| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,857,170 | G→A | G195R (GGA→AGA) | nixA → | High‑affinity nickel‑transport protein NixA |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,857,170 | 0 | G | A | 95.8% | 66.1 / ‑3.3 | 25 | G195R (GGA→AGA) | nixA | High‑affinity nickel‑transport protein NixA |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (8/15); total (8/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.46e-01 | |||||||||||
CGTCGTGAACACATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTGGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTA > USA300TCH1516_ALE/2857038‑2857295 | cgtcgtGAACACATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGt > 1:130337/1‑141 (MQ=255) acacATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATAc < 1:65452/141‑1 (MQ=255) gTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTa > 1:760/1‑141 (MQ=255) tGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGc > 2:87354/1‑141 (MQ=255) aTTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATcaca < 1:202876/141‑1 (MQ=255) aTTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATcaca < 1:35931/141‑1 (MQ=255) tGGTTTCTGGATGTGTAGGACTTTATTGCAAATTAATCTCGCGTAGTTGGCACGTATTGCAACTTGGCTTTTTATTTTGACTTGGTTTTGGTACAGCTAGTGAAATTGCGTTATTCGCTTTTTCTTCAGGTGCATCacaac < 2:82910/141‑1 (MQ=255) tGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCacaac < 2:60949/141‑1 (MQ=255) tttCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAg > 1:156921/1‑141 (MQ=255) cGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGTCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCGGGCGCATCACAACAAGCcatt > 2:221093/1‑141 (MQ=255) gATTTGTAGGACCTTATTTCAAGTTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTGGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcattt < 1:117722/141‑1 (MQ=255) ttGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcatttcat > 2:97602/1‑141 (MQ=255) tGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcatttcatt < 1:125943/141‑1 (MQ=255) gTAGGACCGTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcatttcattt > 2:43375/1‑141 (MQ=255) gcgTAGTTGGCACTTATTGCCACTTGGGTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCTCAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAAtgtt < 2:147401/141‑1 (MQ=255) gcgTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGCCTTGGTTTTGATCCAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAAtttt < 2:122036/141‑1 (MQ=255) gTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTAt < 1:2373/141‑1 (MQ=255) gTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCg > 2:11017/1‑141 (MQ=255) aTTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCAGCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTAt < 2:148848/141‑1 (MQ=255) ttGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATg < 2:760/141‑1 (MQ=255) ttGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATg < 1:19186/141‑1 (MQ=255) tGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGa < 1:69688/141‑1 (MQ=255) aCTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGttt < 1:11017/141‑1 (MQ=255) cTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTa < 2:173164/141‑1 (MQ=255) cTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTa < 2:93541/141‑1 (MQ=255) | CGTCGTGAACACATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTGGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTA > USA300TCH1516_ALE/2857038‑2857295 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |