Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,143,110 G→A 49.5% V163V (GTG→GTA)  USA300HOU_RS10935 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,143,1100GA49.5% 0.6 / 36.7 32V163V (GTG→GTA) USA300HOU_RS10935hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (9/7);  new base A (9/7);  total (18/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

AAAGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCTGTTCCAAT  >  USA300TCH1516_ALE/2142972‑2143250
                                                                                                                                          |                                                                                                                                            
aaaGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGc                                                                                                                                            >  2:300624/1‑141 (MQ=255)
          attattGCTCGAAAAATACCTATATTTATCTTCTTTGTCTCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAAGCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTattatt                                                                                                                                  <  1:414897/141‑1 (MQ=255)
                 cTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTacaa                                                                                                                           <  1:9678/141‑1 (MQ=255)
                     aaaaaTACCTATATTTATCTTCTTTGTATATATTATTGGTCATTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGt                                                                                                                       >  2:222511/1‑141 (MQ=255)
                         aTACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGt                                                                                                                   <  1:330018/141‑1 (MQ=255)
                           aCCTATATTTATCTTATTTGTATCTATTATTGGTCCTTTGTTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTc                                                                                                                 >  1:186022/1‑141 (MQ=255)
                                           tttGTATCTATTATTGGTCCTTTCTTAGAAGAATGTGTATTCAGAAAAGTAATCTTTGGAAAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCTTTTGTTATTGCTACAACTGTAAGTTCATTAATATTTGccgta                                                                                                 >  1:6257/1‑137 (MQ=255)
                                           taggTAGCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCCTTa                                                                                                 >  2:95223/4‑141 (MQ=255)
                                              gTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGca                                                                                              <  2:551717/141‑1 (MQ=255)
                                              gTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTCTGGTGGCTGAAGTAAGTCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGca                                                                                              <  1:552491/141‑1 (MQ=255)
                                                 tCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACCACAGTACGTTCATTAATATTTGCATTAGcacaa                                                                                           >  2:208359/1‑140 (MQ=255)
                                                 tCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAgacaat                                                                                           >  1:262065/1‑136 (MQ=255)
                                                  cTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATa                                                                                          >  1:355114/1‑141 (MQ=255)
                                                        ttGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGAtt                                                                                    <  1:43982/141‑1 (MQ=255)
                                                            tCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCaa                                                                                <  1:541299/141‑1 (MQ=255)
                                                            tCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCaa                                                                                >  1:188111/1‑141 (MQ=255)
                                                             ccTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCTATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCaaa                                                                               >  1:132000/1‑141 (MQ=255)
                                                                ttattaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAAttt                                                                            >  2:386678/1‑141 (MQ=255)
                                                                ttattaGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAAttt                                                                            >  2:387164/1‑141 (MQ=255)
                                                                ttaatcgaagaaCAAGTATTCGACAACGTAATCTTTGGAGAATTATTTAATGCGATGAAAGGTAATCGTATCGTAGCATTTATTAGTGCTACAACAGTAAGTTCATTAATAGTTGCATTAGCACATAATGATTTCAAAttt                                                                            <  1:126262/135‑1 (MQ=255)
                                                                   taagaagaagaTGTATTCAGAAAGGTAATCTTTTGAGAATTATTTAAGGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTAtt                                                                         <  2:89258/139‑1 (MQ=255)
                                                                     agaagaATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTACCACATAATGATTTCAAATTTATTcc                                                                       >  2:153345/1‑141 (MQ=255)
                                                                           atatGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTa                                                                 <  1:112042/141‑1 (MQ=255)
                                                                               gTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAGTTTCTTCCAGTTTAttgt                                                             >  2:44289/1‑139 (MQ=255)
                                                                                       aaaaGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATggg                                                     <  1:222511/141‑1 (MQ=255)
                                                                                         aaGTAATTTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGgtg                                                   <  2:104739/141‑1 (MQ=255)
                                                                                          aGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGgtgt                                                  >  2:399799/1‑141 (MQ=255)
                                                                                                    ggAGAATTATTTAATGCGATTAAAAGTAATCGGATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATATTGATTTCAAATTTATCCCGGTGTATTTTGGTATAGGGGTCGTTTTTTct                                        >  1:92998/1‑140 (MQ=255)
                                                                                                                             gTAATCGTATCGTGGCATTTATTATGGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGc               <  1:150421/141‑1 (MQ=255)
                                                                                                                              tAATCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGAGTAATTTTTTAATGCGAATATGTATGGACAAACCCGCt              >  2:384931/1‑141 (MQ=255)
                                                                                                                               aaTCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCtt             <  2:355114/141‑1 (MQ=255)
                                                                                                                               aaTCGTATCGTAGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCtt             >  2:448543/1‑141 (MQ=255)
                                                                                                                                          ggCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAAAGGCTTGCTGTTCCAat  >  2:455032/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                            
AAAGCTAATTATTATTGCTCGAAAAATACCTATATTTATCTTCTTTGTATCTATTATTGGTCCTTTATTAGAAGAATATGTATTCAGAAAAGTAATCTTTGGAGAATTATTTAATGCGATTAAAGGTAATCGTATCGTGGCATTTATTATTGCTACAACAGTAAGTTCATTAATATTTGCATTAGCACATAATGATTTCAAATTTATTCCAGTTTATTTTGGTATGGGTGTCATTTTTTCATTAGCATATGTTTGGACAAAACGGCTTGCTGTTCCAAT  >  USA300TCH1516_ALE/2142972‑2143250

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: ‑