Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 875,468 G→C 8.9% S791S (TCG→TCC)  clfA → Clumping factor A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE875,4680GC 8.9% 146.3 / 3.2 61S791S (TCG→TCC) clfAClumping factor A
Reads supporting (aligned to +/- strand):  ref base G (26/28);  new base C (3/3);  total (30/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATTCCGACAGTGACTCAGATTCCGACAGTGACTCAGACTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACTCAGATTCAGATAGTGACTCGGATTCAG  >  USA300TCH1516_ALE/875337‑875607
                                                                                                                                   |                                                                                                                                           
gattccgaccgtgactcagattccgacagtgactcaGACTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGa                                                                                                                                     <  2:178304/140‑1 (MQ=255)
gattccgacagtgactcagattccgacagtgactcaGACTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGa                                                                                                                                     <  1:253784/140‑1 (MQ=255)
gattccgacagtgactcagattccgacagtgactcaGACTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATACAGACAGCGAGTCAGACTCGGACAGCGa                                                                                                                                     >  1:407873/1‑140 (MQ=255)
  ttccgacagtgactcagattccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGAca                                                                                                                                   >  1:228382/1‑139 (MQ=255)
  ttccgacagtgactcagattccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGAAAGCGACTCAGACACGGATCGCGACt                                                                                                                                   >  2:159161/1‑140 (MQ=255)
  ttccgacagtgactcagattccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTACGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACt                                                                                                                                   <  1:295031/140‑1 (MQ=255)
   tccgacattgactcagattccgacagtgactcagaCTCAGACTGTGATTCGGAGTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTc                                                                                                                                  <  1:355917/140‑1 (MQ=255)
   gccgacagtgactcagagtccgacagggactcagaCGCAGACAGCGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTc                                                                                                                                  <  1:565926/139‑1 (MQ=255)
    ccgacagtgactcagattccgacagtgactcagaCTCAGACAGTGATTACGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCg                                                                                                                                 >  1:446859/1‑140 (MQ=255)
     cgacagtgactcagattccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCgg                                                                                                                                <  2:159006/140‑1 (MQ=255)
     cgacagtgactcagattccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCgg                                                                                                                                <  1:63362/140‑1 (MQ=255)
          gtgactcagattccgacagtgacccagcCTCAGACGAAAATATTGATTCAGCGAGGGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCa                                                                                                                           <  1:538659/140‑1 (MQ=25)
            gactcagattccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGCTAGCGACTCGGATTCAgg                                                                                                                         >  1:132733/1‑139 (MQ=255)
              ctcagattccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGGTTCAGATa                                                                                                                       >  1:59374/1‑140 (MQ=255)
                   agtccgacagtggctccgaCTCGGACAGGGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGGGACGCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGAt                                                                                                                  <  2:73163/138‑1 (MQ=25)
                      ccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGAAAAACCGACGCGGACAGTGACGGGCACGCAGAAAGCGACTCAAACACGGAAAGCGACTCAGATTCAGACAGCCAtcca                                                                                                               >  2:405887/1‑137 (MQ=12)
                      ccgacagtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGACTCAGCTAGTCAAGCCGACTCCGACAGTGACTCTGAGTCAGATAGCGACTCAGACTCAGATAGCGACTCAGATTCAAACAGCGATTCg                                                                                                               >  2:463760/1‑140 (MQ=21)
                           agtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGGTGCCGATAGCGGGTCGGAcgc                                                                                                          >  2:300241/1‑138 (MQ=25)
                            gtgactcagaCTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCa                                                                                                         <  1:367816/140‑1 (MQ=255)
                                ctcagactcagaCAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATa                                                                                                     >  1:163986/1‑140 (MQ=255)
                                   tgtctcggacCGTGATTCGCATTCAGCGAGTGCTTCGGATTCAGACAGTGCCTCCGCCTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcg                                                                                                  <  2:506167/137‑1 (MQ=25)
                                    gactcagacAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGGGAAGCGGACGCAGATagcgc                                                                                                 >  2:17180/1‑139 (MQ=255)
                                        cagacAGTGATTCGGATTCAGCGAGTGATTCGGACTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGATTCCGATAACGACTCGGATTTAACTAGCGATTCGCATTCAGATagcgactca                                                                                             >  2:147877/1‑140 (MQ=25)
                                         agcaaGTGATTCAGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCACACAGCGGTTCGGACTGCGATagcgattcag                                                                                            >  2:371435/5‑140 (MQ=25)
                                          gacAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcaga                                                                                           >  2:508525/1‑140 (MQ=255)
                                              tgggttCGGATTCAGGTAGTGATTCGTGTTCAGATAGTGATTCCGACTCGGACAGTTACGCGGATTCAGGTAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatca                                                                                       <  2:228382/136‑1 (MQ=21)
                                                gATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGCTagcgattcagaatcaga                                                                                     >  1:561385/1‑140 (MQ=255)
                                                 aTTCGGATTCAGCGCGTGATTCGGATTCAGTTCGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgatttagaatcagac                                                                                    <  2:500925/140‑1 (MQ=255)
                                                  ttCGGATTCAGCGAGTGATTCGGATTCAGATAGTAATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGACAGCGACTCGGACCCAGCTagcgatccagaaccagaca                                                                                   >  2:207101/1‑140 (MQ=25)
                                                  ttCGGATTCAGCGAGTGATTCGGACCCAGATAGTGATTCCGACTCCGACAGTGACTCGGACTCAGATAGCGACTCCGACTCGGATAGCGACTCCGCTTCAGATAGCGATGCGGCCCCACCTagcgccccagaagccgaca                                                                                   >  2:444952/1‑140 (MQ=21)
                                                   tCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATCCGGACTCAGATagcgattcagactcagacgg                                                                                  >  2:208876/1‑138 (MQ=255)
                                                    cGGATTCAGCGAGTGGTTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGAGTCGGATTCAGATAGAGATTCGGACGCAGATagccattcagactcagacagc                                                                                 >  2:237901/1‑140 (MQ=21)
                                                    cGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGCTaacgattcagagtcagacgac                                                                                 >  1:513439/1‑137 (MQ=255)
                                                      gATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatcagacagcga                                                                               <  1:280930/140‑1 (MQ=255)
                                                       aTTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatcagacagcgat                                                                              >  1:311047/1‑140 (MQ=255)
                                                         cgcgCGAGTGGTTCGGAGTCACATGGGTTTTCTGCTTCCGACAGTGACTCCGATTCAGATAGCGACTCAGACTCCGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatcagacagcgattc                                                                            <  2:551457/137‑1 (MQ=17)
                                                            gccaGTGATTGCGCTTCAGACACTGATCCCGCCCCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatcagacagcgattcaga                                                                         <  1:528120/137‑1 (MQ=18)
                                                                 tGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatcagacagcgattcagaatcag                                                                    <  1:38253/140‑1 (MQ=255)
                                                                 tGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCCGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatcagacagcgattcagaatcag                                                                    <  2:63860/140‑1 (MQ=255)
                                                                 tGATTCGGATTCAGATAGTGATTCCGACCCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATagcgattcagaatcagacagcgattcagaatcag                                                                    <  1:121587/140‑1 (MQ=255)
                                                                        gATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGCTAGCGACTCAGACTCGCATAGCGCCTCGGATTCAGATAGCGATTCGGACTCAGATAGCGAttcagaatcagacagcgattcagaatcagacagcga                                                             <  1:518824/140‑1 (MQ=255)
                                                                         aTTCAGATATCGATTCCGACTCCGACAGTTCCCCCGATTCATATCCCGACTCAAACTCCGATCGCCACTCGGATTCAGCTCCCGATTCGAACCCAGATAGCGATtcagaaccagacagcgattcagaatcagacagcgat                                                            <  2:560919/140‑1 (MQ=19)
                                                                         aTTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATtcagaatcagacagcgcttccgagtcagacagcgat                                                            >  1:69015/1‑140 (MQ=255)
                                                                                 actGATTCCGCCTCCGAGAGTGACCCGGATTCAGATAGCGACTCAGACGCGGACAGCGACTCCGATTCCGATAGCGATTCCGACTCAGATAGCGATTCAGACTCAGACAGCGATTCAGAATCAGACAGCgattcagattc                                                    <  2:263405/138‑1 (MQ=17)
                                                                                    gcgtccgcctcagccAGTGAGTCGGTTCCAGACAGTGAGTCAGCGCCGGACAGCGACTCCGATTCAGACAGCGATTCCGACTCAGATAGCGATTCAGACTCAGACAGCGATTCAGAATCAGACAGCGAttcagattcaga                                                 <  2:566232/137‑1 (MQ=2)
                                                                                           acgccgacAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGAc                                          <  1:343208/137‑1 (MQ=255)
                                                                                            ctccgacAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACt                                         >  1:352966/1‑140 (MQ=255)
                                                                                             tccgacAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGTCAGCGATTCAGATTCAGACAGCGACTc                                        <  1:371435/140‑1 (MQ=255)
                                                                                                 acAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATCCAGATTCAGACAGCGACTCAGAc                                    >  2:398052/1‑140 (MQ=255)
                                                                                                      gACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGa                               <  1:110448/140‑1 (MQ=255)
                                                                                                         tccgactCATATAGTGACTCAGACTCCGATAGCGACTCAGATTCAGATAGCGATTCAGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCATATTCAGACAGCGACTCAGACAGTGACtc                            <  2:258855/134‑1 (MQ=14)
                                                                                                         tCGGAGTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAACCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACtc                            <  1:231937/140‑1 (MQ=255)
                                                                                                          cGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACtca                           >  1:89575/1‑140 (MQ=255)
                                                                                                             aTTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGCCAGCGATTACGATTCAGACAGCGACTCCGACAGGGACtcagac                        >  2:212077/1‑139 (MQ=21)
                                                                                                                cAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACGGTGACtccgattca                     >  1:517381/1‑140 (MQ=255)
                                                                                                                cAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACtcagattca                     >  1:516262/1‑140 (MQ=255)
                                                                                                                  gATCGCGACTCAGACTCGGATAGCGACTCGGATTCGGAGAGCGATTCGGAGTGGGACAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACtcagattcaga                   <  1:566709/140‑1 (MQ=18)
                                                                                                                  gATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATGCAGAATCAGACAGCGATTCAGATGCGGACACCGAATCAGATTCAGACAGCGACTCAGACAGTGACgcagatgcaga                   >  2:65334/1‑140 (MQ=14)
                                                                                                                  gATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGAGTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACacagattcaga                   >  2:351973/1‑140 (MQ=17)
                                                                                                                      gCGACTCAGACTCGGAGAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACTCAGATTCAGATAGt               <  1:17180/140‑1 (MQ=255)
                                                                                                                       cGACTCAGACTCGGATAGCGACTCGGATTCAGATTGCGATGCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACTCAGATTCAGATAGTg              <  1:104913/140‑1 (MQ=255)
                                                                                                                                   ggATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACTCAGATTCAGATAGTGACTAGGATTcgg  >  1:412757/1‑138 (MQ=255)
                                                                                                                                   |                                                                                                                                           
GATTCCGACAGTGACTCAGATTCCGACAGTGACTCAGACTCAGACAGTGATTCGGATTCAGCGAGTGATTCGGATTCAGATAGTGATTCCGACTCCGACAGTGACTCGGATTCAGATAGCGACTCAGACTCGGATAGCGACTCGGATTCAGATAGCGATTCGGACTCAGATAGCGATTCAGAATCAGACAGCGATTCAGAATCAGACAGCGATTCAGATTCAGACAGCGACTCAGACAGTGACTCAGATTCAGATAGTGACTCGGATTCAG  >  USA300TCH1516_ALE/875337‑875607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑