Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 737,162 A→G 7.6% R548R (AGA→AGG)  bceB_1 → Bacitracin export permease protein BceB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE737,1620AG 7.6% 149.2 / 3.0 53R548R (AGA→AGG) bceB_1Bacitracin export permease protein BceB
Reads supporting (aligned to +/- strand):  ref base A (31/18);  new base G (2/2);  total (33/20)
Fisher's exact test for biased strand distribution p-value = 6.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.35e-01

ATATCAAGTTTAACCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAATGGGTACAACGAA  >  USA300TCH1516_ALE/737025‑737302
                                                                                                                                         |                                                                                                                                            
atatCAAGTTTAACCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGGAAg                                                                                                                                           >  1:440006/1‑141 (MQ=255)
atatCAAGTTTAACCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGGAAg                                                                                                                                           >  1:440001/1‑141 (MQ=255)
  atCAAGTTTAACCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCt                                                                                                                                         <  1:132105/141‑1 (MQ=255)
   tCAAGTTTAACCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCtt                                                                                                                                        <  2:470119/141‑1 (MQ=255)
          tAACCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTa                                                                                                                                 <  1:387421/141‑1 (MQ=255)
            aCCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTaca                                                                                                                               >  2:505618/1‑141 (MQ=255)
               ggAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACaa                                                                                                                            >  1:180679/1‑141 (MQ=255)
                       attattTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGCTGAGTTATAGGATTATAGTATTTTGAGAAAGCTTGGATTTACTCAAAAAGatat                                                                                                                    >  1:659314/1‑141 (MQ=255)
                       attattTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGGGAAAGCTTGGATTTACACAAAAAGgtat                                                                                                                    >  1:167416/1‑141 (MQ=255)
                       attattTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGatat                                                                                                                    >  1:659287/1‑141 (MQ=255)
                       attattTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGACAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGatat                                                                                                                    >  2:9459/1‑141 (MQ=255)
                         tattTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATgg                                                                                                                  <  1:162245/141‑1 (MQ=255)
                           tttGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTCTGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCa                                                                                                                <  1:309920/141‑1 (MQ=255)
                               tAACATCATTTTTATGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAggg                                                                                                            <  1:24981/141‑1 (MQ=255)
                                 aCATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGa                                                                                                          >  2:713118/1‑141 (MQ=255)
                                  catcatTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGAc                                                                                                         >  2:65268/1‑141 (MQ=255)
                                      atTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGAAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTaaa                                                                                                     >  1:23351/1‑141 (MQ=255)
                                       tttttAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAg                                                                                                    >  1:533034/1‑141 (MQ=255)
                                                  tACATTCTTGATTGATGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAATATTTTGAGAAATCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTAt                                                                                         >  2:528622/1‑141 (MQ=255)
                                                     aTTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGtt                                                                                      <  2:180679/141‑1 (MQ=255)
                                                          tGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATAGCAAGGGGACTAAAGTTTAAAATTATGTTTAAtt                                                                                 >  1:348868/1‑141 (MQ=255)
                                                          tGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGATTGGATTTACACAATAAGATATGGCGAGTGGACTAAAGTTTAAAATTATGTTTAAtt                                                                                 >  2:532360/1‑141 (MQ=255)
                                                           gATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAAttt                                                                                <  2:171918/141‑1 (MQ=255)
                                                             ttGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGGAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTg                                                                              <  2:440006/141‑1 (MQ=255)
                                                             ttGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGGAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTg                                                                              <  2:440001/141‑1 (MQ=255)
                                                             ttGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTCATTTTg                                                                              >  1:327918/1‑141 (MQ=255)
                                                             ttGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAGTTTTg                                                                              >  1:434303/1‑141 (MQ=255)
                                                                 tGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGtt                                                                          >  2:103465/1‑141 (MQ=255)
                                                                      gTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCtt                                                                     <  2:73400/141‑1 (MQ=255)
                                                                        tGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTa                                                                   <  1:649070/141‑1 (MQ=255)
                                                                         gCATTATCTGCAGAACGCGAGTAGATGAAACGGGAGATGAGGGAGAGAATGATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAg                                                                  >  2:373608/1‑141 (MQ=255)
                                                                         gCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAg                                                                  >  2:607108/1‑141 (MQ=255)
                                                                               tataCATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTg                                                            >  1:64069/1‑141 (MQ=255)
                                                                                   cATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACt                                                        <  1:505618/141‑1 (MQ=255)
                                                                                           aaaTAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATg                                                >  1:600795/1‑141 (MQ=255)
                                                                                           aaaTAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATg                                                >  1:600796/1‑141 (MQ=255)
                                                                                            aaTAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGc                                               <  1:237182/141‑1 (MQ=255)
                                                                                            aaTAGATGAAACCGAAGATGAGATAGAGAATGATAGTATGTTGAGAAAGCTGGGATTTGCACAAAAAGATATGACAAGAGGACTAAAGTTTAAAATTATAGTTAATTTTGGAGTACCTGTAGTTATTGCACTAGCACAtag                                               >  2:224001/1‑139 (MQ=255)
                                                                                               aGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCata                                            >  1:474641/1‑141 (MQ=255)
                                                                                                 aTGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATAtt                                          <  1:510220/141‑1 (MQ=255)
                                                                                                  tGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTCTAGTTATTGCACTATCACATGCATAttt                                         <  2:746539/141‑1 (MQ=255)
                                                                                                  agAAACCGAATAGGAGTTAAAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTATAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATAttt                                         <  1:513844/140‑1 (MQ=255)
                                                                                                          aaGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTAcatcat                                 >  2:283881/1‑141 (MQ=255)
                                                                                                          aaGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTCAcatcat                                 >  1:267310/1‑141 (MQ=255)
                                                                                                           aGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCAtt                                >  1:726835/1‑141 (MQ=255)
                                                                                                           aGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATAAtt                                >  1:481583/1‑141 (MQ=255)
                                                                                                                      agaATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAATATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGa                     <  1:417631/141‑1 (MQ=255)
                                                                                                                            ataGTATTTTGAGAAAGCTTGGATTTAAACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTaa               <  1:480114/141‑1 (MQ=255)
                                                                                                                             taGTATTTTGAGAAGGCTTAGATTTACACAAAAAGATATGGCAAAGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAAt              >  1:422781/1‑141 (MQ=255)
                                                                                                                             taGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAAt              >  2:475933/1‑141 (MQ=255)
                                                                                                                             taGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAAt              >  2:300206/1‑141 (MQ=255)
                                                                                                                              aGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTACAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCAAATGCATATTTTACATCATTAGCATATATTAAATTAATg             >  2:527199/1‑141 (MQ=255)
                                                                                                                                   tttGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAATGGGTAc        <  1:394581/141‑1 (MQ=255)
                                                                                                                                        gaAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAATGGGTACAACGa   >  2:684165/1‑141 (MQ=255)
                                                                                                                                        gaAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTGTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAATGGGTACAACGa   >  2:733643/1‑141 (MQ=255)
                                                                                                                                         aaaTCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAATGGGTACAACGaa  <  2:273362/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                            
ATATCAAGTTTAACCGGAATATTATTATTTGTAACATCATTTTTAGGTATTACATTCTTGATTGCTGTATGTTGCATTATATACATAAAGCAAATAGATGAAACCGAAGATGAGTTAGAGAATTATAGTATTTTGAGAAAGCTTGGATTTACACAAAAAGATATGGCAAGGGGACTAAAGTTTAAAATTATGTTTAATTTTGGGTTACCTTTAGTTATTGCACTATCACATGCATATTTTACATCATTAGCATATATGAAATTAATGGGTACAACGAA  >  USA300TCH1516_ALE/737025‑737302

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑