| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_017635 | 1,637,750 | 0 | A | G | 41.7% | 29.8 / 29.1 | 24 | Q597R (CAG→CGG) | ECW_RS08125 | RHS element core protein |
| Reads supporting (aligned to +/- strand): ref base A (7/7); new base G (4/6); total (11/13) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 6.97e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.86e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAGGCGACCTGACTGCCGTTATCACCCCG > NC_017635/1637704‑1637796 | cGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCAGTa < 1:1596178/50‑1 (MQ=40) tGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATg < 1:1339023/50‑1 (MQ=255) cGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCAGTATGAGTa > 2:127549/1‑50 (MQ=255) ggTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATa > 1:1334104/1‑49 (MQ=11) ggTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATa > 2:1953397/1‑49 (MQ=11) ttAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCAGTATGAGTACaa > 2:844644/1‑50 (MQ=255) aCCTCGGTGAAAGACGCACAGGGCCGTGAAACGCAGTATGAGTACAAcg < 1:817383/49‑1 (MQ=255) cGGTGAAAGACGCACAGGGCCGTGAAACGCGGTATGAATACAAcgccg > 2:388735/1‑48 (MQ=11) ggTGAAAGACGCACAGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAg > 1:1749365/1‑50 (MQ=255) gTGAAAGACGCACAGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAgg > 1:58450/1‑50 (MQ=255) gACGCACAGGGCCGTGAAACGCGGTATGAATACAACGCCGCAGGCGACCt < 2:1370353/50‑1 (MQ=14) aCGCACAGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAGGCGACCTg < 2:856716/50‑1 (MQ=255) cGCACAGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAGGCGACCTGa > 1:1526129/1‑50 (MQ=255) cacaGGGCCGTGAAACGCGGTATGAATACAACGCCGCAGGCGACCTGACt < 2:1569035/50‑1 (MQ=14) acaGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAGGCGACCTGACTg < 1:1783426/50‑1 (MQ=255) acaGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAGGCGACCTGACTg < 2:1196764/50‑1 (MQ=255) aGGGCCGTGAAACGCAGTATGAGAACAACGCCGCAGGCGACCTGACTGcc < 2:1232589/50‑1 (MQ=255) cGTGAAACGCGGTATGAATACAACGCCGCAGGCGACCTGACTGCCGTTAt > 1:1880293/1‑50 (MQ=14) cGTGAAACGCAGTATGAGTACAACGCCGCAGGCGACCTGACTGCCGTTAt > 2:152869/1‑50 (MQ=255) tGAAACGCGGTATGAATACAACGCCGCAGGCGACCTGACTGCCGTTATCa < 2:1262126/50‑1 (MQ=14) tGAAACGCGGTATGAATACAACGCCGCAGGCGACCTGACTGCCGTTATCa < 1:454543/50‑1 (MQ=14) tGAAACGCAGTATGAGTACATCGCCGCAGGCGACCTGACTGCCGTTATCa < 1:1401637/50‑1 (MQ=255) aaaCGCGGTATGAATACAACGCCGCAGGCGACCTGACTGCCGTTATCAcc < 1:132596/50‑1 (MQ=14) cgcgGTATGAATACAACGCCGCAGGCGACCTGACTGCCGTTATCACCCCg < 1:759972/50‑1 (MQ=14) gCAGTATGAGTACAACGCCGCAGGCGACCTGACTGCCGTTATCACCCCg > 1:960689/1‑49 (MQ=255) | CGTGGCCGGTTAACCTCGGTGAAAGACGCACAGGGCCGTGAAACGCAGTATGAGTACAACGCCGCAGGCGACCTGACTGCCGTTATCACCCCG > NC_017635/1637704‑1637796 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |