| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000730 | 1,929,804 | A→G | 40.8% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,929,804 | 0 | A | G | 40.8% | 8.1 / 51.0 | 47 | intergenic (‑887/‑281) | USA300HOU_1794/USA300HOU_1796 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (15/13); new base G (7/12); total (22/25) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.73e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.23e-01 | |||||||||||
TAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTA > CP000730/1929667‑1929941 | taaAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGatat < 1:239638/141‑1 (MQ=255) aaaTCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATCTAACTCATCTGAAGCAAGTGACTGTGCTTGTATATTTGCCgatgatcgaa > 1:29218/1‑137 (MQ=255) aaTCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCCGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATataat > 1:241423/1‑141 (MQ=255) aaTCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGATTGTATATTTGCCGataatataat > 1:254164/1‑141 (MQ=255) tCGCCTACTTTCTTAAATTAACAATATCTATTCTCCTAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAAtag > 1:155225/1‑141 (MQ=255) ttCTTAAATTAACAATATCTATTCTCGTAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGCCTGTGATGGTATATTTGCCGTAGAGATAATGTTagagcggc > 1:122341/1‑137 (MQ=25) aCAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCAAGAATCATATAACTTATCAGAAGCAAGTGACGGTGCTTGTATATTTGCCGATGATATAATAGTAGAGGCGCCTATCTCTCAg > 1:351220/1‑141 (MQ=255) cAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAgg > 1:257350/1‑141 (MQ=255) aGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCAGATGAGATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCa < 1:337362/141‑1 (MQ=255) ttggTCCAAGTAAGTGTAGACGATTCAATCGATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTAAATTTGCCGATAATATAATAGTAGAGTCGCCTATCTCTCAGGCATCAATTTAGACGCagaga < 2:224567/138‑1 (MQ=255) ttGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCagagag < 1:141453/141‑1 (MQ=255) gTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGAGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAgcggg > 2:66977/1‑140 (MQ=255) ccAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGTCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGaggagg > 2:249357/1‑141 (MQ=255) aTTCAATCTATCAGCTAGAATCGTATAACTGATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCtt < 1:272708/141‑1 (MQ=255) aTTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTCGAGTCGCCTATCTCTCAGTCGTCAATTTAGACGCAGAATGGAGATGTA‑TAA‑G‑G‑TGCTGCtt > 2:205052/1‑141 (MQ=255) tCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAt < 1:151651/141‑1 (MQ=255) aaTCCATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAAGAGGTGTA‑TAA‑G‑G‑TGATGCTTAt‑‑tt < 1:206777/141‑1 (MQ=255) tCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTc < 2:257350/141‑1 (MQ=255) gCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTAAATTTAGACGAAGAGAGGAGGTGTA‑GNA‑N‑G‑NGATGCTTAT‑‑TTTAGT‑Tcaca > 1:265429/1‑141 (MQ=255) atatAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCAc < 1:289258/141‑1 (MQ=255) atatAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGAA‑TAA‑G‑G‑TGATGCTTCT‑‑TTTCGT‑TCACATCTTAGCAc > 1:65610/1‑141 (MQ=255) taACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAg < 2:287930/141‑1 (MQ=255) aTCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGtcatca > 2:148616/1‑141 (MQ=255) tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAg > 1:106868/1‑141 (MQ=255) tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAg > 1:134483/1‑141 (MQ=255) tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAg > 1:150063/1‑141 (MQ=255) atcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGc < 1:110454/127‑1 (MQ=255) tcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATATCACCAGTCATCAGTGGCt > 2:106091/14‑141 (MQ=255) ggaagtagataggCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCtgt < 2:14923/129‑1 (MQ=255) gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACTAGTCATCAGTGGCtgtg > 1:346576/11‑141 (MQ=255) gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCtgtg < 1:127911/131‑1 (MQ=255) aagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGc < 1:5700/132‑1 (MQ=255) aagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGc > 2:251848/10‑141 (MQ=255) aGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGc > 2:119275/1‑141 (MQ=255) aGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGc < 1:57279/141‑1 (MQ=255) tagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TTTGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGctgt < 2:205543/135‑4 (MQ=255) gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTTTCAGGTGTCAA‑‑TCGACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg < 1:67338/137‑6 (MQ=255) atatgCTTGTATATTCACAGATGGTATAATAATAGCGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGctgttgc < 2:184533/138‑7 (MQ=255) ttgCTTGTATTCTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCg < 2:245553/140‑1 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GCCGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:291399/2‑141 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:189774/2‑141 (MQ=255) atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:163342/2‑141 (MQ=255) atgCTTGTATATTCACAGAGGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTTAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt > 1:232664/2‑141 (MQ=255) cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt < 2:216324/141‑4 (MQ=255) cTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatt < 2:275754/141‑4 (MQ=255) ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta < 2:173931/141‑5 (MQ=255) ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta < 1:251848/141‑5 (MQ=255) tatattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑TTTGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatac > 1:261721/11‑137 (MQ=255) tataTTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑CTT‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatac < 1:96084/141‑8 (MQ=255) tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTA‑C‑T‑T‑‑TGCTAATGGTTACTTATCACATCATAGCACCAGTCATCAGGGGCTGGGCTGTTGCGTATTATACtt > 1:99374/9‑141 (MQ=255) cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg > 2:197643/5‑141 (MQ=255) acagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTTTTGCGTATTATACTTATTgg < 1:217272/138‑1 (MQ=255) ccGATGATATAATAGTAGAGGCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCCGTTATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg < 2:58816/141‑1 (MQ=255) cagatggtATAATAATAGAGGCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc < 1:175042/139‑1 (MQ=255) cGAGGATATAATAGGAGAGTCGCCGATGTCTCAGGCGGCAATGTAGGCGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCAGAGCACCAGTCATCAGTGGCTGTGCCACTGCGTTTTTTTCTTATTGGc < 1:270609/141‑1 (MQ=255) agatggtATAATAAAAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTAC‑T‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt > 2:243199/2‑141 (MQ=255) gatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACT‑T‑TGCTAATCAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt > 1:87064/1‑140 (MQ=255) | TAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAA‑G‑G‑TGATGCTTAT‑‑TTTCGT‑TCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTA > CP000730/1929667‑1929941 |
| 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: ‑ |