Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,775,041 A→G 12.3% D715D (GAT→GAC)  clfB ← Clumping factor B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,775,0410AG12.3% 114.3 / 2.6 54D715D (GAT→GAC) clfBClumping factor B
Reads supporting (aligned to +/- strand):  ref base A (18/27);  new base G (3/4);  total (21/33)
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

CTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCTGAATCGCTATCTGAGTCTGAATCGCTATCTGAGTCTGAATCACTGTCTGAG  >  USA300TCH1516_ALE/2774901‑2775179
                                                                                                                                            |                                                                                                                                          
cTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGGCTGAGTCGGAGTCGCTCtctgaatctgaa                                                                                                                                            >  2:355255/1‑141 (MQ=14)
cTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGaa                                                                                                                                            <  1:351776/141‑1 (MQ=255)
    ttgtgtctgattcGCTGTCTGTGTCGGAGTCGCTATCTGATTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAGTCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGc                                                                                                                                        <  2:202809/136‑1 (MQ=14)
     tgaatctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAGTCTGAGTCGCt                                                                                                                                       >  2:206973/1‑141 (MQ=255)
      gagtctgactcGCTCTCTGAGTCCGACTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTa                                                                                                                                      <  2:178380/138‑1 (MQ=14)
      gaatctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTCTCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGGCGCtg                                                                                                                                      >  2:264481/1‑140 (MQ=255)
      gaatctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTgtctgagtctgagtcgctgtctgagtctgagtcgctg                                                                                                                                      >  2:214288/1‑140 (MQ=255)
        atctgaatcGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatc                                                                                                                                    <  2:163643/141‑1 (MQ=255)
                cGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTatctgaatctg                                                                                                                            <  1:332254/141‑1 (MQ=255)
                   tGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAATCTGAGt                                                                                                                         >  2:311329/1‑141 (MQ=255)
                                 tCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTgtctgagtct                                                                                                           >  1:200770/1‑141 (MQ=255)
                                       tctgaatctgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGtctgagtcg                                                                                                     >  1:230614/1‑141 (MQ=255)
                                               tgaGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGtctgagtcgctgtctga                                                                                             >  2:317278/1‑141 (MQ=255)
                                                 aGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAATCTGAGTCGCTGTCTGAGtctgagtcgctgtctgaat                                                                                           >  2:107863/1‑141 (MQ=255)
                                                   tCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGtctgagtcgctgtctgaatct                                                                                         >  1:71622/1‑141 (MQ=255)
                                                   tCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGtctgagtcgctgtctgaatct                                                                                         <  1:1342/141‑1 (MQ=255)
                                                           tgagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTGTCTGAATCTGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgcgtcgct                                                                                 >  2:171099/1‑141 (MQ=255)
                                                            gagtctgaATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgagtcgctg                                                                                <  1:105802/141‑1 (MQ=255)
                                                                ctgagtcgctatctgagtctgagtcgctatctgagtCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAATCTGAGTCGCTGTCTGAGtctgagtcgctgtctgaatctgagtcgctgtctg                                                                            <  2:172763/141‑1 (MQ=255)
                                                                   aaTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAAACTGAGTCGCTGTCTGAGTctgagtcgctgtctgaatctgagtcgctgtctgaat                                                                         >  2:299612/1‑141 (MQ=255)
                                                                    gtcgctatctgagtctgagtcgctatctgagtctgagtcgctatctgagtctgagTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCtgagtcgctgtctgaatctgagtcgctgtctgaatc                                                                        <  2:171831/140‑1 (MQ=255)
                                                                    gtCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCtgagtcgctgtctgaatctgagtcgctgtctgaatc                                                                        <  2:171835/140‑1 (MQ=255)
                                                                    aTCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCtgagtcgctgtctgaatctgagtcgctgtctgagtc                                                                        >  2:289854/1‑141 (MQ=255)
                                                                         tATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTctgaatctgaat                                                                   >  1:333354/1‑141 (MQ=255)
                                                                            ctgaatctgaGTCGCTATCTGCGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGc                                                                <  1:90180/141‑1 (MQ=255)
                                                                            ctgaatctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGc                                                                <  2:232578/141‑1 (MQ=255)
                                                                               aatctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTNTCTNAATCTGAGTCGCTGNNTGAATCTGAATCGCTgt                                                             <  1:323404/141‑1 (MQ=255)
                                                                                 tctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtct                                                           <  1:318306/141‑1 (MQ=255)
                                                                                 tctgaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCCGAATCGCTATCTGAATCTGAATCGCGGTCTGGGTCTGAGTCGCTGTCTGGAGCTAAGTCGCTTTCTGAATTCGAGTCGCTgtct                                                           >  2:305267/1‑141 (MQ=11)
                                                                                    gaGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGGATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtctgag                                                        >  1:290919/1‑141 (MQ=255)
                                                                                     aGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTgtctgagt                                                       <  2:348549/141‑1 (MQ=255)
                                                                                      ggcGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtctgagtc                                                      <  1:82377/139‑1 (MQ=255)
                                                                                        cGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTgtctgagtctg                                                    <  1:95652/141‑1 (MQ=255)
                                                                                           tATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGATTCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaat                                                 <  2:153209/141‑1 (MQ=255)
                                                                                           tATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaat                                                 <  1:132251/141‑1 (MQ=255)
                                                                                            ttctgagtctgagtcgctgtctgagtctgagtcgctgTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatc                                                <  2:96026/140‑1 (MQ=255)
                                                                                              ctgagtctgagtcgctgtctgagtctgagtcgctgtCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgc                                              <  2:249517/141‑1 (MQ=255)
                                                                                                    ctgagtcgctgtctgagtctgagtcgctgtctgagtCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctg                                        <  1:56176/141‑1 (MQ=255)
                                                                                                    ctgagtcgctgtctgagtctgagtcgctgtctgagtCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctg                                        <  1:56142/141‑1 (MQ=255)
                                                                                                      gagtcgctatctgagtctgagtcgctgtctgagtctGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgag                                      <  2:102029/141‑1 (MQ=255)
                                                                                                        gtcgctatctgagtctgagtcgctgtctgagtctgaGTCGCTGTCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgagtc                                    <  2:101735/141‑1 (MQ=255)
                                                                                                          cgctgtctgagtctgagtcgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgagtctg                                  <  1:98095/141‑1 (MQ=255)
                                                                                                          cgctgtctgagtctgagtcgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgagtctg                                  <  1:123360/141‑1 (MQ=255)
                                                                                                           gctgtctgagtctgagtcgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgagtctga                                 <  2:326081/141‑1 (MQ=255)
                                                                                                            ctgtctgagtctgagtcgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgagtctgaa                                >  1:121685/1‑141 (MQ=255)
                                                                                                              gtctgagtctgagtcgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGATTATGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgagtctgaatc                              <  1:75007/141‑1 (MQ=255)
                                                                                                               tctgagtctgagtcgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGtctgagtctgaatcgctatctgagtctgaatcg                             >  1:189629/1‑141 (MQ=255)
                                                                                                                    gtctgagtcgctgtctgagtctgaCTCGCTCTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCtgagtctgaatcgctatctgagtctgaatcgctatc                        <  2:256941/141‑1 (MQ=255)
                                                                                                                     tctgagtcgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTgagtctgaatcgctatctgagtctgaatcgctatct                       >  1:181163/1‑141 (MQ=255)
                                                                                                                       tgagtcgctgtctgagtctgaATCGCTATCTGAATCCGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAGTCTGAGTGGCTGgctgagtctgcgtcgctatccgagtctgactcccttttcga                     >  1:212454/1‑135 (MQ=11)
                                                                                                                          ttcgtggtctgagtctgaATCGCAATTTGACTCTCCGTCGCTCTCTTTGTCTGCGTCGCGGTCTGAATCTCTGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCtgaatcgctgtctgagtctgaatcgctatctgagtc                  <  2:252458/135‑1 (MQ=11)
                                                                                                                            cgctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCTGaatcgctatctgagtctgaatcgctatctgagtctg                <  1:249773/141‑1 (MQ=255)
                                                                                                                             gctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAGTCTGAatcgctatctgagtctgaatcgctatctgagtctga               <  2:280180/141‑1 (MQ=255)
                                                                                                                              ctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCTGAAtcgctatctgagtctgaatcgctatctgagtctgaa              >  1:138306/1‑141 (MQ=255)
                                                                                                                              ctgtctgagtctgaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGACTCTGAAtcgctatctgattctgagtcgctatctgattctgaa              >  2:276480/1‑141 (MQ=255)
                                                                                                                                          gaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCTGAATCGCTATCTGAGTCTGAATCGCTATCTGAGTCTGAATCACTGTCTGAg  >  1:160875/1‑141 (MQ=255)
                                                                                                                                          gaATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCTGAATCGCTATCTGAGTCTGAATCGCTATCTGAGTCTGAATCACTGTCTGAg  <  1:175604/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                          
CTGTCTGAATCTGAATCGCTGTCTGAGTCCGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTATCTGAGTCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAGTCTGAATCGCTATCTGAATCTGAGTCGCTGTCTGAGTCTGAGTCGCTGTCTGAATCTGAGTCGCTGTCTGAATCTGAATCGCTGTCTGAGTCTGAATCGCTATCTGAGTCTGAATCGCTATCTGAGTCTGAATCACTGTCTGAG  >  USA300TCH1516_ALE/2774901‑2775179

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: ‑