Predicted mutation | |||||||
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evidence | seq id | position | mutation | freq | annotation | gene | description |
RA | USA300TCH1516_ALE | 792,942 | A→T | 5.5% | intergenic (+27/‑250) | ltaS → / → ettA | Lipoteichoic acid synthase/Energy‑dependent translational throttle protein EttA |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | USA300TCH1516_ALE | 792,942 | 0 | A | T | 5.5% | 384.8 / 10.1 | 110 | intergenic (+27/‑250) | ltaS/ettA | Lipoteichoic acid synthase/Energy‑dependent translational throttle protein EttA |
Reads supporting (aligned to +/- strand): ref base A (33/71); new base T (4/2); total (37/73) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 1.76e-01 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
Only 100 of 123 total aligned reads displayed.
CAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAGATCATTAGCA > USA300TCH1516_ALE/792852‑793032 | cAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATaa < 1:431528/91‑1 (MQ=255) cAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATaa < 1:1559040/91‑1 (MQ=255) cAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATaa < 1:722829/91‑1 (MQ=255) aaaaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATaaa < 1:1198113/91‑1 (MQ=255) aaaaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATaaa < 1:1927053/91‑1 (MQ=255) aaaaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATaaa < 1:312502/91‑1 (MQ=255) aaaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATaaaa > 1:2698534/1‑91 (MQ=255) aaaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCGAAAAAATAATATCTAAACACGAACTCGGATTGATaaaa < 1:1162517/91‑1 (MQ=255) aaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAat < 1:1133456/91‑1 (MQ=255) aaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAat > 1:1598144/1‑91 (MQ=255) aaaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAat < 1:397918/91‑1 (MQ=255) aaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAata < 1:864654/91‑1 (MQ=255) aaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAata < 1:3075112/91‑1 (MQ=255) aaGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAata < 1:1174676/91‑1 (MQ=255) ggTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATc < 1:2513749/91‑1 (MQ=255) gTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATTTAAACACGAACTCGGATTGATAAAATATCa > 1:3279343/1‑91 (MQ=255) gTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCa > 1:3477197/1‑91 (MQ=255) aaTCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATc < 1:1920456/91‑1 (MQ=255) aTCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATcc < 1:422278/91‑1 (MQ=255) aTCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATcc < 1:1073042/91‑1 (MQ=255) tCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCg > 1:466300/1‑91 (MQ=255) ccTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCgg < 1:1721443/91‑1 (MQ=255) ccTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCgg < 1:3093606/91‑1 (MQ=255) tCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACCCGGATTGATATTTTATCAATCCGAGtt < 1:546083/91‑1 (MQ=25) cGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGttt < 1:2752841/91‑1 (MQ=255) gAAGTATAAATGTGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGtttt < 1:3766200/91‑1 (MQ=255) aaGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGttttt < 1:1288403/91‑1 (MQ=255) aaGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGttttt < 1:1561805/91‑1 (MQ=255) aGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTtta < 1:1498709/91‑1 (MQ=255) gTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTttat < 1:1957505/91‑1 (MQ=255) gTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTttat < 1:321946/91‑1 (MQ=255) gTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTttat < 1:2138239/91‑1 (MQ=255) tataAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTttatt > 1:3696717/1‑91 (MQ=255) tataAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTttatt < 1:3151251/91‑1 (MQ=255) tataAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTttatt > 1:301154/1‑91 (MQ=255) ataAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTttatta < 1:3013994/91‑1 (MQ=255) ataAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACGCGGATTGATAAAATATCAATCCGGGTTTttatta < 1:539679/91‑1 (MQ=255) aaaTATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATg < 1:2864862/91‑1 (MQ=255) aaaTATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATg < 1:504078/91‑1 (MQ=255) aaaTATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATg < 1:2559094/91‑1 (MQ=255) aaaTATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATg < 1:2298371/91‑1 (MQ=255) aaaTATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATg < 1:505571/91‑1 (MQ=255) aaTATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGt > 1:2476421/1‑91 (MQ=255) aaTATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGt > 1:3331052/1‑91 (MQ=255) tatGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTc > 1:2682321/1‑91 (MQ=255) tatGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTc > 1:561483/1‑91 (MQ=255) aaCAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTta > 1:2552881/1‑91 (MQ=255) aCAGGCCCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTtat < 1:2440064/91‑1 (MQ=255) aGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTatat > 1:855260/1‑91 (MQ=255) aGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTatat > 1:855809/1‑91 (MQ=255) cTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGt < 1:2845845/91‑1 (MQ=255) aaaGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGttt > 1:3242532/1‑91 (MQ=255) aaGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGtttt < 1:3670451/91‑1 (MQ=255) aaGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGtttt > 1:916421/1‑91 (MQ=255) aaCTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACAtt > 1:1770610/1‑91 (MQ=255) aaCTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACAtt < 1:2016115/91‑1 (MQ=255) aaCTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACAtt > 1:59060/1‑91 (MQ=255) aaCTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACAtt > 1:60363/1‑91 (MQ=255) aCTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATta < 1:3827426/91‑1 (MQ=255) tctAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATtata < 1:2347727/91‑1 (MQ=255) tAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATAtg > 1:2994988/1‑91 (MQ=255) tAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATAtg > 1:749249/1‑91 (MQ=255) aaaaaaTAATATCTAAACACGAACTCGGACTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATAtgt > 1:1766629/1‑91 (MQ=255) aaaaaTAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATAtgtg > 1:625333/1‑91 (MQ=255) aaaaaTAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATAtgtg < 1:260504/91‑1 (MQ=255) aaaaaTAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATAtgtg < 1:1496517/91‑1 (MQ=255) aaaaTAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATgtgt < 1:1280195/91‑1 (MQ=255) aaaaTAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATgtgt < 1:2847340/91‑1 (MQ=255) ataataTCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGa < 1:1620195/91‑1 (MQ=255) atatCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATaa < 1:1839599/91‑1 (MQ=255) tatCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATGTGTGTTGATaaa < 1:3200205/91‑1 (MQ=255) tatCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATaaa < 1:1479037/91‑1 (MQ=255) atCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATaaaa < 1:1707033/91‑1 (MQ=255) tCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATTTGTTGATaaaaa < 1:3173036/91‑1 (MQ=255) tCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATaaaaa < 1:2448777/91‑1 (MQ=255) aaaCACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGt < 1:545859/91‑1 (MQ=255) aaCACGAACTCGGATTGCTAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGta < 1:3553285/91‑1 (MQ=255) aaCACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGta < 1:4130878/91‑1 (MQ=255) aaCACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGta < 1:2893314/91‑1 (MQ=255) aaCACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGta < 1:3637233/91‑1 (MQ=255) aaCACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGta < 1:2217930/91‑1 (MQ=255) cacGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGtata < 1:2862073/91‑1 (MQ=255) acGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTatat < 1:2780464/91‑1 (MQ=255) aCTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTCGATAAAAAGGTATATtata > 1:255145/1‑91 (MQ=255) cccGGATTGATATTTTATCAATCCGAGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaa > 1:1647420/3‑91 (MQ=37) cTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaa < 1:1283089/91‑1 (MQ=255) cTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaa < 1:1306092/91‑1 (MQ=255) cTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaa > 1:318766/1‑91 (MQ=255) cTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaa < 1:3634649/91‑1 (MQ=255) cTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaa > 1:1773087/1‑91 (MQ=255) tCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaaa > 1:2491478/1‑91 (MQ=255) ccGGATTGATATTTTATCAATCCGAGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaaa > 1:3244475/2‑91 (MQ=37) ccGGATTGATATTTTATCAATCCGAGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATaaa > 1:537063/2‑91 (MQ=37) cGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAg < 1:367339/91‑1 (MQ=255) cGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAg < 1:1454594/91‑1 (MQ=255) aTTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAGATc < 1:3265860/91‑1 (MQ=255) aTTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAGATc < 1:3264593/91‑1 (MQ=255) gATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAGATCAtt > 1:1597123/1‑91 (MQ=255) tAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAGATCATTAg < 1:1811458/91‑1 (MQ=255) aaaTATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAGATCATTAGCa > 1:1580616/1‑91 (MQ=255) | CAAAAAGGTAAATCCTTCGAAGTATAAATATGAAACAGGACCTAAAGCAAACTCTAAAAAATAATATCTAAACACGAACTCGGATTGATAAAATATCAATCCGGGTTTTTATTATGTTCTTTTATATTATGTTTTACATTATATGTGTTGATAAAAAGGTATATTATAAAGATCATTAGCA > USA300TCH1516_ALE/792852‑793032 |
Alignment Legend |
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Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |