| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | REL606 | 4,169,232 | 0 | A | T | 26.4% | 177.3 / 22.7 | 72 | intergenic (+48/‑165) | rpoC/htrC | DNA‑directed RNA polymerase subunit beta'/heat shock protein |
| Reads supporting (aligned to +/- strand): ref base A (16/37); new base T (19/0); total (35/37) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.45e-08 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GGTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTAGAGAT > REL606/4169158‑4169307 | ggTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTAt < 1:553322/76‑1 (MQ=255)ggTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTAt < 2:1296698/76‑1 (MQ=255) cTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATggg < 2:304987/76‑1 (MQ=255) cTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTATTTTTggg > 1:607975/1‑76 (MQ=38) ggCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATgggggg < 2:2223194/76‑1 (MQ=255) ggCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATgggggg < 2:1701319/76‑1 (MQ=255) cGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTGTTTTTATgggggggg > 1:23615/1‑74 (MQ=255) ggTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGCGGGGGTTTTTTTTTggggggg > 1:1703857/1‑75 (MQ=37) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGttt > 2:677126/1‑76 (MQ=38) tCTGATAACGAGTAATCGTAAACCCGCAAATAACGTAAAAC‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTa < 1:597695/76‑1 (MQ=38) tGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGtttgg > 1:262886/1‑74 (MQ=37) tGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAgg < 1:2080751/76‑1 (MQ=255) gATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAggg < 1:2057658/76‑1 (MQ=255) aTAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTTgggg > 1:475073/1‑76 (MQ=37) aTAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGa < 2:2192027/76‑1 (MQ=255) aCGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTTGGGGaag > 1:1565847/1‑75 (MQ=37) aCGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTTTTGGGGGGGTTTAGGGAAag > 1:2208660/1‑76 (MQ=37) gAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCTGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAagag < 2:1786249/76‑1 (MQ=255) aGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGc < 2:57850/76‑1 (MQ=255) gTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCCCTTCGGCGGGGGTTTTTTTTTGGGGGGGGGTTGGGGagaggg > 1:680297/1‑74 (MQ=19) aaTCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCAtt < 2:725270/76‑1 (MQ=255) aaTCGTTAATCCGCAAATAA‑GTAAAAACCCCGTTGCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCAtt < 1:1110777/76‑1 (MQ=255) cGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGt > 2:109587/1‑76 (MQ=255) ttAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCa < 2:2160875/76‑1 (MQ=255) tAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAg > 2:118671/1‑76 (MQ=255) tAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAg < 2:1755340/76‑1 (MQ=255) aaTCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGa < 2:1709934/76‑1 (MQ=255) aaTCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGa < 2:126675/76‑1 (MQ=255) aaTCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGa < 1:1987146/76‑1 (MQ=255) aaTCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGGTTAGGGGAAGAGCATTTGTCAGa > 2:940727/1‑76 (MQ=37) aaTCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGa > 2:225789/1‑76 (MQ=255) tCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAat < 2:556099/76‑1 (MQ=255) tCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGGTTTGGGAAAGAGCATTTGTCAGAat > 2:2006397/1‑76 (MQ=37) ccGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAata < 1:1684741/76‑1 (MQ=255) gCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑tt < 1:2160927/76‑1 (MQ=255) gCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGGTTTGGGGAAGAGGATTTGTCAGAATA‑tt > 1:2209135/1‑76 (MQ=25) aaaTAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTa > 2:156488/1‑76 (MQ=255) aaTAACGTAAAAA‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGCATTTGTCAGAATA‑tttta > 2:670613/1‑74 (MQ=25) aTAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTTTGGGGGGGGGTTTGGGGAAGAGCATTTGTCAGAATA‑TTTTAg > 2:1668251/1‑76 (MQ=25) tAACGTAAAAA‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGGGGATTTTTTAGGATA‑TTTTAgg > 2:1312395/1‑76 (MQ=12) aaCGTAAAAA‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGGATTTTTCAGAATA‑ATTAAAGa > 2:1195720/1‑76 (MQ=16) aaCGTAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGGTTTGGGAAAGAGCATTTTTTCGAATA‑TTTAAGGa > 2:2065115/1‑76 (MQ=21) cGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAAt > 1:2189513/1‑76 (MQ=255) cGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAAt < 1:208607/76‑1 (MQ=255) tAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGGTTAGGGGAAGAGGATTTGTCAGAATA‑TTTAAGGAAttt > 1:2225694/1‑76 (MQ=37) tAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAAttt > 2:2107908/1‑76 (MQ=255) tAAAAA‑CCCGCTTCGGC‑‑GGGGTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAAttt > 1:2149404/1‑76 (MQ=255) aaaaa‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTTTGGGAAA‑AGGAATTTTTAGAAAATTTTAAGGAAttt > 1:1455175/1‑76 (MQ=12) aaaaa‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTTTGGGAAA‑AGCATTTTTCCGAATA‑TTTTAGGGATTTc > 2:1501684/1‑76 (MQ=16) aaaaa‑CCCGCTTCGGC‑‑GGGTTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTc > 2:2034370/1‑76 (MQ=255) aaaaa‑CCCGCTTCGGC‑‑GGGTTTTTTTTTGGGGGGGGGTTAGGGGAAGAGCATTTGTCAGAATA‑TTTAAGGAAtttt > 2:765785/1‑75 (MQ=37) aaaaa‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTc > 2:11222/1‑76 (MQ=255) aaaaa‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTc > 2:559097/1‑76 (MQ=255) aaaaa‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGGTTAGGGGAAGAGCATTTATCAGAATA‑TTTAAGGAATTTc > 1:777204/1‑76 (MQ=37) aaaa‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTTGGGGAAA‑AGGAATTTTTAGAAAATTTTAAGGAAtttt > 2:960297/1‑75 (MQ=12) aaaa‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGGAATTTTCAGAATA‑TTTAAAGAAatttt > 2:791127/1‑74 (MQ=16) aaaa‑CCCGCTTCGGC‑‑GGGTTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCt > 2:1984710/1‑76 (MQ=255) aaaa‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGGTTAGGGGAAGAGCATTTGTCAGAATA‑TTTAAGGAAttttt > 2:837291/1‑74 (MQ=37) aaa‑CCCGCTTCGGCG‑GGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGCATTTGTCAGAATA‑TTTTAGGAATTTTTg > 2:1634885/1‑76 (MQ=25) aaa‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGTTTTGGGGAAAAGAATTTTTCAGAATA‑TTTAAGGAAATTTTg > 2:533221/1‑76 (MQ=19) aa‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGa < 2:326457/76‑1 (MQ=255) aa‑CCCGCTTCGGC‑‑GGGGTTTTTTTTTGGGGGGGGTTAGGGGAAGAGGCTTTGTTAGGATA‑TTTTAGGAAATTTTGa > 2:1381868/1‑76 (MQ=12) a‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCtnga < 2:1590321/76‑4 (MQ=255) a‑CCCGCTTCGGC‑‑GGGGTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGaa > 2:54832/1‑76 (MQ=39) ccGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATa < 1:656604/76‑1 (MQ=255) cGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATan < 1:1684902/76‑2 (MQ=255) cTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACta < 1:753784/76‑2 (MQ=255) cTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTc < 1:496975/76‑1 (MQ=255) ttCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCa < 2:1420076/76‑1 (MQ=255) tCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCAt < 1:1297343/76‑1 (MQ=255) gc‑‑ggGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAAt < 2:329421/76‑1 (MQ=255) gc‑‑ggGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAAt < 1:455900/76‑1 (MQ=255) gggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCa > 1:932526/1‑76 (MQ=255) gggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCa < 2:1505323/76‑1 (MQ=255) gggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCa < 1:581409/76‑1 (MQ=255) gggTTTTTTTAGGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCa < 1:697588/76‑1 (MQ=255) gTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAAt > 1:564526/1‑76 (MQ=255) tttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTa < 1:1204213/76‑1 (MQ=255) tttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTa > 2:778781/1‑76 (MQ=255) tttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTa < 2:1649255/76‑1 (MQ=255) ttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTag > 1:1604121/1‑76 (MQ=255) ttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTag > 1:2157967/1‑76 (MQ=255) tttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTaga > 1:1496745/1‑76 (MQ=255) ttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTagag > 1:1073795/1‑76 (MQ=255) aTGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTAGAGAt > 2:771599/1‑76 (MQ=255) | GGTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAA‑CCCGCTTCGGC‑‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTAGAGAT > REL606/4169158‑4169307 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |