| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | AP009048 | 3,824,531:1 | +G | 100% | pseudogene (666/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AP009048 | 3,824,531 | 1 | . | G | 95.2% | 203.8 / 2.2 | 62 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base G (28/31); total (29/33) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
AGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑G‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > AP009048/3824462‑3824595 | aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g < 1:3091346/71‑1 (MQ=255)aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g < 1:3998775/71‑1 (MQ=255)aGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g < 1:1450519/71‑1 (MQ=255) gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g < 1:1215560/71‑1 (MQ=255) gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g < 1:2937648/71‑1 (MQ=255) tGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑g < 1:3200147/71‑1 (MQ=255) aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑ggga < 1:1625377/71‑3 (MQ=255) aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g > 1:401086/1‑67 (MQ=255) ggggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑gggaa > 1:3472279/1‑68 (MQ=255) gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑gg < 1:388939/67‑1 (MQ=255) ggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑GTG‑Gg‑aatc < 1:2204984/71‑1 (MQ=255) gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcg < 1:4456662/71‑1 (MQ=255) gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcg < 1:2059803/71‑1 (MQ=255) ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g < 1:2738779/59‑1 (MQ=255) gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcgaatc > 1:4274375/1‑71 (MQ=255) cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑Gg‑aatcgaatc > 1:3612343/1‑70 (MQ=255) aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCAtt < 1:3388543/71‑1 (MQ=255) aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCAtt > 1:2757799/1‑71 (MQ=255) aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTg < 1:2909006/71‑1 (MQ=255) aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑ggga < 1:633878/58‑3 (MQ=255) aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑ggga < 1:4119877/58‑3 (MQ=255) gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc > 1:1702098/1‑71 (MQ=255) aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCg < 1:1448893/71‑1 (MQ=255) gCCGTTCACGCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCg > 1:1712121/1‑70 (MQ=255) gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑g > 1:726700/1‑49 (MQ=255) gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g‑g‑g > 1:1947211/1‑49 (MQ=255) tCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg > 1:2140511/1‑68 (MQ=255) cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑Aatccaatcca > 1:1904658/1‑56 (MQ=255) cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCa > 1:3302379/1‑56 (MQ=255) cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg < 1:856093/70‑1 (MQ=255) cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg < 1:5323230/70‑1 (MQ=255) cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg < 1:5293998/70‑1 (MQ=255) cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGAGACGCAg < 1:2262496/70‑1 (MQ=255) aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAg < 1:5300224/69‑1 (MQ=255) aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGaa < 1:1001932/71‑1 (MQ=255) aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGa < 1:950119/70‑1 (MQ=255) ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAgg < 1:4097046/71‑1 (MQ=255) ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAgg > 1:2778095/1‑71 (MQ=255) cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGa > 1:2043063/1‑61 (MQ=255) aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCa > 1:132913/1‑51 (MQ=255) aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg < 1:85282/62‑1 (MQ=255) aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAggcg > 1:3040977/1‑71 (MQ=255) aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAggcg < 1:2774330/71‑1 (MQ=255) aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACACAGAAggcg > 1:3598421/1‑71 (MQ=255) gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg < 1:2852550/60‑1 (MQ=255) aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGaa > 1:1324126/1‑64 (MQ=255) aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCAACGCAGAAGgcggcg > 1:2717052/1‑71 (MQ=255) gagCTACTCACCTTGTTGGCGCTGGCCCGA‑G‑G‑GGAAATCGAATCCATTGTAGc > 1:2390187/1‑53 (MQ=255) cTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTa > 1:4981970/1‑48 (MQ=255) cTACTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGc < 1:2534944/55‑1 (MQ=255) aCTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGaa > 1:4265161/1‑57 (MQ=255) cTCACCTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaa < 1:4369559/70‑1 (MQ=255) accTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAggc < 1:1532321/54‑1 (MQ=255) accTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:3446913/3‑70 (MQ=255) accTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt < 1:4733650/68‑1 (MQ=255) ccTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc < 1:3793334/42‑1 (MQ=37) ccTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc < 1:4544717/42‑1 (MQ=37) ccTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc < 1:4647054/42‑1 (MQ=37) cTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGc < 1:3439919/42‑1 (MQ=37) cTTGTTGGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt > 1:1539683/1‑71 (MQ=255) tgttgGCGCTGTCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg < 1:713087/44‑1 (MQ=25) tgttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACg < 1:5249932/44‑1 (MQ=38) tgttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttt > 1:1303322/1‑71 (MQ=255) tgttgGCGCTGGACCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGAc > 1:3093496/1‑43 (MQ=25) gttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt < 1:4712786/69‑1 (MQ=255) gttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt > 1:5183624/1‑68 (MQ=255) gttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGAAGCGACGCAg < 1:4577174/46‑1 (MQ=37) ttgGCGCTGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttttt < 1:2921643/71‑1 (MQ=255) ggCGCTGCCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttt > 1:4531883/1‑67 (MQ=255) gcgctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTaa < 1:2552263/67‑1 (MQ=255) gcgctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAg < 1:2132282/68‑1 (MQ=255) gctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCa > 1:1975428/2‑39 (MQ=37) gctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc > 1:5119228/2‑71 (MQ=255) ctGGCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc > 1:2395866/1‑70 (MQ=255) tGGCCCGA‑G‑GTGG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCg < 1:5060291/70‑1 (MQ=255) ggCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGa > 1:3290394/1‑38 (MQ=38) gCCCGAGG‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGCCt > 1:962756/1‑71 (MQ=255) | AGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑G‑G‑GG‑AATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > AP009048/3824462‑3824595 |
| 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: ‑ |