Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 554,989 T→C 8.4% A315A (GCT→GCC)  lysS → Lysine‑‑tRNA ligase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE554,9890TC 8.4% 150.8 / 5.0 58A315A (GCT→GCC) lysSLysine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base T (22/30);  new base C (3/2);  total (26/32)
Fisher's exact test for biased strand distribution p-value = 6.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

TGAATTATATGAAGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTAAAGATACAATGAAATATG  >  USA300TCH1516_ALE/554854‑555122
                                                                                                                                       |                                                                                                                                     
tGAATTATATGAAGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGAc                                                                                                                                  <  1:170776/141‑1 (MQ=255)
tGAATTATATGAAGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATCGCGAGAAATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGAGCGATTTAGAATCTGCTTGGAc                                                                                                                                  <  1:291849/141‑1 (MQ=255)
 gAATTATATGAAGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACt                                                                                                                                 >  1:171214/1‑141 (MQ=255)
   aTTATATGAAGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACCCg                                                                                                                               >  1:56760/1‑141 (MQ=255)
      atatGAAGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGttt                                                                                                                            <  1:489341/141‑1 (MQ=255)
          gAAGCATATGCAGATTATCATGACAATATGGATTAAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATGCAATGGGGTAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCat                                                                                                                        <  2:355141/141‑1 (MQ=255)
           aaGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCata                                                                                                                       <  1:565797/141‑1 (MQ=255)
           aaGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCata                                                                                                                       <  1:580347/141‑1 (MQ=255)
           aaGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCaca                                                                                                                       >  2:149716/1‑139 (MQ=255)
               atatGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATAttgt                                                                                                                   <  1:63516/141‑1 (MQ=255)
                  tGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGa                                                                                                                <  2:21423/141‑1 (MQ=255)
                    cAGATTCGCATGTCATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATg                                                                                                              <  2:62796/141‑1 (MQ=255)
                     agcttATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGc                                                                                                             <  1:240923/138‑1 (MQ=255)
                       aTTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTg                                                                                                           <  1:572534/141‑1 (MQ=255)
                           tCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTaaa                                                                                                       >  1:162688/1‑141 (MQ=255)
                            cATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTaaaa                                                                                                      >  2:201220/1‑141 (MQ=255)
                            cATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTaaaa                                                                                                      <  1:479709/141‑1 (MQ=255)
                             aTGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAaag                                                                                                     <  1:432171/141‑1 (MQ=255)
                                aCATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTCAaagaag                                                                                                  >  2:348629/1‑141 (MQ=255)
                                            tAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCGTGGACTCGTTTGCATATTGTTGATGGTGTAAAAGCAGCTACTGGTATAg                                                                                      >  2:78940/1‑141 (MQ=255)
                                               cAGAATCAATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGAtt                                                                                   <  2:396288/141‑1 (MQ=255)
                                                   aTCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGCTGCTGTAAAAGAAGCTACTGGTGTAGATTTTTa                                                                               >  2:572170/1‑141 (MQ=255)
                                                   aTCCATGGTGAGACACATTGCCAATGAAGGTTTAGGTTCTGCAAAAGTACAATTGCACGCTCAAACCGTCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTa                                                                               <  1:140917/141‑1 (MQ=255)
                                                      tATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGa                                                                            <  1:609396/141‑1 (MQ=255)
                                                      tATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCCTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGa                                                                            >  1:102391/1‑141 (MQ=255)
                                                      tATGGTGAGACATATTGCCAATGAAGTGGTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCCTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGa                                                                            >  1:25946/1‑141 (MQ=255)
                                                           tGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTa                                                                       <  2:557721/141‑1 (MQ=255)
                                                                   atTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAAAGATCGATTTAGAATCTGCTTGGACTCGTTGGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGtgat                                                               <  1:83023/141‑1 (MQ=255)
                                                                        cAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATgaaga                                                          >  2:438727/1‑141 (MQ=255)
                                                                           tGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGc                                                       >  1:232793/1‑141 (MQ=255)
                                                                            gAAGTGTTAGGTTCTGCAAAAGTGCAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATAGTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCt                                                      <  2:472617/141‑1 (MQ=255)
                                                                            gAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGGTGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCt                                                      <  1:235597/141‑1 (MQ=255)
                                                                            gAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAATGATGAAGAAGCt                                                      >  2:138355/1‑141 (MQ=255)
                                                                             aaGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTa                                                     <  1:434168/141‑1 (MQ=255)
                                                                             aaGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTa                                                     <  2:595762/141‑1 (MQ=255)
                                                                             aaGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTa                                                     >  1:356531/1‑141 (MQ=255)
                                                                              aGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTaa                                                    >  2:50307/1‑141 (MQ=255)
                                                                                     ggTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTa                                             >  1:479526/1‑141 (MQ=255)
                                                                                     ggTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTa                                             >  1:514137/1‑141 (MQ=255)
                                                                                      gTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAg                                            >  1:249825/1‑141 (MQ=255)
                                                                                       ttCTGCAAAAGTACAATACAGTGGGGAAACGATCTATGTAGAATCTGTTTGGACTCGTTTGCTTATTGTTGATGCTGTAAAAGAAGTTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGc                                           <  1:405680/141‑1 (MQ=255)
                                                                                        tCTGCAAAAGTACAATACAATGGGGAAACTATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGATGCTAATGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCt                                          <  2:226779/141‑1 (MQ=255)
                                                                                           gCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAGGCTCAAAGTGATGAAGAAGCTAAAGCTTTCGCTaaa                                       >  2:363670/1‑141 (MQ=255)
                                                                                                  tacaatacaaTGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATg                                <  1:201220/141‑1 (MQ=255)
                                                                                                  tacaatacaaTGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGCTTGCATATTGATGTTGATGTAAAAGAAGCTTTCGGTTTTGTTTTTTTTGGTTTTAGTAGTGATGAAAAATCAAAATCTTTAGCTAAAGAACaag                                >  2:143850/1‑139 (MQ=255)
                                                                                                  gacaatacaagGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATg                                <  2:453462/140‑1 (MQ=255)
                                                                                                      atacaatGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTAt                            <  1:573814/141‑1 (MQ=255)
                                                                                                             ggggAAACGATCGATTTAGAATCTGCCTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGACAtt                     >  2:366236/1‑141 (MQ=255)
                                                                                                              gggAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTa                    >  1:121725/1‑141 (MQ=255)
                                                                                                               ggAAACGATCGATTTAGAATCTGCCTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTaa                   <  2:25946/141‑1 (MQ=255)
                                                                                                               ggAAACGATCGATTTAGAATCGGCCTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTaa                   <  2:102391/141‑1 (MQ=255)
                                                                                                                  aaCGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTAAAGa                >  1:152235/1‑141 (MQ=255)
                                                                                                                  aaCGATCGATTTAGAACCTGCTTGGACTCGTTTGCATAATGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAGAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGCAATTAAAgg                >  1:342021/1‑140 (MQ=255)
                                                                                                                      ttctatTTAGACTCTGTTTGGACTCGTTTGCATGTTGTTGATGCTGTAAAATATGTTACTGTGGTATATTTTTATGAAGTTAAAAGTGATTAAGAACCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTAAAGATACa            <  2:336164/137‑1 (MQ=255)
                                                                                                                       tcgatTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTGAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTAAAGATACaa           >  1:599166/1‑141 (MQ=255)
                                                                                                                          atTTAGAATCTGCTTGGGCTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTAAAGATACAATGa        <  2:56760/141‑1 (MQ=255)
                                                                                                                          atTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTAAAGATACAATGa        >  2:174554/1‑141 (MQ=255)
                                                                                                                                aaTCTGCTTGGAATGATTTGCATTGTTGTGATGTGGCAAAAGAAGATACTGGTGTAGATTTTTAGGAAGTTAAAAGTGATGAAGAAGTTAAAGCTTTAGCTAAAGAACCTGGTATTGAAATTAAAGATACAATGAAatatt  <  2:337845/141‑2 (MQ=255)
                                                                                                                                       |                                                                                                                                     
TGAATTATATGAAGCATATGCAGATTATCATGACATTATGGATTTAACAGAATCTATGGTGAGACATATTGCCAATGAAGTGTTAGGTTCTGCAAAAGTACAATACAATGGGGAAACGATCGATTTAGAATCTGCTTGGACTCGTTTGCATATTGTTGATGCTGTAAAAGAAGCTACTGGTGTAGATTTTTATGAAGTTAAAAGTGATGAAGAAGCTAAAGCTTTAGCTAAAGAACATGGTATTGAAATTAAAGATACAATGAAATATG  >  USA300TCH1516_ALE/554854‑555122

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: ‑