| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,812 | 0 | G | A | 52.7% | ‑5.9 / 70.1 | 55 | intergenic (‑895/‑273) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (11/15); new base A (17/12); total (28/27) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 2.85e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01 | |||||||||||
| Rejected as consensus: E-value score below prediction cutoff. | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
CGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAA > CP000730/1929673‑1929952 | cGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAAtagt < 1:348442/141‑1 (MQ=255) cTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTaga < 1:433613/141‑1 (MQ=255) aCAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAg < 2:190908/141‑1 (MQ=255) tatCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGt < 1:12222/141‑1 (MQ=255) tATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAAt < 1:298298/141‑1 (MQ=255) tctcATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTa > 2:10158/1‑141 (MQ=255) gAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCag < 2:255884/141‑1 (MQ=255) gTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAgagga < 2:203942/141‑1 (MQ=255) gtAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑Gt > 2:329965/1‑141 (MQ=255) ttCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTa < 2:387984/141‑1 (MQ=255) aTCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTAtttt > 1:327432/1‑141 (MQ=255) gattgAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTcaca > 1:248743/5‑141 (MQ=255) gAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCAcatcat > 2:68206/1‑141 (MQ=255) cATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCa > 2:127105/1‑141 (MQ=255) tATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGtcatc < 1:204100/141‑1 (MQ=255) tcggaagtagatatgCTAGTATATTCACAGATGGTATAATAATAGAGTCGCCTACCTCTCAGGCGTCAATT‑‑GACGAAGAGAGAAGGTGCA‑TTACT‑TTGCTAATCATTTACGTTCACATCATAGCACCAGTCATCAGTGGCt > 2:330566/14‑141 (MQ=255) aaGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGc < 1:16825/141‑1 (MQ=255) gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg < 1:44075/131‑1 (MQ=255) aaGTGACTGTGCTTGTATATTTGCCAATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg > 1:290106/1‑141 (MQ=255) gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg > 1:71290/8‑139 (MQ=255) gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg > 2:168459/8‑139 (MQ=255) tagatatgCTTGTATATTCACAGATTGTATAATAATAGAGTCTCCTATCTCTCAGGCGGCAAGT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgt < 1:350334/135‑4 (MQ=255) tagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgt < 1:207285/135‑4 (MQ=255) tagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgt < 1:207455/135‑4 (MQ=255) gACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAt < 2:183901/141‑1 (MQ=255) gACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAt < 2:93420/141‑1 (MQ=255) agatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgtt > 2:62631/6‑137 (MQ=255) agatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGGCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgtt > 2:392242/6‑137 (MQ=255) gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg < 1:125257/137‑6 (MQ=255) gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg > 1:157456/5‑136 (MQ=255) aCTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAtt < 1:10158/141‑1 (MQ=255) tatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCg > 1:410236/3‑141 (MQ=255) tatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCg > 2:33219/3‑141 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 2:124294/2‑141 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt < 2:285202/140‑1 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCACAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:363226/2‑141 (MQ=255) ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta < 1:318392/141‑5 (MQ=255) gTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGtttttt < 1:3211/141‑1 (MQ=255) atatTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTc < 1:417919/141‑1 (MQ=255) attcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatactta > 2:181286/8‑134 (MQ=255) atTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCtt < 1:124244/141‑1 (MQ=255) cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg > 2:78306/5‑141 (MQ=255) acagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtg < 2:130734/113‑1 (MQ=255) acagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtg > 1:130734/4‑116 (MQ=255) cagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc < 1:300150/139‑1 (MQ=255) cagatggtATAATAATAGAGTCGCCTATCTCTCAGGAGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc > 1:59774/3‑141 (MQ=255) atggtATAATAAGAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTCATTGGCtta > 2:85646/1‑139 (MQ=255) atgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTCTTTCTCTTATTGTCTa > 2:389478/1‑141 (MQ=255) tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattat < 1:405295/124‑6 (MQ=255) tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattat > 2:405295/4‑122 (MQ=255) tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAg < 2:198921/138‑1 (MQ=255) ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGt < 1:120233/139‑1 (MQ=255) gatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAg > 2:59458/1‑141 (MQ=255) gatATAATAGTAGAGTCGCCTAGCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGGGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGCTTTTTTCTTATTGGCTGAg > 2:217532/1‑141 (MQ=255) gtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTa > 2:31455/2‑141 (MQ=255) ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc < 2:365298/141‑1 (MQ=255) ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACg > 2:385191/1‑141 (MQ=255) gtagAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCaa < 2:273971/141‑1 (MQ=255) | CGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAA > CP000730/1929673‑1929952 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |