Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 9,710 T→C 6.8% intergenic (+15/+72) gyrA → / ← USA300HOU_0007 DNA topoisomerase (ATP‑hydrolyzing) subunit A/possible carbohydrate kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007309,7100TC 6.8% 148.3 / 4.1 60intergenic (+15/+72)gyrA/USA300HOU_0007DNA topoisomerase (ATP‑hydrolyzing) subunit A/possible carbohydrate kinase
Reads supporting (aligned to +/- strand):  ref base T (30/24);  new base C (2/2);  total (32/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.90e-01

GGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATAC  >  CP000730/9570‑9848
                                                                                                                                            |                                                                                                                                          
ggAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACtt                                                                                                                                            <  2:400733/141‑1 (MQ=255)
ggAAATGCAATTCATACTGAAGGGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATAGAGAATAATAAAAAATAAGACtt                                                                                                                                            >  2:267804/1‑141 (MQ=255)
   aaTGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGAAGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATAAGATGAAGAATAATAAAAAATAAGACATccc                                                                                                                                         >  2:38450/1‑141 (MQ=255)
     tGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCta                                                                                                                                       <  2:91551/141‑1 (MQ=255)
     tGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCta                                                                                                                                       >  1:189100/1‑141 (MQ=255)
     ggCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCta                                                                                                                                       >  2:145611/2‑141 (MQ=255)
       cAATTTATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCtata                                                                                                                                     <  1:527923/141‑1 (MQ=255)
       cAATTCATACTGAAGTGATTGATTCAGAAGAACATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCtata                                                                                                                                     <  1:12970/141‑1 (MQ=255)
       cAATTCATACTGAAGTGATTGATTCAGAAAAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTCCCCtaca                                                                                                                                     <  1:8264/141‑3 (MQ=255)
        aaTTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGCGTTATCTatat                                                                                                                                    >  1:68762/1‑141 (MQ=255)
        aaTTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAACAATAATAAAAAATAAGACTTCCCTatat                                                                                                                                    >  1:317502/1‑141 (MQ=255)
               aCTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAgggg                                                                                                                             >  2:374545/1‑141 (MQ=255)
                cTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGa                                                                                                                            <  1:255560/141‑1 (MQ=255)
                   aaGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTCCCCTACATATAGGGAAGTc                                                                                                                         <  2:327004/141‑1 (MQ=255)
                      tgattgatTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTa                                                                                                                      >  2:399945/1‑141 (MQ=255)
                         ttgattCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATAATCAGATGAAGACTAATAAAAAATAAGACTTCGCGATATGTAGGGGAGTCGTAttt                                                                                                                   >  2:401917/1‑141 (MQ=255)
                            attCAGAAGAAAATGATGAAGATGGACGTAGTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTa                                                                                                                <  2:479582/141‑1 (MQ=255)
                             ttCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTAATGTGTAt                                                                                                               >  1:125918/1‑141 (MQ=255)
                                 gaagaaAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTa                                                                                                           >  2:247364/1‑141 (MQ=255)
                                 aaagaaAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTa                                                                                                           <  1:121175/140‑1 (MQ=255)
                                       aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt                                                                                                     >  2:206278/1‑141 (MQ=255)
                                       aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt                                                                                                     <  2:196079/141‑1 (MQ=255)
                                       aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt                                                                                                     <  2:521018/141‑1 (MQ=255)
                                        atgatgAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTa                                                                                                    <  1:203120/141‑1 (MQ=255)
                                         tgatgaAGATGGACGTATTGAAGTGAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTGTTTTTATGCTAGAAAGTaa                                                                                                   >  1:358346/1‑141 (MQ=255)
                                         tgatgaAGATGGACGGATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTaa                                                                                                   >  1:416016/1‑141 (MQ=255)
                                         tgatgaAGATGGACGCATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTaa                                                                                                   >  1:415945/1‑141 (MQ=255)
                                          gatgaAGATGGACGTATTGAAGTAAGACAAGATTTCATTGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAGAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAAt                                                                                                  <  1:365030/141‑1 (MQ=255)
                                               aGATGGACGTATTGAAGTAAGCCAAGATTTAATGGATAGTGTGGAAGAAGATATACAACAATCATCAGATGAATGATAATAAAAAATACGAATTCTCTATATGTAGGGGGGTCTTATTTTTATACTaagaaaaaaagcttg                                                                                             >  2:418219/1‑127 (MQ=255)
                                               aGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCttt                                                                                             >  1:2237/1‑141 (MQ=255)
                                                  gggACGTATTGAAGTAAGACAAGATTTCATGGATCGGGTTGAAGAAGTTAAATAACAATCATCAGATGGAGAATAATAAAAAATAAGACTGCACTATATGTAGGGGAGTCTTATTTTTATGCTACAAAGTAATGCTTTACt                                                                                          <  2:228553/140‑1 (MQ=255)
                                                    gACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAAAAGACCAGCGACAATCATCAGATGAAGAATAATAAAAAATAAGATTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACtat                                                                                        <  1:181737/141‑1 (MQ=255)
                                                     aCGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATACGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACtatt                                                                                       >  2:493723/1‑140 (MQ=255)
                                                          ttGAAGTTAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGTCTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCaa                                                                                  <  1:209252/141‑1 (MQ=255)
                                                          ttGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCTCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCaa                                                                                  <  1:28895/141‑1 (MQ=255)
                                                              aGTAAGACTAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGAt                                                                              <  2:559004/141‑1 (MQ=255)
                                                                     cAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGTTTAGTaaa                                                                       >  2:508684/1‑140 (MQ=255)
                                                                     cAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAAt                                                                       >  2:149515/1‑141 (MQ=255)
                                                                         aTTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACt                                                                   >  1:54491/1‑141 (MQ=255)
                                                                                ggATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTc                                                            <  2:7327/141‑1 (MQ=255)
                                                                                    cGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAACAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTACTGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAAt                                                        <  2:200975/141‑1 (MQ=255)
                                                                                       gtTGAAGAAGATATACAACAATCATCAGATGAAAAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGt                                                     >  2:93312/1‑141 (MQ=255)
                                                                                           aagaagATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCa                                                 <  2:420619/141‑1 (MQ=255)
                                                                                               agaTATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGc                                             >  1:249310/1‑141 (MQ=255)
                                                                                                 atatACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTATAATTGTTTAAtaacga                                           >  2:418000/1‑136 (MQ=255)
                                                                                                 atatACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTAAAGGTAGGGGAGTCTTATGTTTATGCTAGAAAGTAATGCTTTACTATATTCAAGGATTGGACATGACTAACTTTCTAATTGTTTCATTGAGt                                           >  2:393123/1‑141 (MQ=255)
                                                                                                     acaacaATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTAACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAgg                                       <  1:374545/141‑1 (MQ=255)
                                                                                                         caaTCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGAAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTAtt                                   >  2:414783/1‑141 (MQ=255)
                                                                                                               tcaGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTg                             >  1:473300/1‑141 (MQ=255)
                                                                                                                 aGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGAt                           <  1:257800/141‑1 (MQ=255)
                                                                                                                  gATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTTTCCAGATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATa                          <  1:155296/141‑1 (MQ=255)
                                                                                                                  aaTGAAGAATAATAAAAAATAAGACTGCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATa                          <  1:450215/140‑1 (MQ=255)
                                                                                                                          ataataAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGa                  <  2:323921/141‑1 (MQ=255)
                                                                                                                          ataataAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGa                  >  1:83238/1‑141 (MQ=255)
                                                                                                                                   aaTAAGACTCCCCTACATATAGGGAAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGcac         >  1:538544/1‑141 (MQ=39)
                                                                                                                                     tAAGACTCCCCTACATATAGGGAAGTCTTATTTTTATGCTAGAAAGTACTGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGCcaccc       >  2:88078/1‑140 (MQ=38)
                                                                                                                                       aGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACtt                                                              >  1:391247/1‑84 (MQ=255)
                                                                                                                                       aGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACtt                                                              <  2:391247/84‑1 (MQ=255)
                                                                                                                                       aGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTATAGTTTTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACcaca     >  1:526442/1‑141 (MQ=255)
                                                                                                                                        aaCTTCCCTACTTGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacat    <  1:206122/140‑1 (MQ=255)
                                                                                                                                          cTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTTTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacatac  <  1:224591/141‑1 (MQ=255)
                                                                                                                                          cTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacctac  >  1:189948/1‑141 (MQ=255)
                                                                                                                                          attCCCTAGATGTAGTGGAGTCTTATTTTGATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCacatac  <  2:106738/140‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                          
GGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATAC  >  CP000730/9570‑9848

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: