| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,027,672 | C→A | 100% | G92V (GGC→GTC) | vraS ← | Sensor protein VraS |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,027,672 | 0 | C | A | 95.0% | 57.3 / ‑4.8 | 19 | G92V (GGC→GTC) | vraS | Sensor protein VraS |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (9/9); total (10/9) | |||||||||||
| 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. | |||||||||||
TTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGG > USA300TCH1516_ALE/2027553‑2027808 | tttCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTg < 1:572377/141‑1 (MQ=255) tCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGaa < 1:187762/141‑1 (MQ=255) tGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTc > 1:429559/1‑141 (MQ=255) aGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCaa < 1:47337/141‑1 (MQ=255) gCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCGTTCCATTAAACGCTCAATTTGCGTCTTACTCCAATCAt > 1:535940/1‑141 (MQ=255) aTGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAACTCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGACCGCTCAATTTGCGTCTTAATCCAATCATTTTGCtg < 1:173366/141‑1 (MQ=255) ttAAAGGTACAAGTGTATGGTATAAATCTAACGTCTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAg < 1:157283/141‑1 (MQ=255) aGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAg > 1:171034/1‑141 (MQ=255) gtgtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAAc < 1:451517/141‑1 (MQ=255) aTGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACcaac < 1:256326/141‑1 (MQ=255) aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCATTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTGCCGAACCAACAATAATACAAaat > 1:505025/1‑141 (MQ=255) aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgat > 1:360636/1‑141 (MQ=255) aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgat < 1:50218/141‑1 (MQ=255) tttCTATATTTTGATCATTAATGACAACAGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAt < 1:399183/141‑1 (MQ=255) cTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACAAAATAATATGATGATGAGATTta > 1:525167/1‑141 (MQ=255) tatTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATAAGATGATCAGATTtaaaa > 1:406505/1‑141 (MQ=255) tttGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATAATGATGAGATTtaaaaata > 1:181730/1‑141 (MQ=255) tCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATaaaaaa > 1:236550/1‑141 (MQ=255) aaTGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAACCGAGTACCAAACCAACAATAATACACAATATTATGATGCTGAGATTTAAAAATAAAAAAACTgg > 1:260480/1‑141 (MQ=255) | TTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGG > USA300TCH1516_ALE/2027553‑2027808 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |