Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,289,325 C→A 12.7% Q55H (CAG→CAT)  cdaA ← Cyclic di‑AMP synthase CdaA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,289,3250CA12.7% 157.5 / 9.5 57Q55H (CAG→CAT) cdaACyclic di‑AMP synthase CdaA
Reads supporting (aligned to +/- strand):  ref base C (18/31);  new base A (3/4);  total (21/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.22e-01

AAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGTAAATCAAGGATACTCGTTACAATTT  >  USA300TCH1516_ALE/2289187‑2289449
                                                                                                                                          |                                                                                                                            
aaaGCTACCTCTACCCAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTAATATTAAAGCTAATACCCTCCATTGAATAATGACATCGAATTATTTAGATGTTGTAATCACGATGAATATCATACTTCTctactt                                                                                                                            >  2:404396/1‑140 (MQ=255)
   gCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGAcc                                                                                                                         <  1:41299/141‑1 (MQ=255)
   gCTACCCCTACCAAGTCGATCTAACGCGCATCAAATTGCTGGTTGGAATACTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGAcc                                                                                                                         <  1:431695/141‑1 (MQ=255)
      aactctACCAAGTTCTTCTAACGCACGCCTAATTTCTGCTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCCAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAAt                                                                                                                      <  2:243770/139‑1 (MQ=255)
      aCCTCTACCTAGTTGTTCTCACGCACGTCTAATTTCTTGTTGGAATATTACTATTATAGCTAATTCCCCCCATTTAATACCTATACCGAATAATTTAGATTTTGCAGTCAAGTTCAATATCATACTTATCTTCTGACCAAt                                                                                                                      <  2:211148/141‑1 (MQ=255)
        ctctACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAAtca                                                                                                                    >  2:341557/1‑139 (MQ=255)
         tctACCAAGTTGTTCTAACGCTCGTCTGATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAAc                                                                                                                   <  1:433939/141‑1 (MQ=255)
         tctACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATACTTTAGATGTTGCAGTCAAGTTCCCTATCATACGTATCTGCTGACCAATAAc                                                                                                                   <  2:492697/141‑1 (MQ=255)
                cgttggtCTAACGCACGTCTAATTTCTGTTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACt                                                                                                            <  2:693964/140‑1 (MQ=255)
                cgttcttCTAACGAAACTCTAATTCCTGGATGTAATATTACTATGAAAGCTAATTCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACt                                                                                                            <  2:306698/140‑1 (MQ=255)
                aGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTACAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACt                                                                                                            <  1:76643/141‑1 (MQ=255)
                    gttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGATGACCAATAACAATTACTAata                                                                                                        <  2:209031/141‑1 (MQ=255)
                    aatccaaCGCACATCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAATGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAata                                                                                                        <  2:516633/136‑1 (MQ=255)
                     ttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAatat                                                                                                       >  1:138446/1‑141 (MQ=255)
                     ttCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAatat                                                                                                       <  2:468730/141‑1 (MQ=255)
                     ttCTAACCAACGTCTAATTTCTGGTTTGAATATTACTATTAAACCTAATACCCCCCATCTAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAatat                                                                                                       <  2:207085/141‑1 (MQ=255)
                          aCGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCGAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCtt                                                                                                  >  1:643231/1‑141 (MQ=255)
                              aCGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTTAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAg                                                                                              <  2:530182/141‑1 (MQ=255)
                                  ttAATTTCTTTTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGATGACCAATAACAATTACTAATATCCCTTTAAGTAAt                                                                                          <  1:256274/140‑1 (MQ=255)
                                   tAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATACTTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAAATACTAATAGCCCTTCCAGTAAtt                                                                                         >  2:514484/1‑141 (MQ=255)
                                            tttGGAAGATTACTATTAAAGCTATTACCCCCCATTGAATAACGATATTGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCtt                                                                                <  1:213594/140‑1 (MQ=255)
                                            gTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGATGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCtt                                                                                <  1:217909/141‑1 (MQ=255)
                                              tGGAATTTTTCTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGATGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTa                                                                              <  1:568141/141‑1 (MQ=255)
                                                        cTATTAAATCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTaa                                                                    <  2:526158/141‑1 (MQ=255)
                                                         tATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTaaa                                                                   >  2:204661/1‑141 (MQ=255)
                                                           tcaaaGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGa                                                                 <  1:83037/139‑1 (MQ=255)
                                                            tAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGAc                                                                <  1:447256/141‑1 (MQ=255)
                                                              aaGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCg                                                              <  2:434638/141‑1 (MQ=255)
                                                              aaGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCg                                                              <  2:562847/141‑1 (MQ=255)
                                                              aaGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCg                                                              <  2:59184/141‑1 (MQ=255)
                                                               aGCTACTACCCCTCATTGATCAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGt                                                             <  2:196664/141‑1 (MQ=255)
                                                               aGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTTAAGTTCGATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAATTAATTGTATCGCTTTAGTTCCCTTAAAGACCGt                                                             <  2:459526/141‑1 (MQ=255)
                                                               aGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGt                                                             <  2:379496/141‑1 (MQ=255)
                                                                gCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGtg                                                            >  2:568468/1‑141 (MQ=255)
                                                                      aCCCTCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATgaga                                                      <  1:188657/141‑1 (MQ=255)
                                                                       ccccccATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTGCCTTAAAGAACGTGATGagaa                                                     >  2:112781/1‑141 (MQ=255)
                                                                        cccccATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGATGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATAGCTTTAGTTCCCTTAAAGACCCTGATgagaga                                                    >  1:85872/1‑139 (MQ=255)
                                                                        cccccATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTAATCTGATGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGagaag                                                    >  2:186693/1‑141 (MQ=255)
                                                                        cccccATTAAATAACGATATCGAATAATTTAGATGTTACAGTCAAGTTCAATATCATACTTATCTGATGACCAATAACAATTACTAATATCCCTTTAGGTAATGGTATAGCTTTACATCCCTTAAAAACCTGGATGagaaa                                                    >  2:98894/1‑140 (MQ=255)
                                                                          cccATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGataagaa                                                  >  1:280904/1‑140 (MQ=255)
                                                                             aTTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAAAAGATaaa                                               >  1:153210/1‑141 (MQ=255)
                                                                                taaTAACGATATCGAAGAATATAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTAAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTa                                            <  1:399147/140‑1 (MQ=255)
                                                                                gAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTa                                            <  1:571172/141‑1 (MQ=255)
                                                                                  ttAACGATATCGATTAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACa                                          <  2:167170/140‑1 (MQ=255)
                                                                                    aaCGATATCGAATAATTTTGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATa                                        >  2:579999/1‑141 (MQ=255)
                                                                                      cGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATAcc                                      >  1:128927/1‑141 (MQ=255)
                                                                                      cGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATAcc                                      >  1:371207/1‑141 (MQ=255)
                                                                                      cGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATAGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGAGAAAGTAcgagac                                      >  2:430280/1‑136 (MQ=255)
                                                                                            cGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTa                                <  1:516925/141‑1 (MQ=255)
                                                                                                taatTTAGATGTTTCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAg                            <  1:481727/141‑1 (MQ=255)
                                                                                                 aatTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGATCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGATTTATTTCCCTTAATGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGt                           <  1:576357/141‑1 (MQ=255)
                                                                                                     tAGATGTTGCATTCAGGTTCAATATCATACGTATCTGCTGACCAATAACAATTACGAATATACCTATAGGGAATTGTAACGCTTTGGTTGCATTAAGGACCGTGATGAGAAGATAAAGTACATACCAACCTATCGATAAAt                       >  2:174672/1‑141 (MQ=255)
                                                                                                      aGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAAACCGTGATGAGAAGATAAAGTACATACAAAACTCTCAGTAAATc                      >  2:343839/1‑141 (MQ=255)
                                                                                                            tGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGTAAATCAAGGAt                <  2:138446/141‑1 (MQ=255)
                                                                                                                gTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGTAAATCAAGGATACTc            >  1:685667/1‑141 (MQ=255)
                                                                                                                   aaGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGTAAATCAAGGATACTCGtt         >  2:521290/1‑141 (MQ=255)
                                                                                                                   aaGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGTAAATCAAGGATACTCGtt         >  2:566660/1‑141 (MQ=255)
                                                                                                                          atatTATACTTATCGGGTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGTAAATCAAGGATACTCGTTACAAttt  <  2:672938/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                            
AAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAGACCGTGATGAGAAGATAAAGTACATACCAAACTATCAGTAAATCAAGGATACTCGTTACAATTT  >  USA300TCH1516_ALE/2289187‑2289449

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑