Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,097,015 T→C 7.4% M270T (ATG→ACG)  ythB → Putative cytochrome bd menaquinol oxidase subunit II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,097,0150TC 7.4% 151.7 / 3.5 55M270T (ATG→ACG) ythBPutative cytochrome bd menaquinol oxidase subunit II
Reads supporting (aligned to +/- strand):  ref base T (23/26);  new base C (2/2);  total (25/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.96e-01

ATTCTGAACATTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGTGATTGTCTTTATTTTAGGTT  >  USA300TCH1516_ALE/1096877‑1097143
                                                                                                                                          |                                                                                                                                
aTTCTGAACATTTTTATTCAGCTGTTTTTGACTATTGGTGGCTGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACATatg                                                                                                                                 >  2:131151/1‑140 (MQ=255)
   cTGAACATTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAatgatg                                                                                                                              >  1:346986/1‑140 (MQ=255)
      aaCATTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTc                                                                                                                           <  1:108373/140‑1 (MQ=255)
        cATTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTcgc                                                                                                                         <  1:94401/140‑1 (MQ=255)
        cATTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTcgc                                                                                                                         <  1:637123/140‑1 (MQ=255)
         attttgattttgCTGTTTTTGAGTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTcgcg                                                                                                                        <  2:80013/140‑1 (MQ=255)
         aTTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTcgcg                                                                                                                        <  1:10867/140‑1 (MQ=255)
         aTTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTcgcg                                                                                                                        <  1:365775/140‑1 (MQ=255)
              tATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCGTTTGTATTTGTTATTTTACAACTGATGGTCGCGTCCtt                                                                                                                   >  1:78357/1‑140 (MQ=255)
                        tttttGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATCTTTTATATTATGTTCGCGTTCTTTGGCTATGGa                                                                                                         <  1:134993/140‑1 (MQ=255)
                            tGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTa                                                                                                     <  1:400145/140‑1 (MQ=255)
                             gACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAg                                                                                                    <  2:46386/140‑1 (MQ=255)
                              aCTATTGGTGGATGTTTGGTATAAGTTTATTATTAAGAGCATTAGCTTCATTGTTACCATTCTTTAAGAAAACACTTGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATTCTCTCGTTCTTTTTCTCTGTAATTAGt                                                                                                   >  2:503321/1‑140 (MQ=255)
                               cTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATTATTTGTCTTTTGTATCCATTTTTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTa                                                                                                  <  2:501167/140‑1 (MQ=255)
                               cTAGTGGTGGATGTTTGGTATAAGTTTCTTAGTCTTTGCAGTAGCTTCATGGTTGACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAAGGATGTTCGCGTTCTTTGGCTATGGAATTAGTa                                                                                                  <  2:221594/140‑1 (MQ=255)
                                     gtggATGTTTGGTATAATGTTCGTATTCTTTGCATTAGCTTCTTTGTTAACCTTCTTTACGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGc                                                                                            <  2:138412/140‑1 (MQ=255)
                                       gtaTGTTTGGTATAAGTTTTTTATTCTTTGCATTAGCTTCATTGTTGACATTGTTTTATAAAAAACATGGTTTCGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCa                                                                                          <  2:683744/138‑1 (MQ=255)
                                       ggATTTTTTGTATAAGTTTCTTATTCTTTGCATTATCTTCATTGTTAACATTCTTTAAGAAAAAACATTGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCa                                                                                          <  2:360937/140‑1 (MQ=255)
                                       ggATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCa                                                                                          <  1:206811/140‑1 (MQ=255)
                                           gTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAACGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATAcc                                                                                      >  2:483804/1‑140 (MQ=255)
                                           gTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAACGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATAcc                                                                                      >  2:478231/1‑140 (MQ=255)
                                              tGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGATATGGAATTAGTAAATTGAAATAGCttt                                                                                   >  2:621769/1‑140 (MQ=255)
                                                   taAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGTATTAGTAAATTGCCATACCTTTTatat                                                                              >  2:552952/1‑140 (MQ=255)
                                                    aaGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACGTTTTATATc                                                                             >  2:697110/1‑140 (MQ=255)
                                                         tCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGttt                                                                        >  1:55709/1‑140 (MQ=255)
                                                           ttATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGt                                                                      >  1:651690/1‑140 (MQ=255)
                                                               tCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGGTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTATATTGCCATACCTTTTATATCCGTTTGTaaaa                                                                  >  1:629828/1‑140 (MQ=255)
                                                                cTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTaaaaa                                                                 >  2:685476/1‑140 (MQ=255)
                                                                  tttcATTAGTTTCATTGTTAACATTGTTTATGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAAtt                                                               <  2:547980/137‑1 (MQ=255)
                                                                    gCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTAc                                                             >  1:394364/1‑140 (MQ=255)
                                                                                  gctatcATTCCTCAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTa                                               <  1:400578/135‑1 (MQ=255)
                                                                                  gTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATGTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTa                                               <  1:453769/140‑1 (MQ=255)
                                                                                   ttAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAACGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTaa                                              <  1:483804/140‑1 (MQ=255)
                                                                                   ttAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAACGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTaa                                              <  1:478231/140‑1 (MQ=255)
                                                                                      aCATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATcc                                           <  1:204296/140‑1 (MQ=255)
                                                                                             ttAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATg                                    >  2:208056/1‑140 (MQ=255)
                                                                                             agcataaaaatCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGAGACATATGTTAATCAAGaaaag                                    >  2:257446/6‑138 (MQ=255)
                                                                                                  aaaaaaCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTg                               >  1:336281/1‑140 (MQ=255)
                                                                                                    aaaaCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGa                             <  1:685476/140‑1 (MQ=255)
                                                                                                     aaaCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGAc                            >  1:442786/1‑140 (MQ=255)
                                                                                                     aaaCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGAGATGGAc                            >  2:614570/1‑140 (MQ=255)
                                                                                                     aaaCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTACGGCACTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCACAAATGGGCTggtc                            >  1:444902/1‑138 (MQ=255)
                                                                                                     aaaCATGGTTTGGCGTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGAc                            >  1:505330/1‑140 (MQ=255)
                                                                                                      aaCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACa                           <  1:232786/140‑1 (MQ=255)
                                                                                                      aaCATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACa                           >  2:542762/1‑140 (MQ=255)
                                                                                                      aaCATGGTTTGGCTTTTGTATTTGTTATTTGACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACa                           <  2:655219/140‑1 (MQ=255)
                                                                                                        cgtggtttggttTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACAtt                         <  2:307963/138‑1 (MQ=255)
                                                                                                         aTGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAACCTTACAGATGCATATGTTAATCCAGAAATGGGCTGGACAttg                        >  1:32319/1‑139 (MQ=255)
                                                                                                          tGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTAGACAtgaa                       >  2:238017/1‑137 (MQ=255)
                                                                                                           ggTTTGGCTTTTGTGTTTGTTATGTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGt                      <  2:441878/140‑1 (MQ=255)
                                                                                                              ttGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTTGCTATTGTTTTTGTTTGCCACCAAACCATTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGTGAt                   <  1:514731/140‑1 (MQ=255)
                                                                                                                 gCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATTCATATGTTAATCCAGAAATGGGCTGGAGATTGGTGATTGt                >  1:623797/1‑140 (MQ=255)
                                                                                                                 gCTTTTGTAGTTGTTATTTTACAAAGGTGGTTCTCTTTCTTTTGCTATGGAACTAGGAATTTTGCATTACTTCTATATCCGTTTGTAAAAATTACAGATGCATATGTTATTCCAGAAATGGGCTAGACATTAGTGATTGt                <  2:342442/140‑1 (MQ=255)
                                                                                                                   ttttGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGTGATTGTCt              <  2:657540/140‑1 (MQ=255)
                                                                                                                    tttGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGTGATTGTCtt             >  1:389560/1‑140 (MQ=255)
                                                                                                                            tGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATCTCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGTGATTGTCTTTATTTTaa     >  2:200307/1‑139 (MQ=255)
                                                                                                                               tATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGTGATTGTCTTTATTTTAGGtt  <  1:224255/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                
ATTCTGAACATTTTTATTCAGCTGTTTTTGACTATTGGTGGATGTTTGGTATAAGTTTCTTATTCTTTGCATTAGCTTCATTGTTAACATTCTTTAAGAAAAAACATGGTTTGGCTTTTGTATTTGTTATTTTACAAATGATGTTCGCGTTCTTTGGCTATGGAATTAGTAAATTGCCATACCTTTTATATCCGTTTGTAAAAATTACAGATGCATATGTTAATCCAGAAATGGGCTGGACATTAGTGATTGTCTTTATTTTAGGTT  >  USA300TCH1516_ALE/1096877‑1097143

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: ‑