Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 168,397 G→C 31.4% P28R (CCC→CGC)  USA300TCH1516_00148 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE168,3970GC31.4% 43.1 / 39.0 53P28R (CCC→CGC) USA300TCH1516_00148hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (13/21);  new base C (7/9);  total (21/32)
Fisher's exact test for biased strand distribution p-value = 7.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.67e-01

AAACTCTTTAAGGATTATGTTAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATGGTATTTTTTTGCTGT  >  USA300TCH1516_ALE/168258‑168535
                                                                                                                                           |                                                                                                                                          
aaaCTCTTTAAGGATTATGTTAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATggg                                                                                                                                           >  1:595181/1‑141 (MQ=255)
  aCTCTTTAAGGATTATGTTAATGAAAATATATAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTTAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTa                                                                                                                                         <  1:253268/141‑1 (MQ=255)
        tAAGGATTATGTTAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCttt                                                                                                                                   <  2:106361/141‑1 (MQ=255)
        tAAGGATTATGTTAATAAAAATAAAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCttt                                                                                                                                   <  2:594019/141‑1 (MQ=255)
          aGGATTATGTTAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTa                                                                                                                                 >  1:660259/1‑141 (MQ=255)
             aTTATGTTAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACtt                                                                                                                              >  1:390138/1‑141 (MQ=255)
               tATGTTAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGAACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGTGTATTCTTTTACTTGa                                                                                                                            >  1:596628/1‑141 (MQ=255)
                    tAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAAttt                                                                                                                       >  2:45315/1‑141 (MQ=255)
                           aaTAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTcc                                                                                                                >  2:672261/1‑141 (MQ=255)
                             tAGAGAATATAATATAACGAATCTATATAAATTAGGCACCAATATTTAAACATCGAGCTGAAACGATCATCATTTCAGTTCGAGGCTTTTTATTTTATCCTCTTTATATGGGTATTCTTTTACTTCAAATTTGTTTTCCTg                                                                                                              >  2:671529/1‑141 (MQ=255)
                             tAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTg                                                                                                              <  2:494476/141‑1 (MQ=255)
                              agagAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGGAATTTGTTTTCCTGt                                                                                                             <  2:94286/141‑1 (MQ=255)
                              agagAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGt                                                                                                             <  2:44529/141‑1 (MQ=255)
                              agagAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGt                                                                                                             <  1:96098/141‑1 (MQ=255)
                              agacAATATTATGTAGCGGATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGt                                                                                                             <  2:529120/141‑1 (MQ=255)
                                   atataatataACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATTGGTATCCTTTTACTTGAAATTTGTTTTCCTGtttttt                                                                                                        <  2:524193/141‑1 (MQ=255)
                                      taatataaCGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTAt                                                                                                     <  2:588183/141‑1 (MQ=255)
                                       aatataaCGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTAtt                                                                                                    >  2:410558/1‑141 (MQ=255)
                                        atataaCGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTATATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTAttt                                                                                                   >  2:295071/1‑140 (MQ=255)
                                         tataaCGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAGGATCATGATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGt                                                                                                  <  2:268269/141‑1 (MQ=255)
                                           taaCGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTaa                                                                                                >  2:458997/1‑141 (MQ=255)
                                           taaCGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTaa                                                                                                >  1:278308/1‑141 (MQ=255)
                                            aaCGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTaaa                                                                                               <  2:96995/141‑1 (MQ=255)
                                                   gtatataAATGAAGCAGCTATATTTAATTCTCGAGCTGAAAAGATCATCATTTCAGTTCGTGGTTTTTTATTTTATTCTTTTTGTATGGGTATTTTTTTACTTGTAATTTGTTTTCCTGTTTTTTTATTGTAAATTTttat                                                                                        <  2:153229/140‑1 (MQ=255)
                                                          aataaGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAg                                                                                 <  1:577619/141‑1 (MQ=255)
                                                           ataaGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGt                                                                                >  1:391570/1‑141 (MQ=255)
                                                              aGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATc                                                                             >  1:501100/1‑141 (MQ=255)
                                                                      atatTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTta                                                                     <  1:451489/141‑1 (MQ=255)
                                                                       tatTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTTTATTTTTATTACATTGTATTTTTAGTtat                                                                    >  2:22895/1‑141 (MQ=255)
                                                                              aCCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGa                                                             <  2:259679/141‑1 (MQ=255)
                                                                               ccTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGAc                                                            <  1:410558/141‑1 (MQ=255)
                                                                                cTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACa                                                           <  2:484163/141‑1 (MQ=255)
                                                                                cTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACa                                                           <  2:455761/141‑1 (MQ=255)
                                                                                cTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACa                                                           <  1:407045/141‑1 (MQ=255)
                                                                                 tCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACAt                                                          <  2:479568/141‑1 (MQ=255)
                                                                                  cGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACAtt                                                         >  1:90739/1‑141 (MQ=255)
                                                                                    aGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAACTTTTTATTACATAGTATCCTAAGTTATATCCTGCCAtttt                                                       >  2:61880/1‑140 (MQ=255)
                                                                                     gCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTTTAAGTTTTTATTACTTATTATGCGATGTTTTATCTTGTCTTTTGt                                                      >  2:82781/1‑141 (MQ=255)
                                                                                       tGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTtc                                                    <  2:595181/141‑1 (MQ=255)
                                                                                            aGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAg                                               >  1:689885/1‑141 (MQ=255)
                                                                                                    atgtCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTAttttta                                       <  1:79666/138‑1 (MQ=255)
                                                                                                    atTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTAttttta                                       <  2:278308/141‑1 (MQ=255)
                                                                                                        cAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTAtttttagttt                                   <  2:352627/141‑1 (MQ=255)
                                                                                                             tgaagTTTTTTAATTTATCTTCTTTGTTCCTGTCTCCTTGTGCTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTAtttttagttttttag                              <  2:726680/137‑1 (MQ=255)
                                                                                                               aGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTATTTGAAATTTTTTTCCCTGTTTTTTTATTTTAATTTTTTATTCCTTTGTATCCTAATTTATATCCTAACTTTTGTTCTCCATTAtttttttttttttgtta                            >  2:90287/1‑137 (MQ=255)
                                                                                                                 gTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAgg                          <  2:140466/141‑1 (MQ=255)
                                                                                                                           ttatTCTCTTTGTATGTTTATTCTTTTACTTGAAATTTGTTTTCTTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATgg                <  1:464194/141‑1 (MQ=255)
                                                                                                                           ttatTCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATgg                <  2:348577/141‑1 (MQ=255)
                                                                                                                             atCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTGGGAACATAATGGTa              >  1:22849/1‑141 (MQ=255)
                                                                                                                              tactctTTGTAGGGGTATTCCTTTGCGTTAAATGTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATGGTAt             <  1:581513/139‑1 (MQ=255)
                                                                                                                               ccTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATGGTAtt            <  1:219497/141‑1 (MQ=255)
                                                                                                                                   tttGTATGCGTATTCTTTTACTTGAAATCTAGTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATGGTAtttttt        <  1:318075/141‑1 (MQ=255)
                                                                                                                                       tATGCGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCTAGTATTTTTAGTTTTTTAGTAGGAATATAATGGTAtttttttttt    >  2:239336/1‑138 (MQ=255)
                                                                                                                                         tGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATGGTATTTTTTTGCTGt  >  1:43340/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                          
AAACTCTTTAAGGATTATGTTAATGAAAATAGAGAATATAATATAACGAATCTATATAAATAAGGCACCAATATTTAAACCTCGAGCTGAAAAGATCATCATTTCAGTTCGAGGTTTTTTATTTTATCCTCTTTGTATGGGTATTCTTTTACTTGAAATTTGTTTTCCTGTTTTTTTATTGTAAATTTTTATTACATAGTATCCTAAGTTATATCCTGACATTTGTTCTCCAGTATTTTTAGTTTTTTAGTAGGAACATAATGGTATTTTTTTGCTGT  >  USA300TCH1516_ALE/168258‑168535

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: ‑