| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000730 | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 2,455,698 | 0 | C | A | 93.9% | 85.8 / 0.8 | 33 | coding (1216/1260 nt) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); major base A (19/11); minor base . (1/1); total (20/13) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| 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. | |||||||||||
| * | CP000730 | 2,455,699 | 0 | A | T | 100.0% | 81.0 / ‑6.5 | 36 | H406L (CAT→CTT) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (0/1); major base T (20/14); minor base C (0/1); total (20/16) | |||||||||||
| 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. | |||||||||||
CAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT > CP000730/2455567‑2455833 || cAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaaa > 1:143484/1‑141 (MQ=255) caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAGAAACTGAAGAACa > 2:195011/1‑141 (MQ=255) ccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAAt > 1:253223/1‑141 (MQ=255) ccacAAAGTGACGATCTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAACACCTATCGAAAGATCTGAAGAACAAt < 2:260336/141‑1 (MQ=255) acaAAGTGACGATTTAACAAACGATTCAAAGAAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACCGTCGTGCAGCAGTTGT‑ATTGCGGTCAAAAAAATTATCGAAAAAACTGAAGAACAATCt < 1:130058/141‑1 (MQ=255) aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCtta > 2:182865/1‑140 (MQ=255) aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAACCTGAAGAACAATCTTc > 2:263564/1‑141 (MQ=255) aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCGGGCACTTATAGAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAAATGAAGAACAATATTc > 2:230994/1‑141 (MQ=255) aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaa > 1:255977/1‑141 (MQ=255) aCGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCAATAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaa > 2:144305/1‑141 (MQ=255) ttCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa > 2:141139/1‑141 (MQ=255) ttCAAATGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATGGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaa < 1:171563/141‑1 (MQ=255) tCACATGAAGAACAAAAAGAGCAATCTTGAAGAGAACCCGCGACTTATAAAGAAGACAGACGTTCATAAGTTGTAATTGATGCA‑AAACAATTATCGAAAAAACTGAAGAACAATCTTCAGAAAAAAacaaacaaacacgaa > 2:269560/1‑134 (MQ=255) gttagaaTAGAGCAATCATTAAAAGAACCTTCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCATCAGATAAAAACAAATAATAACAAAGCGCTTGCt < 1:123199/136‑1 (MQ=255) gATGAAATGGAGCAATCATTAAAAGATCCGTCGACTTAGAAAGAAGACAGACAGTCATAAGTTGCAATGTATTCA‑AAAAAATTATCGAAAAAGCTGAAGAACAATCTTCAGATAAAAACAATTAAGAACAAAGCGCTGGCt < 2:29078/141‑1 (MQ=255) aaaTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTa < 1:268117/141‑1 (MQ=255) aTAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTAcc > 2:78287/1‑141 (MQ=255) agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCtt > 1:268823/1‑141 (MQ=255) agCAATCATCAAAAGAACCTGCGAATTATAAAGAAGACAGACGTTCATCAATTGTTGTTGTTGCA‑AAAATATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCtt > 1:197813/1‑141 (MQ=255) gCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTa > 2:136065/1‑141 (MQ=255) cAATCATTACAAGAACCTGCGCCTTATAAAGAAGACAGACGTGCATCAATATTAATTGATGCA‑AAGAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATACAAACAAACCGCATACTAGTaattctaca > 2:84564/1‑133 (MQ=255) taTTAAAATAACCTTCGAATTATAAAGAAGACAGACGTTCATTATTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAg < 1:63781/140‑1 (MQ=255) cggCGACTTATAAAGAAGACAGACGTTCATCAGTTGCAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa < 2:73539/139‑1 (MQ=255) cTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa < 1:4402/141‑1 (MQ=255) tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa < 1:14418/141‑1 (MQ=255) tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTAAAAAGATGAGGCTAGCaa > 1:41374/1‑141 (MQ=255) acgaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta < 1:15212/139‑1 (MQ=255) aagtagACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAACAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTCGTACCTCTTAAAAAAATGATGCTAACAAGAGCTTTTcta > 2:3860/1‑141 (MQ=255) acagacGTGCATCAGTTGTAATTGATGCA‑AAAAAAATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat < 2:179832/141‑1 (MQ=255) agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATAATGCTAGCAAGCGCTTTTCTATACtatat > 1:65749/1‑141 (MQ=255) acGTTCAGCAGTTGTAATTGATG‑AAAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATTACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat < 2:188447/141‑1 (MQ=255) tcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt > 2:32961/1‑141 (MQ=255) aTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAttt > 1:110195/1‑141 (MQ=255) ttgaagaaaaaaaaTTATCGAAAAAACCGAAGAACAATCTTCAGATAAAAACCAATAATAACAAAGCGCTTGCTAGTAACTCTTAAAAAGATGATTCTAGCAATCGCTTTTCTATACTATATATTATTTTTCTAAAAtttt < 1:93371/133‑1 (MQ=255) caaaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACAcc < 1:70636/139‑1 (MQ=255) aaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCct < 1:205832/141‑1 (MQ=255) || CAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT > CP000730/2455567‑2455833 |
| 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: ‑ |