Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,480,567 C→T 8.6% R113H (CGC→CAC)  USA300HOU_RS12775 ← putative ABC transporter permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,480,5670CT 8.6% 111.8 / 4.2 47R113H (CGC→CAC) USA300HOU_RS12775putative ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base C (25/17);  new base T (2/2);  total (28/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.47e-01

CTCTATAACTAGTTGAATTATTTTTAAAATGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCACTAAGTTGCGATT  >  USA300TCH1516_ALE/2480439‑2480705
                                                                                                                                |                                                                                                                                          
ctctATAACTAGTTGAATTATTTTTAAAATGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGTGTTGTTGTTTa                                                                                                                                 >  1:446189/1‑140 (MQ=255)
ctctATAACTAGTTGAATTATTTTTAAAATGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGTGTTGTTGTTTa                                                                                                                                 >  1:446184/1‑140 (MQ=255)
ctctATAACTAGTTGAATTATTTTTAAAATGTAATCTATCCCCGACTCTAATGTTGTCTCCAGCTAACTTATCATTAATAACGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAATTTGTATGCGTTGTTGtttg                                                                                                                                 >  2:519970/1‑139 (MQ=255)
    ataACTAGTTGAATTATTTTTAAAATGTAAGCTATCCCCGACTCTAATGTTGTCTGCGACTAACTTATCATTAATAGAGACCTAATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTTTATGCGTTGTTGTTGAACGt                                                                                                                             >  2:239235/1‑140 (MQ=255)
     taACTAGTTGAATTATTTTTAAAATGTAATCTATCCCCGACTCTATTGTTGTCGGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAAAGtc                                                                                                                            >  1:106441/1‑140 (MQ=255)
        cTAGTTGAATTATTTTTAAAATGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGtcatt                                                                                                                         <  1:412966/140‑1 (MQ=255)
             tGAATTATTTTTAAAATGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTg                                                                                                                    >  1:297216/1‑140 (MQ=255)
                     ttttAAAATGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATcaca                                                                                                            >  2:34930/1‑140 (MQ=255)
                       ttAAAATGTAATCTATCCTCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATc                                                                                                          <  2:237119/140‑1 (MQ=255)
                          aaaTGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTTTTTTTTATGCGTTGTTGATTAACGTCATTCATTGTAATCACATCTTg                                                                                                       >  2:520294/1‑140 (MQ=255)
                             tGTAATCTAACCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTc                                                                                                    <  1:353194/140‑1 (MQ=255)
                                       ccccGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGAGCTCATGAGCATGTTTAGGATAATCACCTTTTTTAAGTCGTATGCGTTGTTGTTTAAAGTCATTCATTGTAATCACATCTTGTTCTttattctgt                                                                                          >  2:504531/1‑136 (MQ=255)
                                        cccGACTCTAATGTTGACTGCGGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATa                                                                                         >  2:391320/1‑140 (MQ=255)
                                           gACTCTAATGTTTTGTGCAGCTAACTATCCATTAATAGTTACCGCATGAGCATTTTTAGGTTAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAAtt                                                                                      <  1:385815/140‑1 (MQ=255)
                                           gACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTATGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAAtt                                                                                      <  1:4974/140‑1 (MQ=255)
                                               ctAATGTTGTCTGCGGCTAACTTATCATTAATTGCGACCTCATGAGCATTTTTAGGATAATCTCCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCaa                                                                                  <  1:489408/140‑1 (MQ=255)
                                               ctAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCaa                                                                                  <  1:164868/140‑1 (MQ=255)
                                                 aaTGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATg                                                                                >  1:263883/1‑140 (MQ=255)
                                                  aTGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATATAAAAGATAAAAACCTATTTTAAGAAGTATGCGATGTTGTATAACGTCATTCATTGTAATCACATCTTGTTCTTGATTAGATAATTTCAATGt                                                                               >  1:11123/1‑140 (MQ=255)
                                                             aGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCa                                                                    >  1:148545/1‑140 (MQ=255)
                                                                 aaCTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCAtttt                                                                >  1:224126/1‑140 (MQ=255)
                                                                   cTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTtac                                                              >  2:487650/1‑139 (MQ=255)
                                                                     tATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTTTATTCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTatat                                                            >  2:392017/1‑140 (MQ=255)
                                                                      aTCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATg                                                           <  1:455533/140‑1 (MQ=255)
                                                                         aTTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGtt                                                        <  2:179818/140‑1 (MQ=255)
                                                                             aTAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTATGTTTTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTTTtg                                                    >  2:36737/1‑140 (MQ=255)
                                                                             aTAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTtg                                                    <  2:218886/140‑1 (MQ=255)
                                                                               aGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTTTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTTTATGGTTCTtgat                                                  >  1:189687/1‑140 (MQ=255)
                                                                                      tCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGAGGTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGCATATTCATTTTATATGGTTCTTGATGAATTAc                                           >  2:388516/1‑140 (MQ=255)
                                                                                       taTGAGCATTTTTACGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTTGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTAcc                                          <  2:51465/139‑1 (MQ=255)
                                                                                          gAGTATTTTTAGGATAATTACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTTTTCTTTATTACTTTATCTGAATGTTTGAATATTCAATTTATATGGTTCTTGATGAATTACCttt                                       <  1:290499/140‑1 (MQ=255)
                                                                                          gAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTTATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCttt                                       <  1:290454/140‑1 (MQ=255)
                                                                                          gAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCttt                                       <  1:172251/140‑1 (MQ=255)
                                                                                              aTTTTTAGGTTAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCAATCATTGTAATCACATCTTGTTCTTTATTAGAGAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTaa                                   <  1:129629/140‑1 (MQ=255)
                                                                                              aTTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTTTTGATGAATTACCTTTTTaa                                   >  1:315993/1‑140 (MQ=255)
                                                                                                 tttAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTTTTTAACGTCTTTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAAttt                                <  1:12523/140‑1 (MQ=255)
                                                                                                 tttAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAAttt                                >  1:531641/1‑140 (MQ=255)
                                                                                                        tAATCACCTTTTTTATGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATTTTCATTTTATATGGTTCTTGATTAATTACCTTTTTTATTTGATTCtt                         >  2:442984/1‑139 (MQ=255)
                                                                                                                  ttttAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCa               >  1:56908/1‑140 (MQ=255)
                                                                                                                   tttAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCAc              >  1:351848/1‑140 (MQ=255)
                                                                                                                   tttAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCAc              >  1:204108/1‑140 (MQ=255)
                                                                                                                    ttAAGTTGTATGTGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCACt             <  2:446184/140‑1 (MQ=255)
                                                                                                                    ttAAGTTGTATGTGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCACt             <  2:446189/140‑1 (MQ=255)
                                                                                                                      aaGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCACTag           >  1:433187/1‑139 (MQ=255)
                                                                                                                       tgttttttGCGTTGTTGTTTAACGACATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCTATGTTTGAATATTCATTTTATATTGTTCTTGATGAATTAACTTTTTAATTTGATTCTGTTGCTTATCACTAAg          >  2:414722/8‑140 (MQ=255)
                                                                                                                          tttATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCACTAAGTTg       <  2:440456/138‑1 (MQ=255)
                                                                                                                               gCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCAATTTATATGGTTCTTGATGAATTACCTTTTTAATTTGGTGCTGGTGCGTGTCACTAAGTGGCGAtt  >  1:7175/1‑140 (MQ=255)
                                                                                                                                |                                                                                                                                          
CTCTATAACTAGTTGAATTATTTTTAAAATGTAATCTATCCCCGACTCTAATGTTGTCTGCAGCTAACTTATCATTAATAGCGACCTCATGAGCATTTTTAGGATAATCACCTTTTTTAAGTTGTATGCGTTGTTGTTTAACGTCATTCATTGTAATCACATCTTGTTCTTTATTAGATAATTTCAATGTTTGAATATTCATTTTATATGGTTCTTGATGAATTACCTTTTTAATTTGATTCTGTTGCGTATCACTAAGTTGCGATT  >  USA300TCH1516_ALE/2480439‑2480705

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: ‑