Predicted mutation | |||||||
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evidence | seq id | position | mutation | freq | annotation | gene | description |
RA | USA300TCH1516_ALE | 41,166 | G→A | 16.8% | intergenic (‑33/‑67) | pbp ← / → mecR1 | Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | USA300TCH1516_ALE | 41,166 | 0 | G | A | 16.8% | 863.2 / 148.6 | 354 | intergenic (‑33/‑67) | pbp/mecR1 | Beta‑lactam‑inducible penicillin‑binding protein/Methicillin resistance mecR1 protein |
Reads supporting (aligned to +/- strand): ref base G (168/124); new base A (13/46); total (182/172) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 6.57e-07 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-03 |
Only 100 of 373 total aligned reads displayed.
TACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTA > USA300TCH1516_ALE/41076‑41256 | taCCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTgtag < 2:3414985/91‑1 (MQ=255) ccAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTgtagta < 1:3602199/91‑1 (MQ=255) cAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGtat < 1:2804050/91‑1 (MQ=255) aaaCCCGACAACTACAACTATTAAAGTAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGtata < 1:3689920/91‑1 (MQ=255) aaaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtata < 1:1909851/91‑1 (MQ=255) aaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATGCTCCTTATATAAGACTACATTTGTAGTatat < 1:2647675/91‑1 (MQ=255) aaCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTatat < 1:2216636/91‑1 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATAtt > 1:2833892/1‑91 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact < 2:1205889/91‑3 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact < 1:2336755/91‑3 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact < 2:2193053/91‑3 (MQ=255) aCCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatact < 2:494716/91‑3 (MQ=255) cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatacta < 1:3850049/91‑4 (MQ=255) cccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAAtatacta < 1:2519789/91‑4 (MQ=255) ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTAc > 1:894902/1‑91 (MQ=255) ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac < 1:2770270/91‑1 (MQ=255) ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac < 2:3642166/91‑1 (MQ=255) ccGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTATCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac < 1:876067/91‑1 (MQ=255) cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATCTTTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATAtactac < 1:3043828/91‑1 (MQ=255) cGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACa > 1:1984079/1‑91 (MQ=255) caactacaactaTTAAAATAAGTGGAACCATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACaaaa > 2:1391945/1‑90 (MQ=255) caactacaactaTTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAATATACTACAAAt < 2:3142198/91‑1 (MQ=255) actacaactaTTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACCCCTTATATAAGACTACATTTGTAGTATATTACAAATgt > 2:763508/1‑91 (MQ=255) acaactaTTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATgtagt > 1:468190/1‑91 (MQ=255) taTTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTa > 2:1186657/1‑91 (MQ=255) taTTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTa < 1:3233105/91‑1 (MQ=255) aTTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTAt > 1:1619673/1‑91 (MQ=255) ttAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATg > 2:2860388/1‑91 (MQ=255) ttAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATg > 2:3048069/1‑91 (MQ=255) tAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGt < 1:1339448/91‑1 (MQ=255) aaaTAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCa < 1:2118424/91‑1 (MQ=255) aTAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCaaa > 2:1016979/1‑91 (MQ=255) aaGTGGAACAATTTTTTTT‑TTTTTCTTCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaat > 2:3797166/1‑91 (MQ=255) aaGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaat > 1:1739175/1‑91 (MQ=255) aaGTGGAAATATTTTTATG‑TTTTTCATCAATATACGCCTTATATATAACTACATTTGTTGTATATTACAAATGTAGTATTTATGTCaaatt < 2:3717257/91‑3 (MQ=255) gTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaataa > 2:2085621/1‑91 (MQ=255) tGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAaataat > 1:2727425/1‑91 (MQ=255) tGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAAGGTAGTATTTATGTCAAaataat < 2:1427106/91‑1 (MQ=255) ggAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATg > 1:1282943/1‑91 (MQ=255) ggAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATg > 2:411462/1‑91 (MQ=255) gAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGt < 1:3453174/91‑1 (MQ=255) gAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGt > 1:816602/1‑91 (MQ=255) aaCAATTTTTATC‑TTTTTCATCAATATGCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCATAATAATGtt < 2:1547504/91‑1 (MQ=255) aaCAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGtt < 2:2798256/91‑1 (MQ=255) aaCAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGtt < 2:576144/91‑1 (MQ=255) cAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat < 2:2779881/91‑1 (MQ=255) cAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat > 2:654540/1‑91 (MQ=255) cAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTGGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTtat < 2:321614/91‑1 (MQ=255) cAATTTTTAGC‑TTTTGCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAGATGTAGTATTTATGTCAAAATAATGTtat < 2:1301731/91‑1 (MQ=255) tttttATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAt < 2:1261851/91‑1 (MQ=255) ttATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAtttt < 2:3661688/91‑1 (MQ=255) tATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAAttttt > 2:3110749/1‑91 (MQ=255) tC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTtgt < 1:1409637/91‑1 (MQ=255) tttttCATCGATATACTCCTTATATAAGACTACATTTGTTGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGa < 2:1439916/91‑1 (MQ=255) tttttCATCAATATACTCCTTATATAAGGCTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGa < 2:2323584/91‑1 (MQ=255) ttttCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTCTAATTTTTGAGat > 2:1863247/1‑91 (MQ=255) tcatcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATg > 2:3544989/1‑91 (MQ=255) atcaATATACTCCTTATATAAGACTACCTTTGTATTATATTACTAATGTTGTATTTATGTCAAAATTATGTTCTCATTTTTGTTATATGGa > 2:1583698/1‑91 (MQ=255) atcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGa < 1:2256149/91‑1 (MQ=255) tcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg > 1:3118016/1‑91 (MQ=255) tcaATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAg < 2:2452646/91‑1 (MQ=255) caATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg > 2:1135497/1‑91 (MQ=255) caATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAgg > 1:329698/1‑91 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt > 2:1626156/1‑91 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt > 2:3336010/1‑91 (MQ=255) aaTATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgt > 2:2720485/1‑91 (MQ=255) atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg > 1:1818216/1‑91 (MQ=255) atatACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtg < 1:1213878/91‑1 (MQ=255) tataCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGgtgt > 2:1871334/1‑91 (MQ=255) ataCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTa < 1:2690149/91‑1 (MQ=255) ataCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTa < 2:3907597/91‑1 (MQ=255) taCTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAg > 2:3791128/1‑91 (MQ=255) ccTTATATAAGACTACATTTGTAGTATATTACAGATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAgcatg > 2:2519821/1‑87 (MQ=255) ccTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAgg < 1:540295/91‑1 (MQ=255) ccTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAgg > 2:2975537/1‑91 (MQ=255) cTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgt > 1:2426146/1‑91 (MQ=255) cTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgt > 1:144248/1‑91 (MQ=255) tatataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGgtgt < 1:791792/91‑1 (MQ=255) aatataAAACTACATTTGTAGTATATTACAAATTTACTATTTATGTCAAAATAATTTTAGAATTTTTGTGAGATGGATGTGTAGAAGgtgt < 2:3573316/90‑1 (MQ=255) tataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTa < 2:1642747/91‑1 (MQ=255) tataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTa < 2:2597300/91‑1 (MQ=255) ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat > 2:1844566/1‑91 (MQ=255) ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat < 2:1499582/91‑1 (MQ=255) ataAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTat < 1:3003922/91‑1 (MQ=255) aGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTatcat > 2:2992803/1‑91 (MQ=255) cTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtt > 2:212611/1‑91 (MQ=255) tACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttt < 2:1820461/91‑1 (MQ=255) tACATTTGTAGTATATTACAAATGTAGAATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttt > 2:2027637/1‑91 (MQ=255) aCATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCtttt < 1:1855412/91‑1 (MQ=255) cATTTGTAGTATATTACAAATGTAGTCTTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt > 2:2239689/1‑91 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATTTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt < 1:3371523/91‑1 (MQ=255) cATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCttttt > 1:1042040/1‑91 (MQ=255) aTTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGCTATGGAGGTGTAGAAGGTGTTATCATCtttttt > 2:932276/1‑91 (MQ=255) tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa > 2:1087607/1‑91 (MQ=255) tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa > 1:642662/1‑91 (MQ=255) tttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTa < 1:1136271/91‑1 (MQ=255) ttGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGGTATGGAGGTGTAGAAGGTGTTATCATCTTTTTTaa < 2:228753/91‑1 (MQ=255) ttGTAATATACTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTaa > 2:586524/1‑91 (MQ=255) agtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGtt > 1:1000001/1‑91 (MQ=255) gtaTATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTa < 1:3197510/91‑1 (MQ=255) | TACCAAACCCGACAACTACAACTATTAAAATAAGTGGAACAATTTTTATC‑TTTTTCATCAATATACTCCTTATATAAGACTACATTTGTAGTATATTACAAATGTAGTATTTATGTCAAAATAATGTTATAATTTTTGTGATATGGAGGTGTAGAAGGTGTTATCATCTTTTTTAATGTTA > USA300TCH1516_ALE/41076‑41256 |
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |