| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | REL606 | 4,169,232 | 0 | A | T | 25.0% | 163.0 / 14.7 | 72 | intergenic (+48/‑165) | rpoC/htrC | DNA‑directed RNA polymerase subunit beta'/heat shock protein |
| Reads supporting (aligned to +/- strand): ref base A (20/34); new base T (18/0); total (38/34) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 8.64e-07 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
AGGTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAATGTAGAGA > REL606/4169157‑4169306 | gggTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCTGAAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTa < 2:241797/75‑1 (MQ=255)aGGTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTa < 2:172264/76‑1 (MQ=255) tCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATgg < 2:1413387/76‑1 (MQ=255) tCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATgg > 2:157524/1‑76 (MQ=255) gggCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTtgggg > 2:569687/1‑76 (MQ=38) gggCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTtgggg > 2:569682/1‑76 (MQ=38) gggCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTggggg > 2:1665766/1‑76 (MQ=255) ggCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATgggggg < 2:1037275/76‑1 (MQ=255) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAACCCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGttt < 2:1003157/76‑1 (MQ=255) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGttt < 2:1626344/76‑1 (MQ=255) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGttt < 2:1566956/76‑1 (MQ=255) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGttt < 2:1534845/76‑1 (MQ=255) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGttt < 1:85217/76‑1 (MQ=255) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGttt < 2:727847/76‑1 (MQ=255) tCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTTGGGGGGGtttt > 2:607971/1‑75 (MQ=37) gATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAggg < 2:1471697/76‑1 (MQ=255) tAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGaa < 1:1533984/76‑1 (MQ=255) aaCGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGaaa < 2:1338426/76‑1 (MQ=255) aCGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAag < 2:544038/76‑1 (MQ=255) aCGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAag < 2:1494751/76‑1 (MQ=255) cGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAaga < 1:1458329/76‑1 (MQ=255) gAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTAAGGGGGGAGGTTAGGGAAagac > 2:574446/1‑75 (MQ=255) aGTAATCGTTAATCCGAAAATAACGTAAAACCCCGCTTCGGG‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGc < 1:1362681/76‑1 (MQ=255) tAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCAt > 2:238751/1‑76 (MQ=255) tAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCAt < 1:316622/76‑1 (MQ=255) aaTCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCAtt < 1:315005/76‑1 (MQ=255) aaTCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGGTTAGGGAAAGAGCAtt > 1:1735625/1‑76 (MQ=38) aTCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTTGGGGAAGAGCAttt > 1:1735598/1‑76 (MQ=37) tCGTTAATCCGCAAATACCGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTg < 1:1759056/76‑1 (MQ=255) gTTGATCCGCGTATAAGATAAAAGCCCTCGTCGGC‑GGGTTTGTTTGTGGGGGGTGTTTAGGGAAAGAGCATTTGTc < 2:8/76‑1 (MQ=255) ttAATCCGCAAATAACGTAAAAACCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGGATTTTTCa > 2:811532/1‑76 (MQ=21) tAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAg > 2:268326/1‑76 (MQ=255) tAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAg > 2:222572/1‑76 (MQ=255) aaTCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGa < 1:305293/76‑1 (MQ=255) aTCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGaa > 2:1593118/1‑76 (MQ=255) tCCGCAAATAACGTAAAAACCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTT‑GGGAAAAAGGAATTGTTAGaaa > 2:1193088/1‑75 (MQ=16) tCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAat > 2:290686/1‑76 (MQ=255) tCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAat < 2:1156935/76‑1 (MQ=255) tCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAat < 1:47441/76‑1 (MQ=255) tCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAat < 1:758456/76‑1 (MQ=255) ccGCAAATAACGTAAAAACCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGGATTTTTTAGaaaa > 1:385940/1‑74 (MQ=16) gCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATAtt > 1:1742156/1‑76 (MQ=255) aaaTAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTa < 1:900789/76‑1 (MQ=255) tAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAgg < 1:657317/76‑1 (MQ=255) aaCGTAAAAACCCGCTTCGGC‑GGGTTTTTTTTTGGGGGGAGGTTTGGGGAAGAGGATTTGTCAGAATATTTAAGGa > 2:1004060/1‑76 (MQ=25) aaCGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGa < 1:306962/76‑1 (MQ=255) aaCGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGa > 2:1562433/1‑76 (MQ=38) aaCGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGa > 2:1098201/1‑76 (MQ=38) aCGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGaa < 1:1768054/76‑1 (MQ=255) ttAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGGTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAAtt > 2:1213597/2‑76 (MQ=38) gTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAAtt > 1:1666715/1‑76 (MQ=38) tAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAAttt > 2:397811/1‑76 (MQ=255) tAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAAttt > 2:56968/1‑76 (MQ=255) tAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTTGGGGAAGAGCATTTGTCAGAATATTTAAGGAAttt > 2:1151188/1‑76 (MQ=37) tAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTTGGGGAAGAGCATTTGTCAGAATATTTAAGGAAttt > 2:1151184/1‑76 (MQ=37) tAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTTGGGAAAAAGCATTTGTCAGAATATTTAAGGAAttt > 2:947236/1‑76 (MQ=37) aaaaaCCCGCTTCGGC‑GGGTTTTTTTTTGGGGGGGGTTTTGGGAAAGAGCATTTTTTAGAATATTTAAGGAAtttt > 1:383707/1‑75 (MQ=37) aaaaaCCCGCTTCGGC‑GGGTTTTTTTATGGGGGGTGTTTTGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTc > 2:1765194/1‑76 (MQ=255) aaaaCCCGCTTCGGC‑GGGTTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAAttttt > 2:122167/1‑74 (MQ=38) aaaaCCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGAGGTTTGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCt > 2:1296501/1‑76 (MQ=38) aaaaCCCGCTTCGGC‑GGGGTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCt > 2:1247906/1‑76 (MQ=255) aaaCCCGCTTCGGC‑GGGTTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTg > 2:654451/1‑76 (MQ=255) aaaCCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTTGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTg > 2:734478/1‑76 (MQ=38) aaCCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGa > 2:9262/1‑76 (MQ=255) aaCCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGa > 2:542372/1‑76 (MQ=39) aCCCGCTTCGGC‑GGGGTTTTTTATGGGGGGGGTTTAGGGGAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGaa > 2:1326009/1‑76 (MQ=39) cGCTTCGGC‑GGGGTTTTTTATTGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTTTTAATAc > 2:308753/1‑76 (MQ=255) cTTCGGC‑GGGTTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTc > 2:683022/1‑76 (MQ=255) tCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCAt < 2:1738862/76‑1 (MQ=255) ggc‑ggGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATaa < 2:1457888/76‑1 (MQ=255) c‑ggGTTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATc > 2:1209900/1‑76 (MQ=255) c‑ggGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATc > 1:242852/1‑76 (MQ=255) gggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCa < 2:706458/76‑1 (MQ=255) ggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCaa < 1:1195030/76‑1 (MQ=255) ggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCaa < 1:1051206/76‑1 (MQ=255) gTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAAt < 1:505770/76‑1 (MQ=255) tttttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAATg < 1:511714/76‑1 (MQ=255) ttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAATGTag > 1:380766/1‑76 (MQ=255) ttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAATGTagag > 1:236699/1‑76 (MQ=255) ttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAATGTagag > 2:1442608/1‑76 (MQ=255) tATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAATGTAgaga < 1:154064/76‑1 (MQ=255) | AGGTCTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATATTTAAGGAATTTCTGAATACTCATAATCAATGTAGAGA > REL606/4169157‑4169306 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |