| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | USA300TCH1516_ALE | 2,072,011:1 | +A | 6.6% | intergenic (+506/+67) | USA300HOU_RS10445 → / ← USA300HOU_RS10450 | hypothetical protein/hypothetical protein |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 2,072,011 | 1 | . | A | 6.6% | 240.5 / 11.2 | 61 | intergenic (+506/+67) | USA300HOU_RS10445/USA300HOU_RS10450 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (32/25); new base A (2/2); total (34/27) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 | |||||||||||
TGCCAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCAATAT > USA300TCH1516_ALE/2071921‑2072100 | tGCCAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGat < 1:3718522/91‑1 (MQ=34)tGCCAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGat > 1:1427398/1‑91 (MQ=33) ccAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGat‑at > 1:3668929/1‑91 (MQ=34) ccAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGat‑at > 1:668533/1‑91 (MQ=34) aGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑Attt < 1:2357263/91‑1 (MQ=34) tCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTc > 1:1291046/1‑91 (MQ=34) aGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACAAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAAt > 1:4138943/1‑91 (MQ=21) gACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAAtt < 1:2832130/91‑1 (MQ=34) aCCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑g < 1:1547509/91‑1 (MQ=34) aCCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑g < 1:653558/91‑1 (MQ=34) aCCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑g < 1:1547496/91‑1 (MQ=34) aCCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑g > 1:1341409/1‑91 (MQ=34) ccAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑Ga > 1:3244420/1‑91 (MQ=33) cAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑Gaa > 1:461948/1‑91 (MQ=32) cAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑Gaa < 1:2194429/91‑1 (MQ=32) cAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑Gaa < 1:2194372/91‑1 (MQ=32) aGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTa < 1:1384085/91‑1 (MQ=31) gTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTaa < 1:2010221/91‑1 (MQ=32) tATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTaaa > 1:602115/1‑91 (MQ=33) tATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTaaa > 1:2077910/1‑91 (MQ=33) aTTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAAt > 1:2298306/1‑91 (MQ=34) ttGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATg > 1:1412371/1‑91 (MQ=35) tGTATAAATAGAGAACAGCAGTAAGAA‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGt < 1:3030107/91‑1 (MQ=255) gTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGtt > 1:2181391/1‑91 (MQ=38) gTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGtt > 1:1293517/1‑91 (MQ=38) tataAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGtta > 1:4128324/1‑91 (MQ=39) ataAATAGAGAACAGCAGTAAGATAATTTTCAATTA‑GAAAA‑TATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGttat < 1:1269775/91‑1 (MQ=11) ataAATAGAGAACAGCAGTAAGATAATTTTC‑AATTAGAAAA‑TATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGttat < 1:1269383/91‑1 (MQ=11) ataAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGttat < 1:1778918/91‑1 (MQ=40) ataAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGttat < 1:1777900/91‑1 (MQ=40) aaaTAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGttatta > 1:3992393/1‑91 (MQ=255) aaaTAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGttatta > 1:3522207/1‑91 (MQ=255) aaTAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAg < 1:2132211/91‑1 (MQ=255) aTAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGt < 1:3768336/91‑1 (MQ=255) aTAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGt < 1:1762033/91‑1 (MQ=255) aTAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGt < 1:3400672/91‑1 (MQ=255) tAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGtt > 1:685406/1‑91 (MQ=255) tAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGtt < 1:1387606/91‑1 (MQ=255) tAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGtt < 1:222444/91‑1 (MQ=255) gagaACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTAt > 1:361944/1‑91 (MQ=255) agaACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTAtt > 1:2995190/1‑91 (MQ=255) agaACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTAtt > 1:3456973/1‑91 (MQ=255) agaACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTAtt < 1:2725666/91‑1 (MQ=255) gaACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTAttt > 1:4084601/1‑91 (MQ=255) aaCAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTAtttt < 1:2748919/91‑1 (MQ=255) aCAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCAGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTAttttt > 1:1562629/1‑91 (MQ=255) cagcagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTa > 1:2126812/1‑91 (MQ=255) agcagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTAc > 1:2775860/1‑91 (MQ=255) agcagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTAc > 1:2775970/1‑91 (MQ=255) gcagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACt > 1:501990/1‑91 (MQ=255) gcagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACt > 1:4148700/1‑91 (MQ=255) gcagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACt < 1:4108091/91‑1 (MQ=255) cagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACtt > 1:403928/1‑91 (MQ=255) cagTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACtt < 1:2016248/91‑1 (MQ=255) cagCAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTACTTATTTTTACtt < 1:3206976/91‑1 (MQ=255) agTAAGATAATTTTC‑AATTAGAAAA‑TATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCAAAATGTTATTAGTTATTTTTACttt > 1:2810516/1‑91 (MQ=17) agTAAGATAATTTTC‑AATT‑AGAAAATATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACttt > 1:3804176/1‑91 (MQ=18) agTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACttt > 1:3835218/1‑91 (MQ=255) agTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACttt > 1:597378/1‑91 (MQ=255) agTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACttt < 1:1064889/91‑1 (MQ=255) aaGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCaa > 1:656141/1‑91 (MQ=255) aaGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCaa > 1:2135407/1‑91 (MQ=255) aaGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCaa > 1:1692801/1‑91 (MQ=255) aGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCAat < 1:3794742/91‑1 (MQ=255) gAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCAata > 1:3081622/1‑91 (MQ=255) at‑atTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCAatat < 1:1713566/91‑1 (MQ=255) | TGCCAGTCGAAGACCAAGGCTGAGACGGCACCCTAGGAAAGCGAAGCCATTCAATACGAAGTATTGTATAAATAGAGAACAGCAGTAAGAT‑ATTTTCTAATT‑GAAAATTATCTTACTGCTGTTTTTTAGGGATTTATGTCCCAGCCTCTAAATGTTATTAGTTATTTTTACTTTCAATAT > USA300TCH1516_ALE/2071921‑2072100 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |