| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,709,439 | Δ1 bp | 100% | coding (1488/1812 nt) | oatA_2 ← | O‑acetyltransferase OatA |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,709,439 | 0 | T | . | 83.3% | 67.0 / 12.7 | 24 | coding (1488/1812 nt) | oatA_2 | O‑acetyltransferase OatA |
| Reads supporting (aligned to +/- strand): ref base T (4/0); new base . (8/12); total (12/12) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 9.32e-02 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| 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. | |||||||||||
TACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCA > USA300TCH1516_ALE/2709306‑2709574 | tACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCtttttagc < 2:230193/141‑4 (MQ=255) ccTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACTTTTTTTAGCa > 1:347495/1‑141 (MQ=255) cATAATCTCTAGGTACTCTAATAGAAACTAAATATCTGTCTGCTTTTCCAAAACTATCCATTAGTTCATTTAGTTGATCTTTCGTAAATGCCCCATTTGTACTCAGCTCTACTACACCTTTTTGACC‑TTTTTAGCATattt > 2:43016/1‑138 (MQ=255) aTAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCt > 2:262848/1‑141 (MQ=255) gTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCAGAGTCTTTATATTGCGa > 2:308405/1‑141 (MQ=255) atatGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATc < 1:296663/141‑1 (MQ=255) atGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCaa < 1:194688/141‑1 (MQ=255) ttcccAAAACTATCCAATAGTTCATTTAATTGAACTTTCGTAAATGCCCCAATTGTCCCAAGCACTACTACAACTTTTTGACCTTTCTTAGCATAGTCGTTATATTGCGATTTCACACTTGTTATAACATCAACGAGTTGc > 2:356824/4‑141 (MQ=255) ccAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTGCTACAACTTTTCGACC‑TTTTTAGCATAGTCTTTATATTGCAATTTCACAATTGGTGTTGCATCAACGAGTTGCCGTc > 1:12173/1‑141 (MQ=255) aCTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACt > 2:243319/1‑141 (MQ=255) cAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCa < 2:337407/141‑1 (MQ=255) aaTTGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCAt < 2:361685/141‑1 (MQ=255) aaTAGTTCATTTAATTGATCTTTCGTAAATGCCTCATTTGTACCAAGCTCTACGAGAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTGCACAATTGGTGTAGCATCAACGACTTGCCGTCCAACTTTACCAt < 2:216360/141‑1 (MQ=255) aTAGTTCATTTAATTGAGCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATc < 1:48948/141‑1 (MQ=255) tttAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTtgtg < 2:302087/141‑1 (MQ=255) tGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGCTTTCACAAGTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTg < 2:163202/141‑1 (MQ=255) aTCTTTCGTAAATGCCCCATGTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTGTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGt > 1:256193/1‑141 (MQ=255) tCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTTCATTTGGTAttt > 2:350020/1‑141 (MQ=255) tCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTAttt > 2:350009/1‑141 (MQ=255) tAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTTTAGCATCAACGAGTTGCCGTCAAACTTTACCATCCATTTGTGCATTTGGTATTTTCtt > 2:177591/1‑141 (MQ=255) tGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTa < 1:377651/141‑1 (MQ=255) ccAAGCTCTACTACAACTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCaa > 1:190655/1‑141 (MQ=255) cAACTTTTTGACC‑CTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGAc < 1:6591/141‑1 (MQ=255) aaCTTTTTGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGAcc < 1:15590/141‑1 (MQ=255) ttGACC‑TTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCa < 1:262848/141‑1 (MQ=255) | TACCTTCATAATCTCTAGGTACTCTAATAGAAACTAAATATATGTCTGCTTTTCCAAAACTATCCAATAGTTCATTTAATTGATCTTTCGTAAATGCCCCATTTGTACCAAGCTCTACTACAACTTTTTGACCTTTTTTAGCATAGTCTTTATATTGCGATTTCACAATTGGTGTAGCATCAACGAGTTGCCGTCCAACTTTACCATCAATTTGTGCATTTGGTATTTTCTTAGTAAAGACATTACCAATATCCACCATGACCGAGTCA > USA300TCH1516_ALE/2709306‑2709574 |
| 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: ‑ |