Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,162,009 C→A 7.6% Q428K (CAA→AAA)  mutS_2 → DNA mismatch repair protein MutS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,162,0090CA 7.6% 167.9 / 2.2 60Q428K (CAA→AAA) mutS_2DNA mismatch repair protein MutS
Reads supporting (aligned to +/- strand):  ref base C (27/27);  new base A (2/3);  total (30/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

ACCGCAAGCAAATTTGTATATCAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGATATTGAGTT  >  USA300TCH1516_ALE/2161874‑2162148
                                                                                                                                       |                                                                                                                                           
aCCGCAAGCAAATTTGTATATCAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCaaaaa                                                                                                                                        <  2:561068/141‑1 (MQ=255)
 ccGCAAGCAAATTTGTATATCAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGGTAATAaaaaaa                                                                                                                                       >  2:239528/1‑141 (MQ=255)
     aagcaaATTTGTATATCAACCTGGAATTGTGTTCACGTCAATGGCAAATGTCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAAtata                                                                                                                                   <  1:592777/141‑1 (MQ=255)
      atcaaATGTTTATATCAACCTGGAAATATATACACATCAATGGCTAATGTAGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTAAAAAAAAAAAAAAAATATAc                                                                                                                                  <  2:385478/139‑1 (MQ=255)
      agcaaAGTTGTATATCAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATAc                                                                                                                                  <  2:278301/141‑1 (MQ=255)
         aaaTTTGGATATCAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGc                                                                                                                               <  2:189607/141‑1 (MQ=255)
                 atatCAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGa                                                                                                                       <  2:90588/141‑1 (MQ=255)
                     cAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGaa                                                                                                                   <  1:299499/141‑1 (MQ=255)
                      aaCCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGaaa                                                                                                                  <  1:448560/141‑1 (MQ=255)
                         cTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATGAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAAGATACTGCTTTATAGATGAAAttt                                                                                                               >  2:239084/1‑141 (MQ=255)
                           ggAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGaaaatggg                                                                                                             >  2:580028/1‑136 (MQ=255)
                           ggAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAAttttt                                                                                                             >  2:165909/1‑141 (MQ=255)
                           ggAATTGTGTTCACGTCAATAGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAAttttt                                                                                                             >  1:371417/1‑141 (MQ=255)
                             aaTTGTGTTCACGTCAATGGCAAATGCCGATGATGGGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGAAGAAATTTTTaa                                                                                                           >  2:24459/1‑141 (MQ=255)
                                tgttTTCACGTCGATGGGAATTGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAgg                                                                                                        <  2:149692/141‑1 (MQ=255)
                                   gtTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGCTAGGTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTAc                                                                                                     >  1:118359/1‑141 (MQ=255)
                                   gtTCACGTCAATGGAAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTAc                                                                                                     <  1:363800/141‑1 (MQ=255)
                                      cACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGACTTCACGCCTCGATAAATGATATACTGCTTTATAGATGAAATTTTTAAAGGTAGCaa                                                                                                  >  1:288782/1‑141 (MQ=255)
                                       aCGCCAATGCCAAATGGCAAAGATGTGTAAGAAGGCGATAATAACTTTATACATAAATTAAAATCAAGTAAGCCTTTTTTTGAAAAAAAAAAAAAAAAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAac                                                                                                 <  2:207283/141‑1 (MQ=255)
                                             aTGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCAAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACACCt                                                                                           >  2:600240/1‑141 (MQ=255)
                                               ggaaaaaGCCGAAGATGAGTAAAAAAGCGATAGTTAATTTAAGGCTAAATTAAAATATATTAAGCGTATTGTTGAAAAAAAAAAAAAAAAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGa                                                                                         <  2:412560/138‑1 (MQ=255)
                                                 cAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAAc                                                                                       <  1:154195/141‑1 (MQ=255)
                                                  aaaTGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAACTATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACg                                                                                      >  1:35350/1‑141 (MQ=255)
                                                  aaaTGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAAGACAACTAAACg                                                                                      >  2:150199/1‑141 (MQ=255)
                                                  aaaTGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATAAAAAAATAGACTTCTTTATAGATGAAATTTTTAAAGGTACCAACACCACTGAACg                                                                                      >  1:15855/1‑141 (MQ=255)
                                                     tGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAAt                                                                                   >  1:445385/1‑141 (MQ=255)
                                                      gCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTAAATGAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAAtt                                                                                  >  2:401497/1‑141 (MQ=255)
                                                       ccGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTTTAGATGAGATTTTTAAAGGTACCAACACAACTGAACGAATTg                                                                                 >  2:165822/1‑141 (MQ=255)
                                                       ccGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACCAAtag                                                                                 >  1:286674/1‑139 (MQ=255)
                                                          atgatgTGTTATCAGGCGATAGGTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCg                                                                              >  2:5277/1‑141 (MQ=255)
                                                          agcatgTGTTATCAGGCCATAGTTATTTCAGGGCGGTATTAAATTCTACTAAGCGTAGTGTTGATACCACCGGTTGTCACACCATAGGCTGCTGTATAGATTAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCg                                                                              <  1:143240/138‑1 (MQ=255)
                                                           tgatgTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGc                                                                             <  1:550093/141‑1 (MQ=255)
                                                           ggatgTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGc                                                                             <  1:81588/140‑1 (MQ=255)
                                                            gttggtttATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCt                                                                            <  2:300739/135‑1 (MQ=255)
                                                              tgtgTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTc                                                                          <  1:331841/141‑1 (MQ=255)
                                                                       aGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGt                                                                 <  1:35127/141‑1 (MQ=255)
                                                                          cGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAAAAGAACTGAACGAATTGCCGCTTAAGAATCAGTACt                                                              >  2:342838/1‑141 (MQ=255)
                                                                             tAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATc                                                           >  1:15592/1‑141 (MQ=255)
                                                                              aGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCa                                                          <  1:279905/141‑1 (MQ=255)
                                                                                        tGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGGTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGATGCAGAATCGGTACTATCATTTTTACAta                                                >  2:230484/1‑140 (MQ=255)
                                                                                                     aTCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACtt                                   >  1:544465/1‑141 (MQ=255)
                                                                                                       cTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTa                                 <  2:579032/141‑1 (MQ=255)
                                                                                                         aTTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTaga                               >  1:7983/1‑141 (MQ=255)
                                                                                                         aTTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTaga                               <  1:529058/141‑1 (MQ=255)
                                                                                                              gCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGACAAATCTAACTTTAGAGatat                          >  1:56886/1‑141 (MQ=255)
                                                                                                              gCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTAt                          <  1:210513/141‑1 (MQ=255)
                                                                                                               cGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTAtt                         >  2:329931/1‑141 (MQ=255)
                                                                                                                 tATTGTTGAAATTCCAGCTAATCAAAAAATATACTGCTTTCTAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTgc                       >  1:267094/1‑141 (MQ=255)
                                                                                                                     gttgAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATAATTTTTACATGAAAAATCTAACTTTAAAGATATTgcagca                   >  2:169026/1‑141 (MQ=255)
                                                                                                                       tgAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAac                 >  2:49081/1‑141 (MQ=255)
                                                                                                                            ttCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATg            >  1:190343/1‑141 (MQ=255)
                                                                                                                            ttCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATg            <  1:329931/141‑1 (MQ=255)
                                                                                                                              tcAGATAATCAAAAAATATAATGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAAATTTAGAGTTATTGCAGCAACACATGat          <  1:464536/140‑1 (MQ=255)
                                                                                                                              ccAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGat          <  2:104079/141‑1 (MQ=255)
                                                                                                                                aGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACACCTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGatat        >  1:20807/1‑141 (MQ=255)
                                                                                                                                aGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGatat        <  1:165909/141‑1 (MQ=255)
                                                                                                                                aGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGatat        <  1:580028/141‑1 (MQ=255)
                                                                                                                                  aTAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTACCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGATATTg      >  1:86460/1‑141 (MQ=255)
                                                                                                                                    aaTCAAAAAATATACTGCTGTATAGATAAAAGTTTTAAAGGTACATACACAACGTAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGATATTGAg    <  1:289188/141‑1 (MQ=255)
                                                                                                                                      tCAAAAAATATACTGCTTTAGAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCACCACATGATATTGAGtt  <  1:363505/141‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                           
ACCGCAAGCAAATTTGTATATCAACCTGGAATTGTGTTCACGTCAATGGCAAATGCCGATGATGTGTTATCAGGCGATAGTTATTTTATGGCTGAATTAAAATCTATTAAGCGTATTGTTGAAATTCCAGATAATCAAAAAATATACTGCTTTATAGATGAAATTTTTAAAGGTACCAACACAACTGAACGAATTGCCGCTTCAGAATCAGTACTATCATTTTTACATGAAAAATCTAACTTTAGAGTTATTGCAGCAACACATGATATTGAGTT  >  USA300TCH1516_ALE/2161874‑2162148

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: ‑