| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | AP009048 | 3,685,129 | T→A | 100% | pseudogene (993/1645 nt) | ilvG ← | ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AP009048 | 3,685,129 | 0 | T | A | 98.3% | 176.5 / ‑4.1 | 60 | pseudogene (993/1645 nt) | ilvG | ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base A (30/29); total (30/30) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-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. | |||||||||||
GCGTAGATAGCGTCACCGGGATGGTCGTAACGCCAGGAATGTTCATCACGCAGCTGCGCGCAGTGTTGCTGCCAGTCATTG‑‑ATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATCACCTTGTA > AP009048/3685063‑3685193 | gcgTAGATATCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTagctg > 1:4367778/1‑71 (MQ=255)gcgTAGATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTagctg > 1:694240/1‑71 (MQ=255) gTAGATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTagctgc > 1:4663149/1‑70 (MQ=255) tAGATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTagctgc > 1:3723704/1‑69 (MQ=255) aGATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAg > 1:1363533/1‑71 (MQ=255) aGATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAg > 1:2098383/1‑71 (MQ=255) gATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGt > 1:1042082/1‑71 (MQ=255) gATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGt < 1:927534/71‑1 (MQ=255) gATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGt < 1:4553081/71‑1 (MQ=255) gATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGt > 1:3717561/1‑71 (MQ=255) gATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGt < 1:3103130/71‑1 (MQ=255) gATAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGt < 1:1445725/71‑1 (MQ=255) aTAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTagctgc < 1:3043912/66‑1 (MQ=39) aTAGCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGt > 1:4836522/1‑70 (MQ=255) aTAGCGGCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCTGTGTAGCTGCCAGTc < 1:4043269/71‑1 (MQ=255) tAGCGTCACCGGGATGGTCGTAACGCCAGGAATGTTCATCACGCAGCTGCGCGCAGTGTTGCTGCCAGTCa < 1:440402/71‑1 (MQ=255) gCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCATCTGCGCGCAGTGTAGCTGCCAGTCAtt < 1:4656863/71‑1 (MQ=255) gCGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCAtt < 1:2116878/71‑1 (MQ=255) cGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCATTCa > 1:95048/1‑68 (MQ=39) cGTCACCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCAtt > 1:2871414/1‑70 (MQ=255) aCCGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTG‑‑Atat > 1:1800685/1‑69 (MQ=255) ccGGGATGGTCGTAACGCCAGGCATTTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTG‑‑Atat > 1:1545280/1‑68 (MQ=255) cGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCAt < 1:518618/63‑1 (MQ=39) cGGGATGGTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTG‑‑Atatt > 1:3494401/1‑67 (MQ=255) gTCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGgc < 1:5023601/70‑1 (MQ=255) tCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGgctg < 1:689229/71‑1 (MQ=255) tCGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGgctg > 1:4744227/1‑71 (MQ=255) cGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTg > 1:3813373/1‑56 (MQ=38) cGTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGgctgc > 1:3545106/1‑71 (MQ=255) gTAACGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTg > 1:4249660/1‑55 (MQ=38) aCGCCAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTa < 1:4638299/71‑1 (MQ=255) cAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGc > 1:1389621/1‑71 (MQ=255) cAGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGc < 1:2156418/71‑1 (MQ=255) aGGCATGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCt > 1:2117376/1‑71 (MQ=255) ggcaTGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTg < 1:3849777/68‑1 (MQ=255) gcaTGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTgg > 1:3587445/3‑71 (MQ=255) gcaTGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTgg > 1:645535/3‑71 (MQ=255) gcaTGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTgg > 1:2264061/3‑71 (MQ=255) tGTTCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTaa < 1:19571/71‑1 (MQ=255) ttCATCACGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAAc < 1:4705480/70‑1 (MQ=255) tcatcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTg > 1:100507/1‑64 (MQ=255) tcatcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTaa > 1:3696058/1‑68 (MQ=255) catcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACa > 1:157192/1‑69 (MQ=255) catcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACa > 1:4347544/1‑69 (MQ=255) catcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACa > 1:3252745/1‑69 (MQ=255) atcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACagag < 1:3077584/71‑1 (MQ=255) atcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACagag < 1:1152044/71‑1 (MQ=255) atcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACaga < 1:1409951/70‑1 (MQ=255) tcaCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGc < 1:414004/71‑1 (MQ=255) aCGCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTa > 1:5043966/1‑53 (MQ=255) gCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACa > 1:558433/1‑63 (MQ=255) gCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCAttt < 1:1437913/71‑1 (MQ=255) gCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCAttt < 1:3653848/71‑1 (MQ=255) gCAGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCAtt > 1:650774/1‑70 (MQ=255) aGCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTaa < 1:1399324/71‑1 (MQ=255) aGCTGCGCGCAGTGTAGCTGACAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTaa < 1:3119657/71‑1 (MQ=255) gCTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTaa < 1:3723044/70‑1 (MQ=255) cTGCGCGCAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAAt < 1:181027/71‑1 (MQ=255) gcgcgcAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGt < 1:467718/44‑1 (MQ=25) cgcgcAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATc < 1:1418786/69‑1 (MQ=255) cgcgcAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATCAc < 1:5119457/71‑1 (MQ=255) gcAGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATCACCtt > 1:730421/1‑71 (MQ=255) aGTGTAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATCACCTTg > 1:624899/1‑70 (MQ=255) gtgtAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATCACCTTGt > 1:4992908/1‑70 (MQ=255) gtgtAGCTGCCAGTCATTGATATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATCACCTTGTa < 1:1304208/71‑1 (MQ=255) | GCGTAGATAGCGTCACCGGGATGGTCGTAACGCCAGGAATGTTCATCACGCAGCTGCGCGCAGTGTTGCTGCCAGTCATTG‑‑ATTTAACGGCTGCTGTAATGCTGGTAACAGAGCATTTAAATCACCTTGTA > AP009048/3685063‑3685193 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |