| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | rpoA_2 → | DNA‑directed RNA polymerase subunit alpha |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,856,087 | 0 | T | A | 100.0% | 112.1 / NA | 36 | P80P (CCT→CCA) | rpoA_2 | DNA‑directed RNA polymerase subunit alpha |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (13/23); total (13/23) | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
ATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATT > USA300TCH1516_ALE/2855953‑2856222 | aTGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGt < 1:510315/141‑1 (MQ=255) tGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCACCTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGACGTGTCATGCAATCATGCGCCAAAACGTcaaca > 1:448598/1‑141 (MQ=255) ttcgTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAATTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCAGGCGCCAAAACGTCAACAAATGa < 1:167882/138‑1 (MQ=255) ccTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGAt > 1:182055/1‑141 (MQ=255) ccTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATACAATCATGCGCCAAAACGTCACCAAATGATAGAt > 1:15297/1‑141 (MQ=255) aaaGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGAtttt > 1:665208/1‑141 (MQ=255) atatCAATATTGGAACAAGCTTTATTTCAGCACCAACTACCTTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGACACCAACTGATCGATTTTATAgtt > 1:506278/1‑141 (MQ=255) tatTGGAACAATCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcag < 1:131975/141‑1 (MQ=255) atTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTAcagc < 1:530516/141‑1 (MQ=255) aaCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAt < 1:327987/141‑1 (MQ=255) aCAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAACCGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCAtt > 1:55941/1‑141 (MQ=255) cAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTa < 1:257525/141‑1 (MQ=255) gCTTTATTTCAGCACCAACTACATTTTAAAGCGGAAGTTCAGTCATCATTACCTTGTGAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCGGCGTTAGat > 1:346824/1‑141 (MQ=255) tATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTg < 1:635992/141‑1 (MQ=255) cACCAACTACATTTTTAAACGGAAGTTCAGTCATCATAACTTTATAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAACGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAAtcatta < 1:474770/141‑1 (MQ=255) ccAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTAGTTCCAGCAGACTTATATATTGAATTATTACg > 1:181041/1‑141 (MQ=255) cATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGGGGTTATAACAGCATTAGATAATGAATTGATACGATCACTg > 1:497947/1‑141 (MQ=255) acgtacgTTCAGTTATCATTCCCCTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTacaaca < 1:199411/135‑1 (MQ=255) aCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTacaaca < 1:218584/141‑1 (MQ=255) ttCAGTCATCATTACCTTTTAAGTTAACAGGGGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAattta < 1:307006/141‑1 (MQ=255) tcatcaTTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTgg < 1:515693/141‑1 (MQ=255) atcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCCGCATTAGAGATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTc < 1:523572/141‑1 (MQ=255) atcatTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTc < 1:96566/141‑1 (MQ=255) catTACCTTTTAAGTTAACAGGAGATGTTTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTg < 1:381552/141‑1 (MQ=255) ccTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGCTAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTAACTGGTTACAACAGACTTTATTTGGTCTGTCCCt < 1:141273/141‑1 (MQ=255) ttaagttaagAGGAGATGTGCCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGcc < 1:314134/141‑1 (MQ=255) ttAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGcc > 1:291395/1‑141 (MQ=255) tAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCg < 1:440427/141‑1 (MQ=255) aCAGGAGATGTTACATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTTCCTGGCCGCTTTGAc < 1:246878/141‑1 (MQ=255) gtgtgTCATGCAATCAGGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACg < 1:95828/140‑1 (MQ=255) gtgtCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGa > 1:48163/1‑141 (MQ=255) ttgcATGCAATCATGCGCCAAAACGTCAACAAATGAGAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGAc < 1:98741/138‑1 (MQ=255) tCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATCCGGACCt > 1:539717/1‑141 (MQ=255) aaTGCGCCAAAACGTCAACAAAGGATAGATTTTATAGTTGTTACAGCAGCATTAGATATCGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTa < 1:511416/140‑1 (MQ=255) aTGCGCCAAAACGTCAACAAATGATAGAGTTTATAGTTGTTAAAGTTATTGGAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa < 1:486084/141‑1 (MQ=255) gcgcCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAAtt > 1:43855/1‑141 (MQ=255) | ATGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAATT > USA300TCH1516_ALE/2855953‑2856222 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |