| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | REL606 | 4,169,232 | 0 | A | T | 22.4% | 113.3 / 11.5 | 49 | intergenic (+48/‑165) | rpoC/htrC | DNA‑directed RNA polymerase subunit beta'/heat shock protein |
| Reads supporting (aligned to +/- strand): ref base A (12/26); new base T (11/0); total (23/26) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.64e-05 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTAGAG > REL606/4169161‑4169305 | cTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTATggg > 1:58291/1‑76 (MQ=255) tGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATgggg < 1:753937/76‑1 (MQ=255) ggCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTtggggg > 1:1115652/1‑76 (MQ=38) ggTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGCGGGGTTTTTTTTTgggggggg > 2:965259/1‑74 (MQ=38) ggTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGGGt > 2:1102661/1‑76 (MQ=255) gTTCTGATAACGAGTACTCGTTAATCCGCAAATAACGTGAAAACCCGCTTCTGG‑GAGATGTTTTATTGGGGGGGtt > 1:632553/1‑76 (MQ=255) ttCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGttt < 2:599072/76‑1 (MQ=255) tCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGttt > 1:1236749/1‑76 (MQ=37) tCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTa < 2:68654/76‑1 (MQ=255) tCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTa < 1:648477/76‑1 (MQ=255) ttGATAACGGTTATTCGTTAATCCGCAAATAAGGTGAAACCCGGTTTCGGG‑GGGTTTTTTTATGGGGGGAGTTTAg < 1:352122/75‑1 (MQ=255) tGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAgg < 1:1175314/76‑1 (MQ=255) tAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTTGGGGa > 1:148317/1‑76 (MQ=37) tAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGaa < 1:15529/76‑1 (MQ=255) aaaCGAGTAATCGTTAATCCGCAAATAACGTAAAACCCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGaa < 1:1202419/75‑1 (MQ=255) aGTATTCGTTAAGCGGGAAATGCTGTAAAACCCCGCTCGGGG‑GGGTTTTTTTATGGGGGGAGTTTAGGTAAAGAGc < 1:456473/76‑1 (MQ=16) tAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCAt < 2:311756/76‑1 (MQ=255) tCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGGTTAGGGAAAGAGCATTTg > 1:1037906/1‑76 (MQ=38) cGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTTTGGGGGGGGTTTTGGGGAAGGGCGTTTGt > 2:760498/1‑76 (MQ=25) tAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAg < 1:36319/76‑1 (MQ=255) aaTCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGa > 2:202741/1‑76 (MQ=255) aaTCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTTGGGGGGGGTTAGGGAAAGAGGATTTGTCAGa > 2:451249/1‑76 (MQ=25) aTCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGTTTTGGGGAAGAGGATTTGTCAGaa > 2:333617/1‑76 (MQ=25) cGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAata‑t < 2:132838/76‑1 (MQ=255) cAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑ttt < 1:143026/76‑1 (MQ=255) aaTAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTaa < 2:716466/76‑1 (MQ=255) aTAACGTAAAAACCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGGAATTTTTAGAATA‑TTTTAg > 1:250421/1‑76 (MQ=12) aTAACGTAAAAACCCGCTTCGGC‑GGG‑TTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAgg < 1:243809/76‑1 (MQ=255) aaCGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGa > 2:983336/1‑76 (MQ=255) aaCGTAAAAACCCGCTTCGGC‑GGGGTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGa > 2:1120637/1‑76 (MQ=255) aCGTAGAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGaa < 2:1249644/76‑1 (MQ=255) tAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGGGCTTTGGGAAAGAGGATTTGTCAGAATA‑TTTAAGGGAttt > 2:43970/1‑76 (MQ=25) tAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAAttt > 2:878192/1‑76 (MQ=255) aaaaaCCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTTGGGGAAA‑AGGATTTTTTAGGAAA‑TTTTAAGAAtttt > 2:716080/1‑75 (MQ=9) aaaaaCCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGGATTTTTTAGAATATTTTAAGGAAttc > 2:788439/1‑75 (MQ=16) aaaaaCCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTTAGAATA‑TTTAAGGAAtttt > 2:319374/1‑75 (MQ=255) aaaaaCCCGCTTCGGC‑GGGGTTTTTTTTGGGGGGGGGTTTGGGGAAGAGCATTTGTCAGAATA‑TTTTAGGAAtttt > 2:1089825/1‑75 (MQ=25) aaaaCCCGCTTGGGC‑GGGTTTTTCTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCt < 2:637331/76‑1 (MQ=255) aaaCCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTT‑GGGGAAGAGCATTTTTTAGAATA‑TTTTAGGAATTTCTg > 2:603076/1‑76 (MQ=19) aaCCCGCTTCGGCGGGGTTTTTTTTTGGGGGGGGTTTGGGGAAAAAG‑ATTTTGCAGAAAA‑GTTTAAGAATTTTTGa > 2:787257/1‑76 (MQ=9) aaCCCGCTTCGGC‑GGGGTTTTTTATGGGGGGGGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGa > 2:242492/1‑76 (MQ=255) ccGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATa < 1:1084604/76‑1 (MQ=255) gCTTCGGC‑GGGTTTTTTTTTGGGGGGGGTTTTGGGGAAGAGCATTTGTTAGAATA‑TTTAAGGAATTTTTGAATACt > 2:505226/1‑76 (MQ=255) ttCGGC‑GGGGTTTTTTTTGGGGGGGGGTTAGGGGAAAAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCa > 2:335746/1‑76 (MQ=255) cggc‑ggGTTTTTTTTTTGGGGGGGGGTAGGGGAAGAGCATTTTTTAGAATA‑TTTTAGGAATTTTTGAATACTCATa > 2:788833/1‑76 (MQ=255) ggc‑ggGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATaa < 1:940478/76‑1 (MQ=255) gc‑ggGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAAt > 2:1163499/1‑76 (MQ=255) c‑ggGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATc > 1:959970/1‑76 (MQ=255) gggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCa < 1:478609/76‑1 (MQ=255) gggTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCa < 2:246849/76‑1 (MQ=255) gTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAAt > 1:1273341/1‑76 (MQ=255) tttttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATg < 1:105650/76‑1 (MQ=255) tttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTa < 1:1109278/76‑1 (MQ=255) ttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTag < 2:1013880/76‑1 (MQ=255) ttttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTag < 2:959970/76‑1 (MQ=255) ttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTagag < 2:721447/76‑1 (MQ=255) ttATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTagag > 1:916742/1‑76 (MQ=255) | CTGGGCGGTTCTGATAACGAGTAATCGTTAATCCGCAAATAACGTAAAAACCCGCTTCGGC‑GGGTTTTTTTATGGGGGGAGTTTAGGGAAAGAGCATTTGTCAGAATA‑TTTAAGGAATTTCTGAATACTCATAATCAATGTAGAG > REL606/4169161‑4169305 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |