| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,963,768 | C→G | 100% | V365L (GTA→CTA) | hemY ← | Protoporphyrinogen oxidase |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 1,963,768 | 0 | C | G | 96.5% | 173.0 / ‑0.9 | 58 | V365L (GTA→CTA) | hemY | Protoporphyrinogen oxidase |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base G (33/22); total (34/24) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.61e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
CTTTTCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATG > USA300TCH1516_ALE/1963632‑1963901 | cTTTTCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATa > 1:460505/1‑140 (MQ=255) tttCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACg > 2:394633/1‑140 (MQ=255) actaTTGACAATTGTAACTTCAGGATCACCTTTCAAAGTCATCATTTCACTTAAACCTCTACGCACAATCGATACTAATTCAATATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCa < 2:190685/137‑1 (MQ=255) aCGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCa < 2:489347/140‑1 (MQ=255) tGACAATTGTAAATTAAGGATCACCTTTACCTGTCATCATTTGACTTTAATCTCTAAGTGCACTCGATACTAATTCATTATATGTATGATCATCAACCCCAGTATCACCTCGTTTACCTAGATACGCACGGATCATAacc > 2:141462/1‑140 (MQ=255) aCAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAacctt > 2:488146/1‑140 (MQ=255) ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACTTTCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct < 1:538255/140‑1 (MQ=255) ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTTATTCTTTATATGTATGATCATCAACCACAGTATAACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct < 1:478337/140‑1 (MQ=255) ttGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct < 2:407615/140‑1 (MQ=255) tGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacctt > 1:358102/1‑140 (MQ=255) aaTTCAGGATCACGTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTCGATACCCACGAATCAAAACCTTACCTTCCgg > 2:524792/1‑140 (MQ=255) gATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTgtagta > 2:522313/1‑140 (MQ=255) tCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTaaa > 2:522208/1‑140 (MQ=255) ttAAATGTCATCATTTGACTTAAATCTCTACCTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCa < 2:400263/140‑1 (MQ=255) tcatcaTTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATTTTCTACCACAGTATCTCCTGGTTTTCTTAGATTCGAGCTATTCATAATCTTTCCTTTCGGTGTAGTAATTGGCATTTTTTTc > 1:125046/1‑140 (MQ=255) catTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATg > 1:304531/1‑140 (MQ=255) catTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATg < 1:522313/140‑1 (MQ=255) catTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGGATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATg < 2:132917/140‑1 (MQ=255) ttAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTa < 1:504635/140‑1 (MQ=255) ttctACGTACAATTGTTTCTATTTCATGTTTTGTATTATCATCAACCACATTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCg < 2:312982/139‑1 (MQ=255) tctACGTACAATCGATACTAATTCATTATCTGTATGATCATCTACCACATTATGACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTGCAAGTACATGCgg > 1:290993/1‑140 (MQ=255) tcgaCGTACAATCGATACGAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGTTGTTCTAGAACATCCgg > 2:531725/4‑140 (MQ=255) aCAATCGCTACTAACTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAGACCTTACCTTCTGGCGTAGTAAATGGCCATGTTTTCCATGTCCAAGTGCCTGCggccaggtc > 2:398387/1‑133 (MQ=255) aCAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCACAACCTTACCTTCCGCTGTAGTAAATGGCCATTTTTTTGATGTCCCAGTACGTGCGGTACTGta > 2:398386/1‑139 (MQ=255) cAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGAACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTCATGTCt > 1:139940/1‑140 (MQ=255) aTCGATACTAATTCATTATCTGTATGATCATCAACCACTGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGt < 1:87414/140‑1 (MQ=255) cGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGGGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAAGATCTGTAt > 2:515969/1‑140 (MQ=255) gATACTCATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATc < 2:435429/140‑1 (MQ=255) gATACTATTTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATc < 1:256544/140‑1 (MQ=255) ttCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTTGATTTTCAATTCCATGCGGTAATGTCTGTATCACTCGTtc > 2:69176/1‑140 (MQ=255) cATTATCTGTATGATCATCAACCACAGTCTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCAGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTtctc > 1:355326/1‑140 (MQ=255) cATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTtctc > 1:418499/1‑140 (MQ=255) aTTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTAAATGCGGTAATGTATGTATCACTAGTTCTCg < 2:186624/140‑1 (MQ=255) aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCaa > 1:248487/1‑140 (MQ=255) tCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAt < 1:228254/140‑1 (MQ=255) cTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATAAGCAAGAATAAAAATCTTACATTCAGGTGTAGTAAATGGCAATTTTTTCGATGTCAAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAAtt > 1:18855/1‑140 (MQ=255) gTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTAc < 2:399423/140‑1 (MQ=255) tGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATTTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGaa > 1:352661/1‑140 (MQ=255) catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCTTTTTTTCGATGTCAAACTACACGCGTTAAAGTCTGTATCAACCGTTATCGCAATTAAGAAACCa > 1:101954/1‑140 (MQ=255) catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCTTTTTTTTTTTCCATGCGGACATGTCTGTATCACTCGTTCTCGCCGTTTCGAACCCa > 2:146219/1‑140 (MQ=255) aaCCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTAc > 2:57773/1‑140 (MQ=255) cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTAccgt > 2:506970/1‑138 (MQ=255) cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTAAGAAGCCAGTACcat > 1:184993/1‑140 (MQ=255) cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGCGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcat > 2:207033/1‑140 (MQ=255) cacaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCAACGAAGAAAATAGCCATATTATCGATGTCCAAGTACATGCGGTAATGACTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcat > 1:165448/1‑140 (MQ=255) cacaGTATCACCTGGTTTACCTAGATACGCACGAATAAAGACGTAATCGTCCGGTGTAGTAAATGGCCATTTTTTCGTTGTCCAAGTACATGCGGTAATGTCTGTATCACTAGTTCTCGCAATTACGAAAGCAGTACcaa > 2:413586/1‑139 (MQ=255) cacaGTATAACTACGGTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAGATGGCCATTTTTTCGATGTCCAACTACATGCGGTAATGTATGTATCACTCGTTCTGCCACTTACGAAGCCAGTACcat > 2:172833/1‑140 (MQ=255) cacaGTAACACCTGGTTGACCTAGATACTGGCGAGTGAAAACCTTAGCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTAGTTCTCGCCATTACGAAGCCAGTACcat > 2:543763/1‑140 (MQ=255) aGTATCACCTGGTTTACCTAGATACGCACGAATCAACACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACcatcat > 1:20209/1‑140 (MQ=255) ttATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTATCTTCCTGTGTAGTAAATGGCCAGTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATg < 1:185646/139‑1 (MQ=255) aTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATggg < 1:443890/140‑1 (MQ=255) tCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGt < 2:117355/140‑1 (MQ=255) aCCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTAt < 1:216747/140‑1 (MQ=255) ccTCGTTTACCTAGATACCCACGACTCAAAACCTTACCTTCTGGTGTAGTAATTGGTCATTTTTTCGATGTCCAAGTACATGTTGCATTGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTAtt < 1:457047/140‑1 (MQ=255) tGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTTGTTTTTTAATTACATGCGGGAATGTCTGTATAACTCGTTCTCTCGATTACGAAGCCACTACCAGCATGGGTActtc > 2:236091/1‑139 (MQ=255) gTTTACCTAGATACGCACGAATCAAAACCTTATCTTCCGTTGTAGTAAATTGCCATTTTTTCGATGTCCAATTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCa < 1:27430/140‑1 (MQ=255) gTTGACCTTTATACTCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCa < 2:487785/140‑1 (MQ=255) tACCTAGATACGCACTAATCAAAACCGTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATg < 2:447902/140‑1 (MQ=255) | CTTTTCGGCAAACGATTGACAATTGTAAATTCAGGATCACCTTTAAATGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACTCGTTCTCGCAATTACGAAGCCAGTACCATCATGGGTATTTTCAATG > USA300TCH1516_ALE/1963632‑1963901 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |