| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | AP009048 | 3,684,921 | A→G | 100% | pseudogene (138/582 nt) pseudogene (1201/1645 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 | 3,684,921 | 0 | A | G | 97.2% | 116.7 / ‑4.0 | 36 | pseudogene (138/582 nt) pseudogene (1201/1645 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 A (0/1); new base G (14/21); total (14/22) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-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. | |||||||||||
TCGTTCGGTCGCGCGACTTGTGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTACCTAAACCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGTGCTGCGCAGCCCACATC > AP009048/3684865‑3684987 | tCGTTTGGTCGCGCGACTTGCGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTgg < 1:3369233/70‑1 (MQ=38)tCGTTCGGTCGCGCGACTTGTGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTACCTAAACCGCTgg < 1:1044510/70‑1 (MQ=255) gTTTGGTCGCGCGACTTGCGCGCCAACCGCTGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAgg > 1:2708162/1‑71 (MQ=38) 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) gcgcgcCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCgg < 1:1711110/68‑1 (MQ=38) cgcgcCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTg < 1:3615071/48‑1 (MQ=25) cgcgcCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAAtttt > 1:1373718/2‑65 (MQ=38) gcgcCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCg < 1:512840/71‑1 (MQ=255) gcCAACCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAg > 1:458317/1‑71 (MQ=255) aCCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGtga < 1:1700949/49‑1 (MQ=25) aCCGCCGCCGGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGtgtg < 1:2662106/71‑1 (MQ=255) cgccgccgGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTggg > 1:1388522/1‑71 (MQ=255) gccgGTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGAt < 1:1387381/71‑1 (MQ=255) ggTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGAtg < 1:1052350/69‑1 (MQ=255) gTAAACCAAAACCCATGGTGCCTAAGCCGCTGGAGGt < 1:2063331/37‑1 (MQ=25) aaaCCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGtgctg > 1:4566964/1‑71 (MQ=255) aaaCCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGtgct > 1:986884/1‑70 (MQ=255) aaCCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGtgctgc < 1:2920532/71‑1 (MQ=255) aCCAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGTCGAGTGTGGGCGATGTGCTgcg < 1:278994/71‑1 (MQ=255) ccAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAAtt < 1:4024006/41‑1 (MQ=38) cAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGa < 1:4561485/50‑1 (MQ=255) cAAAACCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAgt < 1:1386620/52‑1 (MQ=255) aaaaCCCATGGTGCCTAAGCCGCTGGAGGtgatga < 1:536156/35‑1 (MQ=37) aaaaCCCATGGTGCCTAAGCCGCTGGAGGTGATGaaa > 1:3352752/1‑37 (MQ=38) aaaaCCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGTGCTGCGCAg < 1:441740/71‑1 (MQ=255) aaaCCCATGGTGCCTAAGCCGCTGGAGGTGATGAAAtttt > 1:4488356/1‑40 (MQ=38) aaaCCCATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAg < 1:5122902/49‑1 (MQ=39) ccATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGtgctg > 1:3574014/1‑61 (MQ=255) ccATGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGACTGTGGGCGAtgtg > 1:3546176/1‑58 (MQ=38) aTGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGTGCTGCGCAGCCCACAt < 1:4530635/71‑1 (MQ=255) aTGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGTGCTGCGCAGCCCACAt > 1:2679192/1‑71 (MQ=255) tGGTGCCTAAGCCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGTGCTGCGCAGCCCACATc > 1:3227711/1‑71 (MQ=255) | TCGTTCGGTCGCGCGACTTGTGCGCCAACCGCCGCCGGTAAACCAAAACCCATGGTACCTAAACCGCTGGAGGTGATGAAATTTTCCGGGCGAGTGTGGGCGATGTGCTGCGCAGCCCACATC > AP009048/3684865‑3684987 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |