Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,744,545 A→T 6.6% Y43N (TAC→AAC)  apt ← Adenine phosphoribosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,744,5450AT 6.6% 159.1 / 2.2 58Y43N (TAC→AAC) aptAdenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base A (23/30);  new base T (2/2);  total (26/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

ATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAAT  >  USA300TCH1516_ALE/1744409‑1744675
                                                                                                                                        |                                                                                                                                  
aTGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAACCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTGCAAGGATATCACCATCTCCGGCTTTTGCGGATTc                                                                                                                                 >  2:127423/1‑140 (MQ=255)
aTGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCACCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACACCGATATCAACATCTCTGTCTTTTGCGTATTc                                                                                                                                 >  1:381729/1‑140 (MQ=255)
aTGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATACCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATATATGACTTTAGCGTAtta                                                                                                                                 >  2:578606/1‑139 (MQ=255)
   aCTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATACAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTAc                                                                                                                              <  2:731699/140‑1 (MQ=255)
   aCTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTAc                                                                                                                              <  1:419953/140‑1 (MQ=255)
    cTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGCTCCTACAACGCTATCAAACCCTCTGCCCCATGCGCATTCTACa                                                                                                                             >  2:354735/1‑140 (MQ=255)
       cACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTTTTCTACAAtt                                                                                                                          <  2:263140/140‑1 (MQ=255)
       cACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTATACAAtt                                                                                                                          >  1:726798/1‑140 (MQ=255)
        aCGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAAttt                                                                                                                         <  1:222886/140‑1 (MQ=255)
           aGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTAt                                                                                                                      >  2:395253/1‑140 (MQ=255)
             gTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATAATCATCTCTGTCTTTTGCGTATTCTACACTTTTATCt                                                                                                                    >  1:337410/1‑140 (MQ=255)
               aaTTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACTGCCAATCATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGt                                                                                                                  <  1:795727/140‑1 (MQ=255)
               aaTTCCGCTTCTTTTCTCACAGGTGCAAAGCCATTCCCCGTTGACTCAGCTACAGGACAGCCAATGATACAGCCTCGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGt                                                                                                                  <  2:539935/140‑1 (MQ=255)
                 tttCCCTTCTTTTCTACCAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTg                                                                                                                >  1:175466/1‑140 (MQ=255)
                 taccccTTCTTTTCTAACAGTTGCGAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACCATTTTATCTGTTg                                                                                                                <  2:310108/137‑1 (MQ=255)
                    cccGTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTTTTCTACAATTTTATCTGTTGCAt                                                                                                             <  2:580711/140‑1 (MQ=255)
                     ccTTCTTTTCCAACATGTGCAAAGCCAAGCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCTCGCGCTTCAGGTCCTACAACGCTATCAACTTCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATa                                                                                                            <  2:15350/140‑1 (MQ=255)
                           tttCTGACAGGTGCAAAGCCAATCCCCATTTAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCata                                                                                                      <  2:429687/140‑1 (MQ=255)
                            ttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACCGGACAGCCAATGATACCGCCACGCGCTTCAGGTCCTACAACGATCTCCACATCTCTGTCTTTTACGCATTCTCCAATTTTCTCTGTTGCCTCCCCatat                                                                                                     >  1:713974/1‑140 (MQ=255)
                             tCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATg                                                                                                    <  1:172815/140‑1 (MQ=255)
                              cTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGc                                                                                                   <  1:395253/140‑1 (MQ=255)
                                  cAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCa                                                                                               >  1:125292/1‑140 (MQ=255)
                                      tGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCTGTGGGGAAGCCGCGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCAt                                                                                           <  1:546644/140‑1 (MQ=255)
                                      tGCAAAGCAAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCCCGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATGTTATCTGTTGCATAGCCATATGCTTCACCAt                                                                                           <  1:735742/140‑1 (MQ=255)
                                       gCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTTTTCTCCAATTTTATCTGTTGCATAGCCATATTCTTCACCttt                                                                                          >  1:475659/1‑140 (MQ=255)
                                        cAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATCAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTCCGCGTCCTCTACACCCTTATCTGTTACATAGCGATATTCTTAACCAttc                                                                                         >  1:26390/1‑139 (MQ=255)
                                        cAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCCTTa                                                                                         >  1:547775/1‑140 (MQ=255)
                                          aaGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATc                                                                                       >  1:461619/1‑140 (MQ=255)
                                          aaGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATc                                                                                       >  1:174997/1‑140 (MQ=255)
                                             ccAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCAt                                                                                    <  2:175466/140‑1 (MQ=255)
                                                  ccccATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGGCCTACAACGATATCAACATCTCTCTCTTTTGCGTATTCTACAATTTTATCTGTCGCATAGCCATATGCTTCACCATTATCCATATTTg                                                                               >  2:647256/1‑140 (MQ=255)
                                                      aTTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTgtagt                                                                           <  1:430710/140‑1 (MQ=255)
                                                      aTTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTgtagt                                                                           <  1:679745/140‑1 (MQ=255)
                                                      aTTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTgtagt                                                                           <  1:710416/140‑1 (MQ=255)
                                                          caTAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAata                                                                       <  2:665920/139‑1 (MQ=255)
                                                          aaTAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCATGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAata                                                                       <  1:33887/140‑1 (MQ=255)
                                                               gCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCtt                                                                  >  1:512607/1‑140 (MQ=255)
                                                                     ggACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTATGTCTTTTGCGTTTTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAACCt                                                            >  2:736278/1‑140 (MQ=255)
                                                                      gACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATGTCAACATCTCTGTCGTTTGCTTATTCTACAATTTTATCTGTTTCATAGCCATATGCTTCACCATTATCCATGATGGTAGTAATATCCTTggtactg                                                           >  1:359884/1‑134 (MQ=255)
                                                                      gACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTa                                                           >  2:278395/1‑140 (MQ=255)
                                                                        cAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATACTTGAAACTAac                                                         >  2:464218/1‑140 (MQ=255)
                                                                            cAATGATAAAGCCACGCGTTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCt                                                     >  1:186989/1‑140 (MQ=255)
                                                                             aaTGATAAAGGCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCCTAATTGTAGTAATATCCTTGAAACTAACACCTg                                                    <  1:154689/140‑1 (MQ=255)
                                                                               tGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGt                                                  >  2:658179/1‑140 (MQ=255)
                                                                                   aaaGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCg                                              <  1:448726/140‑1 (MQ=255)
                                                                                         aCGCGCTTCAGGTCCTACAACGATAGCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAAt                                        <  2:596667/140‑1 (MQ=255)
                                                                                          ggcgcTTTAGGGCGTACAACGATATCAACGTCTCTGTGTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATc                                       <  2:191504/139‑1 (MQ=255)
                                                                                             gcTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTg                                    <  1:634402/140‑1 (MQ=255)
                                                                                                              gATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTAtt                   <  1:454321/140‑1 (MQ=255)
                                                                                                                 atCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATCATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCt                <  1:628323/140‑1 (MQ=255)
                                                                                                                  tCAACATCTCTGTCTTTTGCGGATTCTACAATTTTATCTGGTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCtt               <  1:327551/140‑1 (MQ=255)
                                                                                                                   cAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCttt              <  1:285946/140‑1 (MQ=255)
                                                                                                                    aaCATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTTGGCCCATCTTGAACTTCTGATACGTATTGCTGTa             >  2:434035/1‑140 (MQ=255)
                                                                                                                       aTCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAAt          <  2:104105/140‑1 (MQ=255)
                                                                                                                            tGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATATCTGCCAGTTTGGCCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCGtt     >  1:796296/1‑140 (MQ=255)
                                                                                                                              tCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCACTCTTGAAGTTCTGATACGTATTGCTTTAAATCCATTaa   >  1:337286/1‑140 (MQ=255)
                                                                                                                               ctgttGCGTAGTCTACAATTTTAGCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTCAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAat  <  1:458249/137‑1 (MQ=255)
                                                                                                                               cTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAat  <  1:354735/140‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                  
ATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAAT  >  USA300TCH1516_ALE/1744409‑1744675

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: ‑