| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | REL606 | 4,574,252 | 0 | T | G | 27.9% | 91.3 / 11.0 | 43 | S5S (TCA→TCC) | hpaX | hypothetical 4‑hydroxyphenylacetate permease |
| Reads supporting (aligned to +/- strand): ref base T (2/29); new base G (12/0); total (14/29) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.93e-09 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
TAATAACCGCCTGTTGTCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATGGCGGATGCGGCGTAA > REL606/4574179‑4574327 | taataaCCGCCTGTTGTCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCaggtga < 2:140467/76‑1 (MQ=255) aataaCCGCCTGTTGTCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCaggtgag < 2:972192/76‑1 (MQ=255) ccGCCTGTTGTCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTc < 2:1823867/76‑1 (MQ=255) ccGCCTGTTGTCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTc < 1:1812616/76‑1 (MQ=255) cGCCTGTTGTCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCg < 1:470329/76‑1 (MQ=255) tgttgtCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCa < 2:2007223/76‑1 (MQ=255) tgttgtCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCa < 2:211184/76‑1 (MQ=255) tgttgtCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCNCa < 2:1461901/76‑1 (MQ=255) tgttgtCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCNCa < 2:1461918/76‑1 (MQ=255) tgttgtCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGGGGGGGCGCTCa > 2:1653814/1‑76 (MQ=255) tgtCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCAttt < 2:688858/76‑1 (MQ=255) tCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCAttttt < 2:476771/76‑1 (MQ=255) tCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCAttttt < 2:1359759/76‑1 (MQ=255) ccGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTttc < 2:723126/76‑1 (MQ=255) ggCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTttctt < 2:1482207/76‑1 (MQ=255) ggCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGGGGGGGGGGTCAtttttttt > 1:484942/1‑76 (MQ=255) cAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGAGGTGTCGCTCAtttttttttt > 2:1449004/1‑74 (MQ=255) aGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCct < 1:462065/76‑1 (MQ=255) cAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGAGGGGTGGCTCATTTTTTTTTCCCTa > 1:1833328/1‑76 (MQ=255) gcgcTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAAt < 1:1356420/76‑1 (MQ=255) cgcTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATg < 2:567845/76‑1 (MQ=255) cgcTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGAGGGGTCGCTCATTTTTTTTCCTCTTATg > 2:1333339/1‑76 (MQ=255) cTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGGGGGGTCGCTCCTTTTTTTTCCTCTTATggg > 1:154155/1‑76 (MQ=255) tttATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGa < 1:347496/76‑1 (MQ=255) tttATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGGGGGGGCGCTCATTTTTTTTCCTCTTATtggg > 1:547532/1‑75 (MQ=255) ttATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGAt < 1:1746158/76‑1 (MQ=255) tATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGGGGGGGCGCTCATTTTTTTTCCTCTTATGGGGtt > 1:1809844/1‑76 (MQ=255) aTGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGAGGGGTCGCTCCTTTTTTTTTCTCTTATTGGGttt > 1:1568403/1‑76 (MQ=255) tGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGAtttt < 1:110174/76‑1 (MQ=255) gATTCGCCGTATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTa < 1:648395/76‑1 (MQ=255) gATTCGCCGGATCGATACTCTCCGGTATGGCAGGGGAGGGGTCGCTCATTTTTTTTCCTCTTATGGGGTTTTTGtt > 2:1801032/1‑75 (MQ=255) cGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGt < 2:1330808/76‑1 (MQ=255) cGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGt < 1:458367/76‑1 (MQ=255) ccGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTAc < 2:1655227/76‑1 (MQ=255) ccGGATCGATACTCTCCGGTATGGCAGGTGAGGGGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTAc > 2:1451409/1‑76 (MQ=255) cGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACg < 2:1442713/76‑1 (MQ=255) tCGATACTCTCCGGTATGGCAGGGGAGGTGTCGCTCATTTTTTTTCCTCTAATGGGATTTTTTTAGGGTACGACaa > 2:1603997/1‑76 (MQ=255) cGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAg < 2:1607896/76‑1 (MQ=255) gATACTCTCCGGTATGGCAGGGGAGGGGTCGCTCCTTTTTTTTTCTCTTATTGGGGTTTTTTTGGGGGCGACAAgg > 1:1392589/1‑76 (MQ=255) tACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGtt < 2:1311735/76‑1 (MQ=255) tACTCTCCGGTATGGCAGGGGAGGGGTGGCTCTTTTTTTTTTCTCTTTTGGGGTTTTTTTTGGGGTCGACAAGGtt > 1:49968/1‑76 (MQ=255) ctctCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTa < 2:423495/76‑1 (MQ=255) ctcCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATg < 1:274478/76‑1 (MQ=255) ctcCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATg < 1:1158164/76‑1 (MQ=255) tGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATGGCGGATgc > 1:253195/1‑76 (MQ=255) cAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATGGCGGATgcggc < 1:1329920/76‑1 (MQ=255) gtgaggtgTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATGGCGGAGGTGGTGTa > 2:148451/1‑76 (MQ=255) tgaggtgTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACANGGTTTATGGCGGATGCGGCGTaa > 1:1966056/1‑76 (MQ=255) tgaggtgTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATGGCGGATGCGGCGTaa > 1:1938748/1‑76 (MQ=255) | TAATAACCGCCTGTTGTCCGGCAGTCAGCGCTTTATGCTGATTCGCCGGATCGATACTCTCCGGTATGGCAGGTGAGGTGTCGCTCATTTTTCTTCCTCTAATGGGATTTTTGTAGGGTACGACAAGGTTTATGGCGGATGCGGCGTAA > REL606/4574179‑4574327 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |