Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,929,918 A→G 50.5% intergenic (‑1001/‑167) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,929,9180AG50.5% ‑2.1 / 70.1 55intergenic (‑1001/‑167)USA300HOU_1794/USA300HOU_1796hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (14/13);  new base G (21/7);  total (35/20)
Fisher's exact test for biased strand distribution p-value = 9.66e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

TGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTA  >  CP000730/1929778‑1930053
                                                                                                                                                 |                                                                                                                                       
tGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATAATAGCACCAGTCATCAGTGGCTGTGCCa                                                                                                                                         >  1:152367/1‑141 (MQ=255)
 gACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCAt                                                                                                                                        >  2:164834/1‑141 (MQ=255)
     ttgCTTGTATATCCACAGATGGTATAATAATAGAGTCGCCTATCTCTCCGGCGTCAATT‑‑GACGAAGAGAGGAGGTTCATTACTTTGCTAATCATTTTCGTTCACATCATAGCCCCAGTCATCAGTGGCTGTGCTGTTGCGt                                                                                                                                   <  2:103232/140‑1 (MQ=255)
        cTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGttt                                                                                                                                 >  1:14277/1‑141 (MQ=255)
         ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta                                                                                                                               <  1:54762/141‑5 (MQ=255)
             atatTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTc                                                                                                                            <  1:285647/141‑1 (MQ=255)
              tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACtt                                                                                                                          >  1:122592/9‑141 (MQ=255)
                 tcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCAAATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTAtt                                                                                                                       >  1:91212/6‑141 (MQ=255)
                  tGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTAtt                                                                                                                       >  2:108555/1‑141 (MQ=255)
                  cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGCAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg                                                                                                                      >  1:152294/5‑141 (MQ=255)
                  cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg                                                                                                                      >  2:42977/5‑141 (MQ=255)
                   gCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGAAACTTATTTTTGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTg                                                                                                                      >  1:77367/1‑141 (MQ=255)
                    cagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                                                    <  2:139902/139‑1 (MQ=255)
                    cagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                                                    >  2:329878/3‑141 (MQ=255)
                     cgttgattgtataGTTGAGTCGTCTATCTCGCAGGCGTCAATTTAGACGCAGAGAGGAGGTTTATAAGGTGATGCTTATTTTCGTTCAAATCATAGCTCCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGc                                                                                                                    <  2:136383/131‑1 (MQ=255)
                     agatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt                                                                                                                   >  1:40252/2‑141 (MQ=255)
                         ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCACTT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATGAGTTGCTGTGCTGTTGCGTATTTTTCTTGTTGGCttata                                                                                                               >  1:11708/3‑137 (MQ=255)
                         ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGt                                                                                                               >  1:310193/3‑141 (MQ=255)
                         ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAA‑‑TGGACGAAGAGAGGAGGTGCATTACTCTGCTAATCATTTTCGGTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGt                                                                                                               <  2:94460/139‑1 (MQ=255)
                          gtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTa                                                                                                              >  2:300018/2‑141 (MQ=255)
                          atatAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGt                                                                                                               >  1:289981/1‑141 (MQ=255)
                           tataATAGTAGAGGCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTa                                                                                                              <  1:321193/141‑1 (MQ=255)
                             taataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATACGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGa                                                                                                            >  1:128062/1‑141 (MQ=255)
                               ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                                                                         <  1:283091/141‑1 (MQ=255)
                               ataGTAGGGTCGCCTATCTCTCAGGCGTTAATTTATACGCAGGGAGGAGGTATATAAGGGGATGCATATTTTCGTTCACATCATCGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTATGtgggag                                                                                                          <  2:252941/141‑6 (MQ=255)
                                  gtagAGTCTGCTATCTCTCAGGCGTCAATTTATACGCAGATAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCaa                                                                                                       <  1:31861/141‑1 (MQ=255)
                                     gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                                                                                                   >  1:194162/1‑137 (MQ=255)
                                      agTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTAATTGGCTTAGTAAACGCaacgaat                                                                                                  >  1:101432/1‑136 (MQ=255)
                                       gccGCCTATCTCTCAGGCGTCCATT‑‑GACGAAGTGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaata                                                                                                 <  1:111180/139‑7 (MQ=255)
                                         cGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaagaat                                                                                               >  2:74143/1‑133 (MQ=255)
                                          gCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAAt                                                                                               <  1:236510/141‑1 (MQ=255)
                                          gCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt                                                                                              >  2:290875/1‑132 (MQ=255)
                                          gCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt                                                                                              >  1:131133/1‑132 (MQ=255)
                                          gCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt                                                                                              >  1:131138/1‑132 (MQ=255)
                                           ccTATCTCTCAGGCGTCAATTTAGACGCAGCGAGGCGGCGTTCAATGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAGTACAAGATa                                                                                              >  2:219080/1‑141 (MQ=255)
                                           ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                             >  2:140636/1‑131 (MQ=255)
                                            cTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATCACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaa                                                                                            <  2:169084/141‑12 (MQ=255)
                                             tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaatgattaat                                                                                           >  2:329713/1‑129 (MQ=255)
                                             tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                           >  1:119945/1‑129 (MQ=255)
                                              aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                          >  2:52411/1‑128 (MQ=255)
                                              aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                          >  1:110041/1‑128 (MQ=255)
                                              aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                          >  2:84230/1‑128 (MQ=255)
                                                   tcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACat                                                                                      >  1:284260/1‑141 (MQ=255)
                                                        cGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACAtatacc                                                                                 >  1:758/1‑139 (MQ=255)
                                                                           aggaggTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATcccc                                                              >  1:254420/1‑141 (MQ=255)
                                                                            ggaggTTTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCt                                                             <  2:256696/141‑1 (MQ=255)
                                                                              aggTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCa                                                           <  2:242382/141‑1 (MQ=255)
                                                                                 tgtATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACtt                                                        >  1:49376/1‑140 (MQ=255)
                                                                                                     ttATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAATAATCCCCTCACTACCGCAAATAGTGAgg                                         <  1:211507/141‑1 (MQ=255)
                                                                                                          ttCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTCTTGTCAAATGATACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGAtt                                    <  1:242614/141‑1 (MQ=255)
                                                                                                          ttCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAGTAGTGGGGGGagt                                    >  1:32641/1‑139 (MQ=255)
                                                                                                          ttCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGAtt                                    <  1:51801/141‑1 (MQ=255)
                                                                                                                      atAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAACCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTa                        >  2:206197/1‑141 (MQ=255)
                                                                                                                              aGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTa                >  2:312972/1‑141 (MQ=255)
                                                                                                                                     aGTGGCTGTGCCATTGCGTTTTTTTCATATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAACCCCCTCACTATCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATATATATTTTCGt         <  1:244606/141‑1 (MQ=255)
                                                                                                                                            gtgCCATGGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTa  <  1:88590/141‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                       
TGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTA  >  CP000730/1929778‑1930053

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: