Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,831,763 T→C 8.9% Q301R (CAG→CGG)  lipA_2 ← Lipase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,831,7630TC 8.9% 157.4 / 4.3 58Q301R (CAG→CGG) lipA_2Lipase 1
Reads supporting (aligned to +/- strand):  ref base T (36/16);  new base C (2/3);  total (39/19)
Fisher's exact test for biased strand distribution p-value = 3.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

CTTCATAAGCTTTGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCATTTTTCTTGTCATTG  >  USA300TCH1516_ALE/2831626‑2831903
                                                                                                                                         |                                                                                                                                            
cTTCATAAGCTTTGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGAt                                                                                                                                           >  1:76414/1‑141 (MQ=255)
  tCATAAGCTTTGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCCCTAAAACGATAGGATCCTGAttt                                                                                                                                         >  1:157796/1‑141 (MQ=255)
    aTAAGCTTTGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGAttttt                                                                                                                                       >  1:191527/1‑141 (MQ=255)
          tttGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCGTGAACTAAGACGATAGGATGCTGATTTTTATACTg                                                                                                                                 >  1:391843/1‑141 (MQ=255)
          tttGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACtc                                                                                                                                 >  2:138894/1‑140 (MQ=255)
           ttGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGc                                                                                                                                >  1:171492/1‑141 (MQ=255)
            tGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGcc                                                                                                                               >  1:117278/1‑141 (MQ=255)
             gTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGccc                                                                                                                              >  1:587340/1‑141 (MQ=255)
                          tctAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACt                                                                                                                 <  1:79836/141‑1 (MQ=255)
                          tctAAATCTTGGCGAATGTTAATTTTAAAATCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACt                                                                                                                 <  2:478714/141‑1 (MQ=255)
                           ctAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAACACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACtt                                                                                                                >  1:161315/1‑141 (MQ=255)
                              aaTCTTGGCGTATGTGCATGTTAGTATCGCCTCAATAATGAGCTAATGCTGAAGGATTAATATCATCTGTAAATCTATTGATACCATGCACTAAAACGTTAGTTTGTTGATGTTGATACTGCCCTTGTTTGGCAACTTTAt                                                                                                             <  2:44975/141‑1 (MQ=255)
                                  ttGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATCCTGCCCTTGTTTGGCAACTTTATTCGt                                                                                                         >  2:526724/1‑141 (MQ=255)
                                   tGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGtt                                                                                                        >  1:555374/1‑141 (MQ=255)
                                         aTGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGatca                                                                                                  >  1:224608/1‑141 (MQ=255)
                                         aTGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGatca                                                                                                  >  1:614693/1‑141 (MQ=255)
                                         aTGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGACAACTTTATTCGTTTGatca                                                                                                  >  1:404951/1‑141 (MQ=255)
                                              cATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATTATCttt                                                                                             >  1:455821/1‑141 (MQ=255)
                                                   tattaCCGCCCCAATAATGAGCTGACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCtt                                                                                        >  2:370531/1‑141 (MQ=255)
                                                      taCCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTg                                                                                     <  1:402519/141‑1 (MQ=255)
                                                       aCCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTTAAACCATGCACTAAAACGATAGGATCCCGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGc                                                                                    >  2:9916/1‑141 (MQ=255)
                                                       aCCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCCGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGc                                                                                    >  2:322425/1‑141 (MQ=255)
                                                        ccGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCa                                                                                   >  1:22408/1‑141 (MQ=255)
                                                        ccGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGAAAGAAAATGGTAGGCTACAACAACGGTTTTTTCGCTTGTTTGGCGACTTTATTCGTTTGATCAGGTTGCGCTTTTGCa                                                                                   >  1:121778/1‑141 (MQ=255)
                                                           ccccAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATAACTTTTTCTGTTCTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTa                                                                                <  1:573158/141‑1 (MQ=255)
                                                                   atGAGCTACCACTGAAGGATTGAGATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCtt                                                                        <  1:399954/141‑1 (MQ=255)
                                                                        cTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTcc                                                                   >  1:503170/1‑141 (MQ=255)
                                                                         tAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTccc                                                                  <  1:185818/141‑1 (MQ=255)
                                                                          aaCACTGAATGATCAATATCATGTGTTAACGCCATGCAATTATTCGCTACAACCATAGTATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCt                                                                 <  2:482057/141‑1 (MQ=255)
                                                                                  aGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTgg                                                         <  1:452125/141‑1 (MQ=255)
                                                                                   ggATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGt                                                        >  1:179090/1‑141 (MQ=255)
                                                                                    gATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTa                                                       <  1:370531/141‑1 (MQ=255)
                                                                                        aaTTTCATCTGTAAACCCATGGAATCCATGCACTAAAACGATAGGATCCTGATTGTTATACTTCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGt                                                   <  2:198288/141‑1 (MQ=255)
                                                                                        aaTATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGt                                                   <  1:598379/141‑1 (MQ=255)
                                                                                        aaTATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGt                                                   >  1:423354/1‑141 (MQ=255)
                                                                                                    aaaCCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGTTACTGCact                                       >  2:202322/1‑141 (MQ=255)
                                                                                                    aaaCCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCATTATATGGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTTTCCCTTTGTTTGGTAACTTTGCTACTGCact                                       >  1:573624/1‑141 (MQ=255)
                                                                                                     aaCCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCacta                                      >  1:114855/1‑141 (MQ=255)
                                                                                                       cccATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCCTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCactact                                    >  2:484869/1‑141 (MQ=255)
                                                                                                          aTTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACtttt                                 <  2:587340/141‑1 (MQ=255)
                                                                                                           ttGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTTTCATTTTGTTTGGTAACGATGCTACTGCACTACttttt                                >  2:39879/1‑141 (MQ=255)
                                                                                                            tGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTta                               >  1:525686/1‑141 (MQ=255)
                                                                                                            tGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTta                               >  2:189623/1‑141 (MQ=255)
                                                                                                            tGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTta                               >  2:511301/1‑141 (MQ=255)
                                                                                                            tGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTta                               >  1:578978/1‑141 (MQ=255)
                                                                                                            tGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGAACATCTTTCGCTTTTGCAGTCAGTTCCTTTTTCCCATTGCTTGGTAACGTTACTCCTGCACTACTTTTta                               >  2:9057/1‑141 (MQ=255)
                                                                                                            tGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTCTATTAGTTTGATGATCTTTCGAAACTCCAGTAATTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTCCTTTTta                               >  1:605784/1‑141 (MQ=255)
                                                                                                            tGAAACCATGCACTAAAACGATAGGATCCTGATTCTTATACTGCCCTTGTTTGGCAACTTTCTTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTTTTAACGTTGCTACTGCACTACtttttt                               >  2:45888/1‑140 (MQ=255)
                                                                                                               aaCCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTtaata                            >  2:270371/1‑141 (MQ=255)
                                                                                                               aaCCAGGCACTAAAGCGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTtaata                            <  2:615195/141‑1 (MQ=255)
                                                                                                                aCCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTCCTACTGCACTACTTTTtcataa                           >  2:566101/1‑141 (MQ=255)
                                                                                                                       aCTAAAACGTGAGGATCCTGATTTTTATACTGCCCTTCTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAACCTCCTTTGTACCATTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAAt                    <  1:124212/141‑1 (MQ=255)
                                                                                                                          aaaaCGATAGGATCCTGATTTTTATACTGCCCTTGTTTGACAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCa                 >  2:106695/1‑141 (MQ=255)
                                                                                                                          aaaaCGATAGGATCCCGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCa                 <  1:322425/141‑1 (MQ=255)
                                                                                                                          aaaaCGATAGGATCCCGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCa                 <  1:9916/141‑1 (MQ=255)
                                                                                                                                 tAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCTTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCATTTTTCt          <  1:324993/141‑1 (MQ=255)
                                                                                                                                    gATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCAATACTTTTTAATAAATTTAATATATTTTTATTGt       >  1:76547/1‑141 (MQ=255)
                                                                                                                                     aTCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCATTTTTCTTGTc      <  1:138894/141‑1 (MQ=255)
                                                                                                                                         tGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCATTTTTCTTGTCATTg  <  1:547589/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                            
CTTCATAAGCTTTGTAACCATTTTCTTCTAAATCTTGGCGAATGTTCATTTTATTACCGCCCCAATAATGAGCTAACACTGAAGGATTAATATCATCTGTAAACCCATTGAAACCATGCACTAAAACGATAGGATCCTGATTTTTATACTGCCCTTGTTTGGCAACTTTATTCGTTTGATCATCTTTCGCTTTTGCAGTAAGTTCCTTTGTCCCTTTGTTTGGTAACGTTGCTACTGCACTACTTTTTAATAAATTTAATCCATTTTTCTTGTCATTG  >  USA300TCH1516_ALE/2831626‑2831903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑