Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,981,418 C→A 42.3% intergenic (‑17/+339) USA300HOU_RS09870 ← / ← liaR hypothetical protein/Transcriptional regulatory protein LiaR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,981,4180CA42.3% 17.4 / 30.2 37intergenic (‑17/+339)USA300HOU_RS09870/liaRhypothetical protein/Transcriptional regulatory protein LiaR
Reads supporting (aligned to +/- strand):  ref base C (8/13);  new base A (5/11);  total (13/24)
Fisher's exact test for biased strand distribution p-value = 7.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTC  >  USA300TCH1516_ALE/1981286‑1981551
                                                                                                                                    |                                                                                                                                     
aaaGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAACCTCTGTCTACCCATTCTGTAAGCTACCTTTCt                                                                                                                                      >  2:66818/1‑134 (MQ=255)
   gTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGtt                                                                                                                                   <  1:232235/134‑1 (MQ=255)
           aGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGAGGAAt                                                                                                                           >  1:71079/1‑134 (MQ=255)
            gAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAAtt                                                                                                                          <  2:258983/134‑1 (MQ=255)
               aGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTa                                                                                                                       <  1:402276/134‑1 (MQ=255)
               aGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTATTATCTACCTTTCTGTTTGGTGAAATTTa                                                                                                                       >  1:419812/1‑134 (MQ=255)
               aGTCCAATGGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTa                                                                                                                       <  2:309443/134‑1 (MQ=255)
                  ccAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGTATTTTAtac                                                                                                                    >  2:203476/1‑132 (MQ=255)
                       tgtgtgCGCCATGGTTTCTGGCGTATAGCCAGCCTCTATACGAAGCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGaca                                                                                                               <  2:595550/134‑1 (MQ=255)
                         tttGCGCCATAGTAACTTGCGTATAACCAGCCTCTATACGAACCATGTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGAcaca                                                                                                             <  1:387826/134‑1 (MQ=255)
                                            cGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATacac                                                                                          <  2:58440/134‑1 (MQ=255)
                                            cGTAGAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATacac                                                                                          <  2:348719/134‑1 (MQ=255)
                                                  aCCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCt                                                                                    <  2:532454/134‑1 (MQ=255)
                                                   ccAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCtt                                                                                   <  2:405393/134‑1 (MQ=255)
                                                        ctctATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCAGGACACAAGAAATTGCAATAATACACATTTCTTGAAac                                                                              >  1:121367/1‑134 (MQ=255)
                                                          ctATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATCATACACATTTCTTGAAacac                                                                            >  2:94369/1‑134 (MQ=255)
                                                             taCGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGa                                                                         <  2:452559/134‑1 (MQ=255)
                                                             taCGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTATGTTATCTACCTTTCTGTTTGGGGAATTTTAGCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGa                                                                         <  1:52482/134‑1 (MQ=255)
                                                               cGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTGATGTGTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGAtt                                                                       <  2:209550/134‑1 (MQ=255)
                                                                   ccATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACAt                                                                   <  1:127603/134‑1 (MQ=255)
                                                                      ttttATATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCtt                                                                <  2:328248/134‑1 (MQ=255)
                                                                      ttttAAATTTTGTTTGAATTAAATATGTAAAACTCTGTCTATCCATTCTGTTATTTATCTTTATATTTGGGGATTTTTATCCTGATACAATAAATTGCAATAATACACAATTCTTGAAACACAAACTAAATCtt                                                                >  2:330106/1‑134 (MQ=255)
                                                                       ttgtaaTTTTGTTTGAATTACATCTGGAAATCTCTGTCTATCCATTCTGTTATCTACCTTTATGTCTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTa                                                               <  2:365764/130‑1 (MQ=255)
                                                                        ttAAATTTTGTTTGACTCAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCAACCTTCCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGAATACATCTTaa                                                              >  2:576936/1‑134 (MQ=255)
                                                                         tAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATACTGTTATCTACCTTTATGTTTGGGGAATTATATCCGGACACAAGAAATTGCAATAATACACATTTAGTGAAACACAGATTACATCTTaag                                                             >  2:212791/1‑133 (MQ=255)
                                                                                           aaTCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAGTAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTACTAAAATGa                                           >  1:404510/1‑134 (MQ=255)
                                                                                            aTCTTTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGaa                                          <  1:547209/134‑1 (MQ=255)
                                                                                            aTCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAAGTATACCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGaa                                          <  1:54626/134‑1 (MQ=255)
                                                                                              cTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGaaaa                                        >  1:203850/1‑134 (MQ=255)
                                                                                                         tGTCTATCCATTCTGTTATCTACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTc                             >  1:595124/1‑134 (MQ=255)
                                                                                                          gTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTca                            >  1:294191/1‑134 (MQ=255)
                                                                                                               tCCATTCTGTTATCTTTCTTTCTGTTTGGGGAATTTTATCCAGACACAAGAAATTGCAATAATACACATGTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACAttt                       <  1:355004/134‑1 (MQ=255)
                                                                                                                             tACCTTTATGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGa         <  1:332212/134‑1 (MQ=255)
                                                                                                                             tACCTTTATAGTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGa         <  2:145072/134‑1 (MQ=255)
                                                                                                                                  ttCTGTTTTGTGAATTTTATCCGGACAGAAGAAAATGCAAAAAGACACAATGCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAg    <  1:492150/134‑1 (MQ=255)
                                                                                                                                  ttCTGTTTGTGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAg    <  1:17706/134‑1 (MQ=255)
                                                                                                                                  ttCTGTTTGGGGAATTTTATCAGGACACAAGAAATTGCAATAATACACATTTCTTAAAACACAGATTACATCTGAATATATTTTTAATAAAATGAAAGGAGTCAATTTCACATTTGTATTAAATTTTGATCAAg    <  1:559537/134‑1 (MQ=255)
                                                                                                                                    cTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTc  >  2:255799/1‑134 (MQ=255)
                                                                                                                                    |                                                                                                                                     
AAAGTCTTTTTAGAAAGTCCAATTGTTTGCGCCATAGTATCTTGCGTATAACCAGCCTCTATACGAACCATTTTAAATTTTGTTTGAATTAAATCTGTAAAACTCTGTCTATCCATTCTGTTATCTACCTTTCTGTTTGGGGAATTTTATCCGGACACAAGAAATTGCAATAATACACATTTCTTGAAACACAGATTACATCTTAATATATTTTTAATAAAATGAAAAGAGTCAATTTCACATTTGTATTAAATTTTGATCAAGTC  >  USA300TCH1516_ALE/1981286‑1981551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑