| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | AP009048 | 3,684,885 | T→C | 100% | pseudogene (174/582 nt) pseudogene (1237/1645 nt) |
ilvG ← ilvG ← |
ECK3760:JW3741:b3768; acetolactate synthase II, large subunit, C‑ter fragment 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 | 3,684,885 | 0 | T | C | 95.3% | 62.2 / ‑3.7 | 21 | pseudogene (174/582 nt) pseudogene (1237/1645 nt) | ilvG ilvG | ECK3760:JW3741:b3768; acetolactate synthase II, large subunit, C‑ter fragment ECK3760:JW3740+JW3741:b4488; large subunit of acetolactate synthase II |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (6/14); total (6/15) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-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. | |||||||||||
TCATCATGAAAGAGCCGTCACCGGAGATACAGACAACGGTATCGTTCGGTCGCGCGACTTGTGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTACCTAAACCGCTGGAGGTGATGAAATTTTC > AP009048/3684824‑3684950 | tcatcaTGAAAGAGCCGTCACCGGAGATACAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCaa < 1:3440394/69‑1 (MQ=255) catcatGAAAGAGCCGTCACCGGAGATACAGACGACGGTATCGTTTGGTCGCGCGACTTgcgc > 1:4901506/1‑63 (MQ=255) tcatTAAAGAGCCGTCACCGGAGATACAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCaa < 1:1063935/66‑1 (MQ=255) cGTCACCGGATATACAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAAcc < 1:1095742/70‑1 (MQ=255) gTCACCGGAGATACAGACGACGGTATCGTTTGGTCGCGCGACTTGcgcg < 1:3699167/49‑1 (MQ=255) gTCACCGGAGATACAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCaa < 1:1436267/71‑1 (MQ=255) tCACCGGAGATACAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCaaa < 1:1657701/71‑1 (MQ=255) ggAGAAACAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTa < 1:3291936/59‑1 (MQ=255) agaTACAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATg > 1:3030120/1‑71 (MQ=39) aCAGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGtgc > 1:1484733/1‑69 (MQ=38) aGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCaa < 1:4585561/39‑1 (MQ=37) aGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAAccgac < 1:5143910/44‑3 (MQ=37) aGACGACGGTATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCa < 1:2509921/56‑1 (MQ=255) tATCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCgg < 1:13402/40‑1 (MQ=38) tCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTgg < 1:3369233/70‑1 (MQ=38) tCGTTCGGTCGCGCGACTTGTGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTACCTAAACCGCTgg < 1:1044510/70‑1 (MQ=255) gTTTGGTCGCGCGACTTGCGCGCCAACCGCTGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAgg > 1:2708162/1‑71 (MQ=38) gTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCaaaa > 1:2640317/1‑46 (MQ=39) gTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAg < 1:1227030/70‑1 (MQ=38) cgcgcgACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGtgatga > 1:2029960/1‑70 (MQ=38) cgcgACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGaa < 1:2375232/69‑1 (MQ=38) gACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAAtttt > 1:1849615/1‑71 (MQ=38) aCTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTc < 1:2247738/71‑1 (MQ=38) | TCATCATGAAAGAGCCGTCACCGGAGATACAGACAACGGTATCGTTCGGTCGCGCGACTTGTGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTACCTAAACCGCTGGAGGTGATGAAATTTTC > AP009048/3684824‑3684950 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |