Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,352,815 G→A 53.0% A92V (GCA→GTA)  rpsI ← 30S ribosomal protein S9

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,352,8150GA53.0% 9.8 / 118.9 83A92V (GCA→GTA) rpsI30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (17/22);  new base A (19/25);  total (36/47)
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

TTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAG  >  USA300TCH1516_ALE/2352728‑2352904
                                                                                       |                                                                                         
ttAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCtt                                                                                        <  1:295580/91‑1 (MQ=255)
ttAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACtt                                                                                        <  1:268491/91‑1 (MQ=255)
ttAAGACCTGGCTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACtt                                                                                        <  1:3764742/91‑1 (MQ=255)
 tAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTc                                                                                       <  1:1162002/91‑1 (MQ=255)
  aaGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCt                                                                                      <  1:3078277/91‑1 (MQ=255)
   aGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCta                                                                                     >  1:2884084/1‑91 (MQ=255)
      ccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCtaata                                                                                  >  1:1146391/1‑91 (MQ=255)
      ccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCtaata                                                                                  >  1:652719/1‑91 (MQ=255)
      ccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaata                                                                                  <  1:2102774/91‑1 (MQ=255)
      ccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaata                                                                                  <  1:2098398/91‑1 (MQ=255)
       cTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaataa                                                                                 >  1:908040/1‑91 (MQ=255)
            tttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCAc                                                                            <  1:421121/91‑1 (MQ=255)
             ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACg                                                                           <  1:1563792/91‑1 (MQ=255)
             ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACg                                                                           <  1:1158365/91‑1 (MQ=255)
               ttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                         <  1:40942/91‑1 (MQ=255)
                 aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCg                                                                       <  1:364774/91‑1 (MQ=255)
                 aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCg                                                                       >  1:757089/1‑91 (MQ=255)
                 aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCg                                                                       >  1:680771/1‑91 (MQ=255)
                   gTTCTTTCATACGTGGGTCACGAGTTAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGAt                                                                     <  1:3859214/91‑1 (MQ=255)
                   gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGAt                                                                     <  1:3200178/91‑1 (MQ=255)
                   gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGAt                                                                     >  1:650933/1‑91 (MQ=255)
                   gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGAt                                                                     <  1:3631288/91‑1 (MQ=255)
                   gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGAt                                                                     <  1:1424357/91‑1 (MQ=255)
                        ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGt                                                                >  1:1555768/1‑91 (MQ=255)
                          cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGa                                                              >  1:2510779/1‑91 (MQ=255)
                           aTACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGAc                                                             >  1:2892002/1‑91 (MQ=255)
                            tACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACg                                                            >  1:1517283/1‑91 (MQ=255)
                             aCGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACgg                                                           >  1:2905122/1‑91 (MQ=255)
                             aCGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACgg                                                           <  1:65249/91‑1 (MQ=255)
                             aCGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACgg                                                           >  1:1053670/1‑91 (MQ=255)
                              cGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGa                                                          <  1:1077559/91‑1 (MQ=255)
                               gTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGAt                                                         <  1:2489029/91‑1 (MQ=255)
                                tGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATa                                                        >  1:3824412/1‑91 (MQ=255)
                                 gggTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATag                                                       <  1:1730759/91‑1 (MQ=255)
                                   gTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagct                                                     <  1:693359/91‑1 (MQ=255)
                                   gTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagct                                                     >  1:1148150/1‑91 (MQ=255)
                                    tCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagctt                                                    <  1:1780195/91‑1 (MQ=255)
                                     cACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttg                                                   >  1:1902272/1‑91 (MQ=255)
                                      aCGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttga                                                  <  1:1325469/91‑1 (MQ=255)
                                       cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                                 <  1:3904383/91‑1 (MQ=255)
                                       cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                                 <  1:2110096/91‑1 (MQ=255)
                                       cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                                 <  1:1331091/91‑1 (MQ=255)
                                        gAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagc                                                <  1:2347492/91‑1 (MQ=255)
                                          gtaagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcatgagctt                                              >  1:2066455/1‑91 (MQ=255)
                                           taagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagcttg                                             <  1:672664/91‑1 (MQ=255)
                                            aagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGt                                            <  1:1833041/91‑1 (MQ=255)
                                             agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                           >  1:2428630/1‑91 (MQ=255)
                                             agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                           <  1:414245/91‑1 (MQ=255)
                                             agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                           >  1:2623832/1‑91 (MQ=255)
                                               taaTCCAGCGCGTTTTAAAGAACCCCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCCTGTCCa                                         >  1:1406943/1‑91 (MQ=255)
                                                aaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAg                                        <  1:4054750/91‑1 (MQ=255)
                                                      gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAac                                  >  1:2176694/1‑91 (MQ=255)
                                                      gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAac                                  >  1:3147593/1‑91 (MQ=255)
                                                      gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAac                                  <  1:1139199/91‑1 (MQ=255)
                                                        gcgTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAacca                                <  1:2336506/91‑1 (MQ=255)
                                                          gTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                              <  1:2184667/91‑1 (MQ=255)
                                                          gTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                              <  1:3075608/91‑1 (MQ=255)
                                                          gTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                              <  1:3263557/91‑1 (MQ=255)
                                                             ttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccacc                           >  1:1149646/1‑91 (MQ=255)
                                                              tAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAAccaccacca                          >  1:2419512/1‑91 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTGCTTCTAATACTGCACGAGCGATTCCGTGACGGATAGCTTGAGCTCGTCCAGTGAAACCACCACCATg                        <  1:1727738/91‑1 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                        >  1:994471/1‑91 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                        <  1:1727799/91‑1 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                        >  1:3655712/1‑91 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                        >  1:557461/1‑91 (MQ=255)
                                                                    aCCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACg                    >  1:2260583/1‑91 (MQ=255)
                                                                     ccTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGt                   >  1:3010174/1‑91 (MQ=255)
                                                                     ccTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGt                   <  1:893129/91‑1 (MQ=255)
                                                                     ccTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGt                   <  1:4095531/91‑1 (MQ=255)
                                                                     ccTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGt                   >  1:4129655/1‑91 (MQ=255)
                                                                        ctGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAGCCACCACCATGAACGTTaa                <  1:2647763/91‑1 (MQ=255)
                                                                        ctGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTaa                <  1:2647283/91‑1 (MQ=255)
                                                                        ctGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTaa                >  1:963614/1‑91 (MQ=255)
                                                                         tGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc               >  1:743008/1‑91 (MQ=255)
                                                                           tATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAGCGTTAACTa             <  1:2086238/91‑1 (MQ=255)
                                                                               cAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAc         >  1:263953/1‑91 (MQ=255)
                                                                                 ggATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcat       <  1:22928/91‑1 (MQ=255)
                                                                                 ggATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcat       >  1:1848447/1‑91 (MQ=255)
                                                                                 ggATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAACTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcat       <  1:22902/91‑1 (MQ=255)
                                                                                 ggATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcat       <  1:711189/91‑1 (MQ=255)
                                                                                 ggATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcat       <  1:711208/91‑1 (MQ=255)
                                                                                  gATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatc      >  1:2044772/1‑91 (MQ=255)
                                                                                      tGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAg  >  1:3002500/1‑91 (MQ=255)
                                                                                       |                                                                                         
TTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAG  >  USA300TCH1516_ALE/2352728‑2352904

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑