 (MQ=255) gggaggtaaGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGAc > 1:13749746/8‑75 (MQ=255) agtaTCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGAc > 1:10920958/4‑75 (MQ=255) ttattcAAGTACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACa > 1:9908054/6‑75 (MQ=255) aaTCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACaa > 1:796377/2‑75 (MQ=255) tcgttaGCAGAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACaaa > 1:12978369/6‑75 (MQ=255) attgaaGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACaaa > 1:7809825/5‑75 (MQ=255) aagaaatcacaGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑CA‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACaa > 1:426049/8‑75 (MQ=255) tgaaaGCACAGAATAAACTGGAGAATCTG‑TATTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATAAAAATGACAAAt > 1:15683670/4‑75 (MQ=255) tatgtacaGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGa > 1:3122536/6‑75 (MQ=255) acgcgagaGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGa > 1:10066208/8‑75 (MQ=255) aggtggggAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGaa > 1:12262807/8‑75 (MQ=255) aaGCTCAGATTATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGaa > 1:1656997/1‑75 (MQ=255) tgtctgAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAAt > 1:8652483/6‑75 (MQ=255) gagtaGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAAt > 1:8667277/5‑75 (MQ=255) cggaGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑CAAAA‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGa > 1:2969741/4‑75 (MQ=255) aaaaaggtataCTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAAtt > 1:9143706/8‑75 (MQ=255) ggcagatatACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGAAAAATGAAATTc > 1:15139500/6‑75 (MQ=255) ggaGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑CA‑‑‑‑AAA‑AAAATTA‑AAGGACTATAAAAATGACAAATGAAAtt > 1:1572320/3‑75 (MQ=255) catggctataCTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTc > 1:13113562/7‑75 (MQ=255) acgtcagtaCTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCa > 1:1541046/8‑75 (MQ=255) agctctgaCTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCaa > 1:62440/8‑75 (MQ=255) gtagataCTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAg > 1:9453393/5‑75 (MQ=255) ggggacttGGAGAATCTGTTTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGAAAAATGAAATTCAAg > 1:16250408/8‑75 (MQ=255) ggcaagttGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGt > 1:195794/8‑75 (MQ=255) ggtaattgagaATCTG‑TTTTAAAGCTTAT‑CAA‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGt > 1:17047340/8‑75 (MQ=255) cacctttgagaATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGa > 1:11170817/8‑75 (MQ=255) attagttgagaATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGa > 1:6229872/8‑75 (MQ=255) aggttcgagaATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGac > 1:7877351/7‑75 (MQ=255) ttaagaaaTCTG‑TTTTAAAGCTTAT‑CAA‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGaca > 1:2796298/7‑75 (MQ=38) tggatgaATCTG‑TTTTAAAGCTTAT‑CA‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGacaa > 1:11340123/6‑75 (MQ=255) tGGAGATTCCG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGacaaca > 1:12469692/1‑75 (MQ=255) aggAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGacaaca > 1:5300042/2‑75 (MQ=255) tggaaaTCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAAcag > 1:16600944/5‑75 (MQ=255) gcagattCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAAcag > 1:689358/7‑75 (MQ=255) cgagaATCTG‑TTTTAAAGCTTAT‑CAAAAAAAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGac > 1:2970823/2‑75 (MQ=255) cttaaTCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAAcagc > 1:5983642/4‑75 (MQ=255) gatgtatttttGAAGCTTAT‑CAA‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAAcagc > 1:1421090/8‑75 (MQ=255) ctaagccttttAAAGCTTAT‑CA‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAAcagca > 1:16743698/8‑75 (MQ=255) tcccatgtttATAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGa > 1:6314059/8‑75 (MQ=255) gtag‑TTTAAAAGCTTAT‑C‑‑‑‑‑AAAGAAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGaa > 1:385751/4‑75 (MQ=255) gaag‑TTTTAAAGCTTAT‑CA‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGaa > 1:11063542/4‑75 (MQ=255) tgg‑TTTTAATGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGAAcg > 1:10231736/3‑74 (MQ=255) aaaGCTTATCC‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGAACAATACCa > 1:678066/1‑75 (MQ=255) tggattAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGAACAATACCaaa > 1:606371/5‑75 (MQ=255) aGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGAACCATACCaaaa < 1:7068791/75‑1 (MQ=255) | CCCGACTAACAAAACTTGAAAACTTAATTGATCCAAGCACAGAATATACTGGAGAATCTG‑TTTTAAAGCTTAT‑C‑‑‑‑‑AAA‑AAAATTA‑AAGGACTATTAAAATGACAAATGAAATTCAAGTGACAACAGCAGAACAATACCAAAA > NC_004302/5643‑5783 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |