| 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 | 97.6% | 93.3 / ‑6.2 | 37 | H406N (CAT→AAT) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (1/2); new base A (20/11); total (22/15) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.44e-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. | |||||||||||
| Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch. | |||||||||||
| * | CP000730 | 2,455,699 | 0 | A | T | 92.3% | 104.2 / 2.3 | 39 | coding (1217/1260 nt) | USA300HOU_2315 | hypothetical membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (20/15); minor base . (1/2); total (22/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 5.77e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
AATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT > CP000730/2455564‑2455833 || aaTCAGTTAAACAAGCGCGACAAAGTGGCGGTTTCCCAAAGGATTCAGAGGAAGATGAAAGAGAGCAATCATTAAAAGAACCTGCGACTTATCAAGAAGACCGGCGTTCATCAGCTGTAGTGGATGGAGGATAAC‑TATCGa > 2:215140/1‑141 (MQ=255) aGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGaaaaa > 1:262910/1‑141 (MQ=255) ttAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAAc > 1:209105/1‑141 (MQ=255) aaaGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGACCAATCtta > 1:139875/1‑140 (MQ=255) aaGTGAAGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCa < 1:71634/141‑1 (MQ=255) aaGAGACGATTTAACAAAGGATTCCAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGGTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCa < 2:130722/141‑1 (MQ=255) gACGAGTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATa < 2:142485/141‑1 (MQ=255) gATTTACCAAACGATTCAAACGAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaaa < 1:189447/141‑1 (MQ=255) cAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGCCCTATAAACAACAGTTACGTTCCACGCAGGTGATTGATGCA‑AAAAAAGTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg > 1:159648/1‑141 (MQ=255) cAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAg > 1:103083/1‑141 (MQ=255) aGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGc < 1:272661/141‑1 (MQ=255) tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGc < 1:118470/138‑1 (MQ=255) tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAg > 1:89568/1‑141 (MQ=255) tGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAAAAATAATAACAAAGCGCTTGc > 2:118470/1‑138 (MQ=255) gAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt < 2:7763/141‑1 (MQ=255) agCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAAACAAGCGCTACCTGGTAccacat > 2:282880/1‑137 (MQ=255) tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa > 1:311178/1‑141 (MQ=255) aTTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAga > 1:133896/1‑141 (MQ=255) aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCACTTGATAGTACCTCTTAAAAAGATGATGCTAg > 1:274571/1‑141 (MQ=255) aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCACTGGCGAGTACCTCTTAAAAAGATGATGCTAg > 1:274554/1‑141 (MQ=255) ccTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc > 2:333057/1‑141 (MQ=255) ctcGACTTAAAAAGACGACCGACGTTCATCAGTTGTAATCGATGCA‑AAAAAATTATCGAACACACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTTAAAAGATGATGCTAGCaa < 2:58315/139‑1 (MQ=255) gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg < 1:107178/141‑1 (MQ=255) gACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcg < 2:311178/141‑1 (MQ=255) aactcagaaaGAAGACATACGTTCATCAGTAGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAACATTCAGCTAAAAACAAATAATAACAAACCGCTTGCTAGTACCTCTTAAGAAGATTATGCTAGCAAgcg < 2:112524/134‑1 (MQ=255) tgttaAAGAAGCCAGACGGTAAGCAGTTGTAATAGATGCAAAAAAAC‑TATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATATTAACGAAGCGTTTGTGAAAATCTCTAAAAAAGATGATGCTAGCAAGCGCtt < 2:2698/138‑1 (MQ=255) ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACATCTTAAAAAGATGATACTAGCAGGCGCtttt > 1:106245/1‑141 (MQ=255) aagaagACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATCCTAACGAAGCGCGGGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta > 1:63012/1‑141 (MQ=255) aagaagACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTcta > 2:276461/1‑141 (MQ=255) agacagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGGGCTTTTctatact > 1:276604/1‑141 (MQ=255) agacagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACGGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatact > 1:260426/1‑141 (MQ=255) acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat > 1:270238/1‑141 (MQ=255) agacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatat > 2:116678/1‑141 (MQ=255) cGTTCATCAGATGTAATTAATGCA‑AAAAAATTATCGAAAAAACTGGAGTACAATGTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCCCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTACCCTAAAtatt > 2:331166/1‑141 (MQ=255) gTTGATCGGGTGTAAGTGATGGAAAAAAAC‑GAGCGAGAAAACGGAGGAAAAATGTTCAAGTTAAAACAAATAAGAACAAAGCGCGTGCTAGTACCTCTTAAAAAGAAGATGCTAGCAAGCGCTTTTCTATACTATAtatta < 2:175745/141‑1 (MQ=255) ataGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAttttt < 2:81431/139‑1 (MQ=255) aTGCAAAAAAA‑TTAGCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAac < 2:98076/141‑1 (MQ=255) aaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCct < 2:237487/141‑1 (MQ=255) aaaaaaTTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCct < 1:166865/141‑1 (MQ=255) || AATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCT > CP000730/2455564‑2455833 |
| 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: ‑ |