| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 3,790 | G→A | 100% | A29T (GCA→ACA) | USA300HOU_RS00015 → | hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 3,790 | 0 | G | A | 92.6% | 76.3 / ‑0.5 | 27 | A29T (GCA→ACA) | USA300HOU_RS00015 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (12/13); total (13/14) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.53e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
AATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCAT > USA300TCH1516_ALE/3668‑3923 | aataTATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCaa < 1:75210/140‑1 (MQ=255) atatatTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAg < 1:116088/140‑1 (MQ=255) aaaGAAATGGAGTGATTATTTTGGATCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTattaatt > 1:492562/1‑140 (MQ=255) aGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAAAATCTAAAAACAGAAGGGAATAAAGAAACTGGAGGACAAACAAAATGGTACTAGCAAAACGTTGAAGTAtaaattaa > 1:15915/1‑140 (MQ=255) tGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGATGTATTAATTAATGGAg < 1:380100/140‑1 (MQ=255) gATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATTTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTg < 1:207166/140‑1 (MQ=255) taaagaagTTGTAGTAGAAGGAGACATTCATTTAGGGCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTcgcg < 1:361858/138‑1 (MQ=255) agTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCGAAAAACAGAAGGGAGTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTAGCGGAaaaa > 1:179710/1‑140 (MQ=255) tagAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGaa > 1:486265/1‑140 (MQ=255) tagAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGaa > 1:762730/1‑140 (MQ=255) gAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACa > 1:539901/1‑140 (MQ=255) aGGAGCCATTAATTTAGGTCAATTTTTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATc < 1:255217/140‑1 (MQ=255) aGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGATGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATc < 1:10879/140‑1 (MQ=255) aGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATc < 1:569810/140‑1 (MQ=255) agaCATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGACAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGAAGGGCGTGAAACACGTCGCGGGAAAAAGTTAGAACATCAAg > 1:636753/1‑140 (MQ=255) aTTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGtata > 1:313454/1‑140 (MQ=255) tttAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAg < 1:671884/140‑1 (MQ=255) aaTTTCTAAATACAGAAGGTATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCa < 1:707191/140‑1 (MQ=255) aaTTTCTAAAAGCAGAATGTATTTTTGAATTTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCa < 1:483578/140‑1 (MQ=255) aaCAGAAGGGATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATACCAGAATTACCTg > 1:81028/1‑140 (MQ=255) gggATTATTGAATCTGGTGTTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGc < 1:24031/140‑1 (MQ=255) gggATTATTGAATCTGGTGGTCAAACAGAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGc < 1:531716/140‑1 (MQ=255) ggATTATTGAATCTGGTGGTCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATTCCAGAATTACCTGAAGATGCt > 1:706236/1‑140 (MQ=255) ggtggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAAt > 1:81317/1‑140 (MQ=255) ggtggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACAAGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTAACTGAAGATGCTGGTTCTTTCTTAAt > 1:581972/1‑140 (MQ=255) tggtCAAACAAAATTGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAAtca < 1:52961/140‑1 (MQ=255) ggtCAAACAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAAATGCTGGTTCTTTCTTAAtcat > 1:407869/1‑140 (MQ=255) | AATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGATGCTGGTTCTTTCTTAATCAT > USA300TCH1516_ALE/3668‑3923 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |