Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,514,408 T→C 7.0% K55E (AAA→GAA)  USA300HOU_1380 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,514,4080TC 7.0% 170.3 / 3.6 57K55E (AAA→GAA) USA300HOU_1380hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (26/27);  new base C (2/2);  total (28/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01

CATTAAACCGTGTGGGACGTCATCATGTTTAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATAACAACCAATGCAATAGA  >  CP000730/1514268‑1514543
                                                                                                                                            |                                                                                                                                       
catTAAACCGTGTGGGACGTCATCATGTTTAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGttt                                                                                                                                         <  2:573193/141‑1 (MQ=255)
              ggACGTCATCATGTTTAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCAtatt                                                                                                                           >  1:222520/1‑138 (MQ=255)
                aCGTCATCATGTTTAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCtttt                                                                                                                         >  1:480531/1‑141 (MQ=255)
                 cGTCATCATGTTTAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCttttt                                                                                                                        <  1:111180/141‑1 (MQ=255)
                       catGCTTAACAATCTCTTGTTTATAAAATGTCGTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGa                                                                                                                  >  2:103538/1‑141 (MQ=255)
                           tttAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAAc                                                                                                              >  2:539845/1‑141 (MQ=255)
                            ttAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACt                                                                                                             >  2:168569/1‑141 (MQ=255)
                                cAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACttttt                                                                                                         <  1:119236/141‑1 (MQ=255)
                                   tctcTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTg                                                                                                      <  2:21860/141‑1 (MQ=255)
                                    ctctTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGc                                                                                                     >  1:303412/1‑141 (MQ=255)
                                     tctTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTTTTCTTTAAATCATTAGATGGTTCTACTTTGATATTATGTTCGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCa                                                                                                    >  2:221491/1‑141 (MQ=255)
                                     tctTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTCGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCa                                                                                                    >  2:221492/1‑141 (MQ=255)
                                           ttATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTa                                                                                              >  1:439234/1‑141 (MQ=255)
                                            tataAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTAt                                                                                             <  1:424964/141‑1 (MQ=255)
                                            tataAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTAt                                                                                             <  1:424878/141‑1 (MQ=255)
                                              taAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTa                                                                                           >  1:187786/1‑141 (MQ=255)
                                                   tGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTAtt                                                                                      >  2:449168/1‑141 (MQ=255)
                                                      cTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCat                                                                                   <  2:633391/141‑1 (MQ=255)
                                                         cccATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCAtata                                                                                >  1:317023/1‑141 (MQ=255)
                                                            atcatcTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAAcc                                                                             <  2:610668/141‑1 (MQ=255)
                                                            atcatcTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAAcc                                                                             <  1:352350/141‑1 (MQ=255)
                                                               atcTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATGACTATTCATATAACCaaa                                                                          >  1:180442/1‑141 (MQ=255)
                                                                  tttAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTTATATAACCAAAATa                                                                       >  2:552023/1‑141 (MQ=255)
                                                                   ttAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATaa                                                                      <  1:81691/141‑1 (MQ=255)
                                                                      gAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTc                                                                   <  1:264487/141‑1 (MQ=255)
                                                                        aaCTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGt                                                                 <  2:495390/141‑1 (MQ=255)
                                                                         aCTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGtt                                                                >  2:251/1‑141 (MQ=255)
                                                                               tttACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGa                                                          <  2:296345/141‑1 (MQ=255)
                                                                                ttACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGAc                                                         <  2:267691/141‑1 (MQ=255)
                                                                                  aCAAAGTCTCCTTTTTTCTTCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGTCTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAATTAAGTCGTTTTTTGACTa                                                       >  2:39865/1‑141 (MQ=255)
                                                                                  aCAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCa                                                                                                    >  1:568583/1‑96 (MQ=255)
                                                                                  aCAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCa                                                                                                    <  2:568583/96‑1 (MQ=255)
                                                                                  aCAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGtttaaaaaaaa                                                       <  2:267129/141‑9 (MQ=255)
                                                                                    aaaGTCTCCTTTTTTCGTCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTc                                                                   >  1:522271/1‑127 (MQ=255)
                                                                                    aaaGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTc                                                                   <  2:522271/127‑1 (MQ=255)
                                                                                                 ttCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTaaa                                        <  2:77646/141‑1 (MQ=255)
                                                                                                   cGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACa                                      >  1:93696/1‑141 (MQ=255)
                                                                                                   cGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGAAAAGAAAAAATCATTAAACa                                      <  2:480531/141‑1 (MQ=255)
                                                                                                           aaTCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACgg                              <  1:449168/141‑1 (MQ=255)
                                                                                                           aaTCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATATTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACgg                              <  2:222520/141‑1 (MQ=255)
                                                                                                            gtaaaaaaaTGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGc                             >  2:275349/9‑141 (MQ=255)
                                                                                                            aTCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGc                             <  2:339034/141‑1 (MQ=255)
                                                                                                              cATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCaa                           >  2:134083/1‑141 (MQ=255)
                                                                                                               aTTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAAt                          >  2:118676/1‑141 (MQ=255)
                                                                                                                  aGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATAcc                       <  1:168569/141‑1 (MQ=255)
                                                                                                                   gATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATACCGAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCa                      >  1:151560/1‑141 (MQ=255)
                                                                                                                      ggTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATa                   <  1:460048/141‑1 (MQ=255)
                                                                                                                       gTTCTACTTTGATATTATGTTCGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATaa                  <  1:221491/141‑1 (MQ=255)
                                                                                                                       gTTCTACTTTGATATTATGTTCGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATaa                  <  1:221492/141‑1 (MQ=255)
                                                                                                                        ttCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATaac                 <  2:91928/141‑1 (MQ=255)
                                                                                                                        ttCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATaac                 >  2:441151/1‑141 (MQ=255)
                                                                                                                         tCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTTTTTTTTTTTTATCATTAAACATACAACGGCAATACCAATaaca                >  2:711385/1‑141 (MQ=255)
                                                                                                                         tCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATaaca                >  1:335764/1‑141 (MQ=255)
                                                                                                                                 gATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCCGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATAACAACCAATGc        <  1:121735/141‑1 (MQ=255)
                                                                                                                                  atatTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGc                                                                                                     <  1:360662/47‑1 (MQ=255)
                                                                                                                                  atatTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGc                                                                                                     >  2:360662/1‑47 (MQ=255)
                                                                                                                                   tattatGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATAACAACCAATGCaa      <  2:65263/141‑1 (MQ=255)
                                                                                                                                       atGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTTTTTTTTTTTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACTAATAACAACCAATGCAATAGa  >  2:517335/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                       
CATTAAACCGTGTGGGACGTCATCATGTTTAACAATCTCTTGTTTATAAAATGTCTTCCCATCATCTTTAGAAACTAATTTTACAAAGTCTCCTTTTTTCGGCTTGAAATCATTAGATGGTTCTACTTTGATATTATGTTTGACTAATCCATCTTTTTCACTGACAACTTTTTCTGCATTTGTATTACTATTCATATAACCAAAATAAGTCGTTTTTTGACTAGAAAAAATCATTAAACATACAACGGCAATACCAATAACAACCAATGCAATAGA  >  CP000730/1514268‑1514543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑