| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,440,085 | G→T | intergenic (‑45/+126) | cspA_2 ← / ← USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 1,440,085 | 0 | G | T | 98.4% | 181.1 / NA | 61 | intergenic (‑45/+126) | cspA_2/USA300TCH1516_01338 | Cold shock protein CspA/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (26/34); minor base A (0/1); total (26/35) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
AAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA > USA300TCH1516_ALE/1439950‑1440221 | aaaaaTGTACGATTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCatat < 2:318269/141‑1 (MQ=255) aaaaTGTAGGAATCCGTCATTTTCTCCTTCAACTGCGATGAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATAtt < 2:433458/141‑1 (MQ=255) aaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTa < 1:586130/141‑1 (MQ=255) aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAc < 1:189421/141‑1 (MQ=255) tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaa > 2:276180/1‑141 (MQ=255) gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa > 2:269183/1‑141 (MQ=255) gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCCTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa > 1:605564/1‑141 (MQ=255) tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa < 1:68422/141‑1 (MQ=255) ttcGTCATTTTCTCCTTCAACTTCGGTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTCCCTTGTTTCATAATCTGAATCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACa < 1:116579/139‑1 (MQ=255) cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATg > 1:299685/1‑141 (MQ=255) gTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAGTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGc > 2:751041/1‑141 (MQ=255) tttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAtt < 1:581724/141‑1 (MQ=255) ttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATACTTATTCTCAGATTACAAAAACTACATGCAAAttt > 2:235215/1‑141 (MQ=255) tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc > 1:39728/1‑141 (MQ=255) cattCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAGATTTCACt < 2:850216/139‑1 (MQ=255) aCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAata < 1:788405/141‑1 (MQ=255) cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCCCTCAAATATTCt > 2:401795/1‑141 (MQ=255) cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt < 2:254160/141‑1 (MQ=255) gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt > 2:302932/1‑141 (MQ=255) gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt < 1:604783/141‑1 (MQ=255) gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt < 1:816194/141‑1 (MQ=255) gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt < 1:816184/141‑1 (MQ=255) cgtaTCCTTTTTCAGCGTTAAAACATCTA‑ACTGTACCTTGTTTCATCATCAGACACCTCCAAGACTAACATTCATCCAATATGCTTATAAACAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCCatat < 2:846601/138‑1 (MQ=255) cGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAGTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCACATATTCTTTGCAatat < 2:667673/141‑1 (MQ=255) ccTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTCAAATTCATTCAATATGCTTATTCTCATATTACAACAAATACATCCAAATTTCACTCCAATATTCTTTGCAATATGGcat > 1:732932/1‑141 (MQ=255) ccTTGTTCATTGTTAAAATAATTA‑GCGGTCCCTCGTTTCATACTCTGAAACCTCCAAGCCTAAAATTCACTCCATACGTTTATTCTCTTATGACAAAAAATACATGCAGATTTCACTCAAATATTCTTTGCAAGAGGGagt < 2:863277/141‑3 (MQ=255) tttttCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa > 1:317692/1‑141 (MQ=255) tttttCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa < 2:745417/141‑1 (MQ=255) ctCACCGTTAAACCATTTACAATG‑ACCATGTTGCATAATCTGAAACCTTCAAGACTAATATTCATTCAATATGCTTATTCTCCTATTACAAAAAATACATGCAACTTTCACTCAAATATTCTTTGCAATATGGAATAatca < 1:855596/140‑1 (MQ=255) aGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCACGACTAAAGTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt < 1:680521/141‑1 (MQ=255) gTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCGGCt > 1:62522/1‑141 (MQ=255) aaCCATTTA‑ACTGTTCCTTGTTCCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATTCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATCGAATAATCATCTGCTTAAc < 2:620912/141‑1 (MQ=255) aTTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt > 2:139791/1‑141 (MQ=255) aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat > 1:42672/1‑141 (MQ=255) tACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAATCAAATATTCTTTGCAATATGGAATAATCATCTGCTTACCTTGTATTAGAGTg > 1:811841/1‑141 (MQ=255) cTTGTTTCATCATCTGAAACCTCCAAGACTAGAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg < 2:732932/141‑1 (MQ=255) tGTTTCATAATCTGAAACCTCAAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt < 2:482684/141‑1 (MQ=255) tttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTGAACTTGTATTATAGTGCAGttat > 1:337229/1‑141 (MQ=255) ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACGCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt < 2:86431/141‑1 (MQ=255) tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatta > 2:290930/1‑141 (MQ=255) tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatta > 2:585478/1‑141 (MQ=255) aTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTAcc < 1:93790/141‑1 (MQ=255) cTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt < 2:299685/141‑1 (MQ=255) aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAataata > 1:189307/1‑141 (MQ=255) atAAAATTCATTCAATATGCTTATTCTCATAATACAAAAAATACATGCAAATTTCACTTAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTCTATCATAGTGCAGTTATTACCAAATTGCAATACAAtaataa < 2:606030/140‑1 (MQ=255) aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATGTGCATTGATCTTGGGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAGTAATaaaa > 1:212895/1‑141 (MQ=255) aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa > 1:894267/1‑141 (MQ=255) aaaaCTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGATTAACTAGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa < 2:604776/141‑1 (MQ=255) aaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaaaa < 1:245442/141‑1 (MQ=255) attcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAGTATTc < 2:317692/141‑1 (MQ=255) attcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTc < 1:776722/141‑1 (MQ=255) caATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATCCAATAATAAAAAATATTCGtt > 1:352322/1‑141 (MQ=255) caATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCAtt < 1:139791/141‑1 (MQ=255) tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa > 1:75642/1‑141 (MQ=255) tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTAAAATATTCTTTGCAATATGGAATAATCATCTGATTAACTTGTATTATAGTGCAGTTATTAACAAATTGCAATACAATAATAAAAAATATTCATTTaa > 1:172431/1‑141 (MQ=255) gCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAAGAATAAAAAATATTCATTTAATCa > 2:836691/1‑141 (MQ=255) tATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatt < 1:302932/141‑1 (MQ=255) tttCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta < 1:570220/140‑1 (MQ=255) aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta < 1:571438/141‑1 (MQ=255) aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta > 1:871002/1‑141 (MQ=255) aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta < 1:290930/141‑1 (MQ=255) | AAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTA‑ACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA > USA300TCH1516_ALE/1439950‑1440221 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |