Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 4,873 T→A 6.8% I312N (ATC→AAC)  recF → DNA replication and repair protein RecF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE4,8730TA 6.8% 165.2 / 5.2 59I312N (ATC→AAC) recFDNA replication and repair protein RecF
Reads supporting (aligned to +/- strand):  ref base T (30/25);  new base A (2/2);  total (32/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.01e-02

CATCGAGATGATATAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTATTGATCATGAAATCATGA  >  USA300TCH1516_ALE/4734‑5004
                                                                                                                                           |                                                                                                                                   
caTCGAGATGATATAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGAAACGTACAACGGCTTTGTCCATTAAATTAGATGAAATTGAATTCAAGAATATCGAAGTTGGGGAATATCCAATc                                                                                                                                    >  2:142314/1‑141 (MQ=255)
  tCGAGATGATATAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCtt                                                                                                                                  <  1:279575/141‑1 (MQ=255)
  tCGAGATGATATAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCtt                                                                                                                                  <  1:253414/141‑1 (MQ=255)
   cGAGATGATATAAGCTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCtta                                                                                                                                 >  1:275683/1‑141 (MQ=255)
    gagaTGATATAAATTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATAGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCttat                                                                                                                                >  1:279958/1‑141 (MQ=255)
         gatATAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCttattatta                                                                                                                           >  2:90161/1‑141 (MQ=255)
         gatATAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCttattatta                                                                                                                           >  1:144952/1‑141 (MQ=255)
          atatAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCGTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAg                                                                                                                          <  2:140670/141‑1 (MQ=255)
             taAGTTTTGATGTGAATGGGATGGATGCTCAAACATATGGTTATCAAGGACAGCAACGTACAACTGCGTTGTACGTTAAATTAGCTGAAAGTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACg                                                                                                                       >  1:295290/1‑141 (MQ=255)
                 ttttGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGt                                                                                                                   <  2:65654/141‑1 (MQ=255)
                          gAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTACTGCAAATCGAACTTGGGGAACATCCCATCTTATTATTAGACGATGTACTCAGTGa                                                                                                          <  1:154222/141‑1 (MQ=255)
                              ggCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCAACTTATTATTAGACGATGTACTCAGTGAATTa                                                                                                      >  1:128828/1‑141 (MQ=255)
                              ggCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCAACTTATTATTAGACGATGTACTCAGTGAATTa                                                                                                      >  1:103822/1‑141 (MQ=255)
                                  tGGGTGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAgatg                                                                                                  <  2:75961/141‑1 (MQ=255)
                                  tGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAgatg                                                                                                  <  1:358716/141‑1 (MQ=255)
                                    gATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTCgatgat                                                                                                >  1:194655/1‑141 (MQ=255)
                                    gATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAgatgat                                                                                                >  1:395920/1‑141 (MQ=255)
                                     aTGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGAtt                                                                                               <  2:343172/141‑1 (MQ=255)
                                         tCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTcgcg                                                                                           >  2:341833/1‑141 (MQ=255)
                                          cAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGt                                                                                          >  1:360504/1‑141 (MQ=255)
                                                    gTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCAtt                                                                                >  1:263727/1‑141 (MQ=255)
                                                    gTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCACTGAATTAGATGATTGGCGTCAAACGCAtt                                                                                <  1:211658/141‑1 (MQ=255)
                                                    gTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACAATGTGCTCAGTGAATTAGATGATTCGCGTCAAAAGAAtt                                                                                >  2:315615/1‑141 (MQ=255)
                                                    gTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCAACTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCAtt                                                                                <  2:128828/141‑1 (MQ=255)
                                                    gTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCAACTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCAtt                                                                                <  2:103822/141‑1 (MQ=255)
                                                    gTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATAACCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCAtt                                                                                <  2:602/141‑1 (MQ=255)
                                                    gTTCGCAAGGAGAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCAtt                                                                                <  2:329875/141‑1 (MQ=255)
                                                           aGGACAGCAACGTATAACGGCTTTTCCCATTAAATTAGCTGAAATTGAGTGAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAg                                                                         <  1:277206/141‑1 (MQ=255)
                                                           aGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGCTTCGCGTCAAACGCATTTATTAAg                                                                         <  1:288665/141‑1 (MQ=255)
                                                            ggACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGCTGATTCGCGTCAAACGCCTTTATTAAGt                                                                        >  2:9349/1‑141 (MQ=255)
                                                              aCAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAGTTAGATGATTCGCGTCAAACGCATTTATTAAGTAc                                                                      >  1:6382/1‑141 (MQ=255)
                                                              aCAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACAATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGtca                                                                      >  2:99841/1‑139 (MQ=255)
                                                                ggCAACGGAACACGCCTTTGTCCATGAAATTAGCTGAAATTGATTAAATTAATATCGAAGTTGGGGAATATCCCATCTTATTATCAGACGACGTACTCAGTGAATTAGATGATTCGCGTCAAACGCAATTATTAAGTACGa                                                                    <  2:97533/140‑1 (MQ=255)
                                                                 gCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGAt                                                                   >  1:44312/1‑141 (MQ=255)
                                                                       tACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCa                                                             <  1:183785/141‑1 (MQ=255)
                                                                           aCGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATaaa                                                         >  1:147698/1‑141 (MQ=255)
                                                                              gCTTTGTCCATTAACGTAGCTGAAAGTGAGCTGATGAATAGTGAATGTGGTGACTCTCCCATCTTATTATTAGACGATGTACCCAGTGAATTAGATGCTTCGCGTCAAACTCATTTATTAAGTCCGATTCAGCATAAAGTa                                                      <  2:309641/141‑1 (MQ=255)
                                                                                 ttGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACaa                                                   >  1:321095/1‑141 (MQ=255)
                                                                                 ttGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACaa                                                   >  1:173596/1‑141 (MQ=255)
                                                                                   gTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGCTTCAACATAAAGTACAAAc                                                 <  1:297898/141‑1 (MQ=255)
                                                                                     ccATTCAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCAAATCTTATTATTAGACGATGTACTAAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGGACGATTCAACAAAAAGTACAAACAt                                               >  2:338013/1‑141 (MQ=255)
                                                                                     ccATTAAATTAGCTGAAATTGAGTTAATGCATATCGAAGTAGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACAt                                               >  1:373928/1‑141 (MQ=255)
                                                                                     ccATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACAt                                               <  2:147717/141‑1 (MQ=255)
                                                                                      cATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACAtt                                              <  2:279958/141‑1 (MQ=255)
                                                                                         tAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGAAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGt                                           <  1:197641/141‑1 (MQ=255)
                                                                                            agtAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCAc                                        >  2:344443/3‑141 (MQ=255)
                                                                                                 cTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGa                                   >  1:232500/1‑141 (MQ=255)
                                                                                                        tGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGCCATTTGt                            <  2:144952/141‑1 (MQ=255)
                                                                                                        tGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGt                            <  1:90161/141‑1 (MQ=255)
                                                                                                        tGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGt                            >  2:81215/1‑141 (MQ=255)
                                                                                                         gAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTa                           >  1:339352/1‑141 (MQ=255)
                                                                                                           gTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGa                         >  1:326105/1‑141 (MQ=255)
                                                                                                                  aaTATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTAtt                  >  1:137876/1‑141 (MQ=255)
                                                                                                                  aaTATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTAtt                  >  2:124344/1‑141 (MQ=255)
                                                                                                                        gAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTATTGatcat            <  2:389972/141‑1 (MQ=255)
                                                                                                                         aaGTTGGGCAATATCCCATGTTATTATTAGCCGATGTACTCAGCCAATTAGATTATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTATTGatcatg           <  1:72999/141‑1 (MQ=255)
                                                                                                                          aGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTATTGatcatga          >  1:364286/1‑141 (MQ=255)
                                                                                                                          aGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATCCGCTGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTATTGatcatga          >  1:250611/1‑141 (MQ=255)
                                                                                                                                  aaTATGCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTATTGatcatgaaatcatga  <  2:144481/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                   
CATCGAGATGATATAAGTTTTGATGTGAATGGCATGGATGCTCAAACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATTGAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGTGAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACATTTGTCACTACGACATCTGTAGATGGTATTGATCATGAAATCATGA  >  USA300TCH1516_ALE/4734‑5004

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑