Predicted mutation | |||||||
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evidence | seq id | position | mutation | freq | annotation | gene | description |
RA | NC_002947 | 5,256,864 | T→A | 8.2% | intergenic (+16/+29) | PP_5703 → / ← PP_4634 | type III effector protein HopJ/alpha/beta family hydrolase |
Read alignment evidence... | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NC_002947 | 5,256,864 | 0 | T | A | 8.2% | 144.5 / 3.5 | 57 | intergenic (+16/+29) | PP_5703/PP_4634 | type III effector protein HopJ/alpha/beta family hydrolase |
Reads supporting (aligned to +/- strand): ref base T (24/27); new base A (2/3); total (27/30) | |||||||||||
Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.65e-01 |
GCCTTCGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATT > NC_002947/5256717‑5257010 | gCCTTCGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTACCGACCATGGCAACATCCGTGAACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCtt > 5:142209/1‑149 (MQ=255) gCCTTCGGCGAGAACTACCGTGATGTGTTGGCCACGACTGAGGGTAGCGACCATGGCAACATCCGTGCACTGTTCAAACACGGTCTGGCGGGCGTGAAGTTTGATGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGACGGGGCCGCtt > 7:334570/1‑149 (MQ=255) ccTTCGGCGATCACTTCCGTGATGTGTTGTCCACGCCTGAGGTTAGCGACCATGGCAACATCCGTGCACTGTTCAAACAGGGTCTGGCGGGCGTTAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCttt < 8:334570/149‑1 (MQ=255) aGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCa < 4:188940/149‑1 (MQ=255) aGCACTACCGTGATGTGTTGGCCACGCCGGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCAAAGCGGccccg < 2:315022/149‑2 (MQ=255) cACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCAAAGCGGccccggc < 4:98168/149‑4 (MQ=255) cTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCATTGCGGCCCCCCGa > 4:196302/1‑148 (MQ=255) tACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATc > 1:3130/1‑149 (MQ=255) tgtTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCAc > 7:88474/1‑149 (MQ=255) ggCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCt < 8:88474/148‑1 (MQ=255) cACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAAt > 8:282768/1‑149 (MQ=255) cACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAAt > 6:2298/1‑149 (MQ=255) cACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAAt > 2:157783/1‑149 (MQ=255) aCGCCTGAGGGTAGCGACCGTGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATc < 7:103553/149‑1 (MQ=255) ccTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCat < 3:197493/149‑1 (MQ=255) cTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCat > 1:117105/1‑148 (MQ=255) aGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGCGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCatgatg < 6:87042/149‑1 (MQ=255) ggTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGc > 7:216698/1‑113 (MQ=255) ggTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGc < 8:216698/113‑1 (MQ=255) ggTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGt < 2:3130/149‑1 (MQ=255) ggTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGt < 7:311466/149‑1 (MQ=255) cGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAg > 7:38272/1‑149 (MQ=255) aCATCCTTGCACTGATCAAACAGGGTGTGGCGGGCGGGAAGTTTGCTGCGCAGCCGCTTGCGGGCAAGGGTTGTGATTGCGGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCt < 3:196302/149‑1 (MQ=255) cGTGCACTGACCAAACACGGTCTGGCGGGCTGGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑Tcc < 6:285059/147‑1 (MQ=255) tGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGcc < 1:232805/149‑1 (MQ=255) cACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTc < 2:117105/149‑1 (MQ=255) aCTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGc < 4:366934/145‑1 (MQ=255) aCTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGc > 3:366934/1‑145 (MQ=255) aCTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTcc > 2:104586/1‑149 (MQ=255) tCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGc > 1:16925/1‑149 (MQ=255) aaCACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATc < 1:302719/88‑1 (MQ=255) aaCACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCCCGTTTCGGCCCCACGaaa > 2:302719/1‑86 (MQ=255) gcgggcgTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGc > 4:237345/1‑147 (MQ=255) tGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTTCCGCCCCACGAAACTGCCCCCACCCAGAAACCAATATAGTTCCCAGACCCCCCCCT‑‑ACCAGCCACCCCACACCCAACCACAGCAAAGGCAcc > 8:22035/1‑149 (MQ=255) gTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGcc > 1:150894/1‑149 (MQ=255) tttGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCca > 7:184210/1‑149 (MQ=255) ctgcGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAgg < 7:282768/149‑1 (MQ=255) gcAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCCCCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCACCCCCTGCAAGGCCCCCGGCCACCGCCttt > 5:371758/1‑149 (MQ=255) cAGCCGCGTGCGCGCATGGCTTGAGATGGCCGGGGCCGCTTGGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTc < 6:276225/149‑1 (MQ=255) gCCGCTGGCGCCAATGGCTTGAGCTGGCGGGGGCCGCTTGGCGCCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTcgc < 1:205623/149‑1 (MQ=255) ccGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGCTCCTGCGCCCCCCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCCCCGGCCACAGGCTTTcgc > 7:83640/1‑148 (MQ=255) ccGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCCGGCCCCCCGCCT‑‑TCCAGCCAACCCAGCCGCAACCACTGCAACGCCCCCCGCCACAAGCATTcgc > 8:229381/1‑148 (MQ=255) gCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGa > 7:161978/1‑148 (MQ=255) gcgcgcAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAAc < 8:161978/147‑1 (MQ=255) gcAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCAGCCCCCACCCACAAACCAAGATGGTGCCACGCCCCCCGCCT‑‑TCCAGCCACCCCATCCGCAACCACTGCAAAGCCACCGGCCACAGGCATTCGCGAAACCCGTc > 2:325325/1‑148 (MQ=255) aaGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATg < 7:229381/149‑1 (MQ=255) ggCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTCCTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATg < 1:325325/149‑1 (MQ=255) ggCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGa < 1:104586/149‑1 (MQ=255) ttGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGaaa > 6:376104/1‑148 (MQ=255) gagaTTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGaaaaa < 5:2298/148‑1 (MQ=255) aTTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCAc < 7:87668/98‑1 (MQ=255) aTTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCAc > 8:87668/1‑98 (MQ=255) ccGGGGCCGCTTTGCGGCCCCACGATCCTGCGCGCACCCTCAATCGATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGATACCGGTCATGGAAAAACGCGAAAt < 7:22035/149‑1 (MQ=255) tggggCCGCAAAGCGGCCCCGCGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCgg > 6:375966/2‑129 (MQ=255) tggggCCGCAAAGCGGCCCCGCGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCgg < 5:375966/128‑1 (MQ=255) cGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATg < 2:16925/149‑1 (MQ=255) ggCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGcc < 3:237345/149‑1 (MQ=255) gCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCg < 6:51270/124‑1 (MQ=255) gCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCg > 5:51270/1‑124 (MQ=255) gCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCTCCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAAtt > 1:332384/1‑149 (MQ=255) | GCCTTCGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCT‑‑TCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAATT > NC_002947/5256717‑5257010 |
Alignment Legend |
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Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |