Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 9,716 T→C 7.3% intergenic (+21/+66) 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
*CP0007309,7160TC 7.3% 126.6 / 2.2 53intergenic (+21/+66)gyrA/USA300HOU_0007DNA topoisomerase (ATP‑hydrolyzing) subunit A/possible carbohydrate kinase
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base C (2/2);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.22e-01

CAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATACATAT  >  CP000730/9577‑9852
                                                                                                                                           |                                                                                                                                        
cAATTTATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCtata                                                                                                                                         <  1:527923/141‑1 (MQ=255)
cAATTCATACTGAAGTGATTGATTCAGAAGAACATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCtata                                                                                                                                         <  1:12970/141‑1 (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                                                                                                         <  2:521018/141‑1 (MQ=255)
                                aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt                                                                                                         >  2:206278/1‑141 (MQ=255)
                                aaTGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGt                                                                                                         <  2:196079/141‑1 (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                      >  1:83238/1‑141 (MQ=255)
                                                                                                                   ataataAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGa                      <  2:323921/141‑1 (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)
                                                                                                                                       ccTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATACatat  <  1:184789/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                        
CAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAATAAAAAATAAGACTTCCCTATATGTAGGGGAGTCTTATTTTTATGCTAGAAAGTAATGCTTTACTATATTCAATGATTAGTAATGACTAACTTTCTAATTGTTTCATTGCGTAAGGTATTTCATTGATAAGTCTTGATGGTGGCACCACATACATAT  >  CP000730/9577‑9852

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: ‑