| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | W3110S.gb | 3,824,533:1 | +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 | ||
| * | W3110S.gb | 3,824,533 | 1 | . | G | 94.7% | 55.7 / ‑3.1 | 19 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (8/10); total (8/11) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| 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. | |||||||||||
AGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGC > W3110S.gb/3824479‑3824593 | aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGG‑gaatcga > 1:2504552/1‑66 (MQ=255) aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCg < 1:2121168/71‑1 (MQ=255) ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑GGGTGAATCGAATCCATTg < 1:1948866/56‑1 (MQ=255) aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGG‑gaatcga > 1:1215668/1‑46 (MQ=255) tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATcc < 1:2002050/49‑1 (MQ=255) tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTg < 1:2331062/53‑1 (MQ=255) gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAggcggc > 1:676895/1‑71 (MQ=255) cTCACCTTGTTGGCGCTGGCCCGAGGGG‑gaatcgaatc < 1:572548/38‑1 (MQ=21) cTCACCTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTg < 1:542296/43‑1 (MQ=25) accTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTg > 1:2249652/3‑63 (MQ=255) accTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:2272440/3‑70 (MQ=255) ccTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa < 1:611850/64‑1 (MQ=255) ccTTGTTGGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGa > 1:1909900/2‑71 (MQ=255) ttgttgGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaaa > 1:1530667/1‑65 (MQ=255) ttgGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttttt < 1:1466265/71‑1 (MQ=255) tgGCGCTGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGAc > 1:1825581/1‑40 (MQ=37) gctGGCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGc < 1:1568465/70‑1 (MQ=255) gCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAg < 1:2260308/36‑1 (MQ=37) gCCCGAGGGG‑GAATCGAATCCATTGTAGCGACGCAg < 1:850822/36‑1 (MQ=37) | AGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGG‑GAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGC > W3110S.gb/3824479‑3824593 |
| 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: ‑ |