| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 1,440,085 | G→T | 100% | 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 | 99.2% | 143.7 / ‑6.5 | 53 | 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 (23/28); minor base A (0/2); total (23/30) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.99e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
AAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTC > USA300TCH1516_ALE/1439951‑1440208 | aaaaTGTACGAATACGACATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAACGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACATCCAAGACTAAAATTGATTCAATTTGCTTATTCTCatat > 1:273117/1‑140 (MQ=255) aTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCGTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTTCAAGACTATACTTCCGTCGACAGGCTTATTCTCGCATTAc < 1:404992/140‑1 (MQ=255) tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAGTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTTTAATATTACa > 2:156597/1‑140 (MQ=255) gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATACTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaa > 2:296243/1‑140 (MQ=255) cGAATACGTCATTTTCTCCTTCAACTTCGGTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaa > 1:119604/1‑140 (MQ=255) gTCATTTTCTTCTTCAACTTCGAAAAAGCCAAATCCTTTTTCAGCGTTAAACCATTTAACTGCACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTAAAAAAAAAAAAAAAATACATg < 2:525602/140‑1 (MQ=255) gTCATTTTCTCCTTCACCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATg < 2:50295/140‑1 (MQ=255) tttCTCCTTCAACTGCTATACAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAt < 2:398364/140‑1 (MQ=255) tctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAATACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAttt < 2:266297/140‑1 (MQ=255) cctttcaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc < 2:276839/134‑1 (MQ=255) ccTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc < 1:325761/140‑1 (MQ=255) cTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAAAAAAAATACCTGCAAATTTCACt > 2:536728/1‑140 (MQ=255) tCAACTTCGATAAAGCCGAATCCTTTTTCAGCTTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCa < 1:220958/140‑1 (MQ=255) aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaaa < 1:220682/140‑1 (MQ=255) aCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAat < 2:363710/140‑1 (MQ=255) tCGTTAAAGCCGAACTCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAACATACATGCAAATTTCACTCAAATAtt < 2:341428/140‑1 (MQ=255) tCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAATACATGCAAATTTCACTCAAATATTc > 2:37483/1‑140 (MQ=255) aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt < 2:147285/140‑1 (MQ=255) aTAAAGCCGAATCCTTTTTCAGCGTTAAAACATTTAACAGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCAGTCAATATGCTTATTAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCtt < 2:27940/140‑1 (MQ=255) aaGCCTAATCCTTTTTCACCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc < 2:131906/140‑1 (MQ=255) gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat < 1:95113/140‑1 (MQ=255) gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCAAATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat < 1:67310/140‑1 (MQ=255) aTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg < 2:94602/140‑1 (MQ=255) ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaa > 2:366229/1‑140 (MQ=255) ttCAGCGTTAAACCATTTAGCTGTACCTTGTTTCATAATCTGAAGCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAttc > 1:302385/1‑140 (MQ=255) cAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat < 1:275903/140‑1 (MQ=255) cGTTAAACCATTTAACTGTACCGTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTGAAATAGTCTTTGCAATATGGAATAATCATCTg < 1:119488/140‑1 (MQ=255) ttAATCCATTTCACTGTACCTTGTTTCATAATATGAAACCTCCAAGACTAAAATTCCTTCAATATGCTTATTCTCATATTAGAAACAATACACGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt < 1:52888/140‑1 (MQ=255) ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAATACTAAAATTCATTCATTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt < 1:431772/140‑1 (MQ=255) tAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat < 1:342311/140‑1 (MQ=255) aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattc > 1:330170/1‑139 (MQ=255) gTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTCATTAACTTGTATTATAg > 2:221681/1‑140 (MQ=255) ccTTGTTTCATAATCTGAAACCTCCAAGAATAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGc < 1:442380/140‑1 (MQ=255) ccTTGTTTCATAATCTGAAACCTACAAGACTAAAATTCAATCAATATGCTTATTCTAATATTACAAAAAATACAAGCAAATTTCAATCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGc < 1:137414/140‑1 (MQ=255) ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCATATATTCTTTGTAATATGGAATAATCATCTGCTTACCTTGTATTATAGTTCAg > 2:42921/1‑140 (MQ=255) ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg > 1:278328/1‑140 (MQ=255) gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt < 1:338151/140‑1 (MQ=255) tttCATAATCTGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtta > 1:133036/1‑140 (MQ=255) tCATGATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt < 2:389252/140‑1 (MQ=255) tCATAATCTGAAACCTCCAAGACTAAAATTCATTCATTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt < 2:31503/140‑1 (MQ=255) tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt < 1:303376/140‑1 (MQ=255) aTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTACTTAACTTGTATTATAGTGCAGTTATTAc > 1:490697/1‑140 (MQ=255) tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCCTCTGCTTACCTTGTATTGTAGTGAATTTATTAca > 2:19048/1‑139 (MQ=255) aaTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa > 2:519009/1‑140 (MQ=255) tGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt > 1:314710/1‑140 (MQ=255) aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc < 2:504968/140‑1 (MQ=255) aCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaa > 1:155339/1‑140 (MQ=255) aCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGAAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATCACCAAATTAcaa > 2:18521/1‑140 (MQ=255) ccTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaat > 1:383313/1‑140 (MQ=255) ccAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACAAAATTGcaataca > 2:433616/1‑140 (MQ=255) aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATTCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataat < 2:21320/140‑1 (MQ=255) ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTc > 2:185548/1‑140 (MQ=255) ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTc > 1:172212/1‑140 (MQ=255) | AAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTC > USA300TCH1516_ALE/1439951‑1440208 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |