Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,581 C→T 37.5% intergenic (‑30/‑493) USA300HOU_0026 ← / → USA300HOU_0028 IS431mec transposase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,5810CT37.5% 63.2 / 55.3 62intergenic (‑30/‑493)USA300HOU_0026/USA300HOU_0028IS431mec transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (21/17);  new base T (14/9);  total (35/27)
Fisher's exact test for biased strand distribution p-value = 7.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.13e-01

ATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATT  >  CP000730/36449‑36717
                                                                                                                                    |                                                                                                                                        
atagTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTCTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAAtt                                                                                                                                  <  2:267572/141‑1 (MQ=21)
    ttCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAAGTATACTATAAATTCAAc                                                                                                                              <  2:283701/141‑1 (MQ=25)
             atCACGATAACTCAATGAATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACa                                                                                                                     <  2:17914/141‑1 (MQ=17)
                aCGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGaa                                                                                                                  >  2:148273/1‑141 (MQ=35)
                 cgaataCTCAATGAATTTTATAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAc                                                                                                                 <  1:377235/136‑1 (MQ=11)
                   atagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAACAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCg                                                                                                               >  1:229571/5‑141 (MQ=1)
                    tagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                                                                                                              <  1:237052/138‑1 (MQ=12)
                    tAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACCGTGATAACATCCTTGTTAATTTGTTTATATCTGAACTAGTTTATTTTGTTTACTCCTTTTTGTTAAATTTATATTATAAATTCAACTTTGCAAGAGAACCGt                                                                                                              >  2:231379/1‑141 (MQ=11)
                    tAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACACCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGt                                                                                                              <  1:186800/141‑1 (MQ=37)
                     agcTCAATGCATATCTTAGATAGTAGCCAACGGCTACCGTGCTAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGta                                                                                                             >  1:175403/3‑141 (MQ=11)
                     aaCTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGta                                                                                                             <  1:103414/141‑1 (MQ=37)
                      aCTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTAAACTTTGCAACAGAACGGtat                                                                                                            >  1:80346/1‑141 (MQ=255)
                       cTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCACCAGAACCGtatt                                                                                                           >  1:71405/1‑141 (MQ=255)
                       cTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatt                                                                                                           >  1:373395/1‑141 (MQ=16)
                       cTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatt                                                                                                           >  1:302406/1‑141 (MQ=18)
                       cTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatt                                                                                                           >  2:353978/1‑141 (MQ=16)
                         caattcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaac                                                                                                         <  2:176324/135‑8 (MQ=11)
                         cAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGtattat                                                                                                         >  1:118197/1‑141 (MQ=40)
                          aaTGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttta                                                                                                        >  1:31516/1‑138 (MQ=255)
                           aTGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATgg                                                                                                       >  1:81945/1‑141 (MQ=255)
                            tgcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatg                                                                                                      <  1:133561/138‑6 (MQ=255)
                            tGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTTTTTTTTTTACTATAAATTCAACTTTGCAACAGAACCGTATTATGGa                                                                                                      >  2:357775/1‑141 (MQ=14)
                            agTATATCTTGGATAGTAGCCACCAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttacta                                                                                                      <  2:369604/140‑11 (MQ=11)
                              catatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtat                                                                                                    <  2:324813/140‑13 (MQ=11)
                              aatatCTTAGATAGTAGCCAACGGCTACAGTGATAACAATCTTGTTAATTTGTTTAGATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAAGTTTGCAACAGAACCGtattttatgag                                                                                                    <  2:238507/140‑8 (MQ=11)
                                tatCTTAGATAGTAGGCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatta                                                                                                  >  1:297111/1‑127 (MQ=11)
                                tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtattc                                                                                                  >  1:339211/1‑127 (MQ=11)
                                tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatta                                                                                                  >  1:231292/1‑127 (MQ=11)
                                tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatta                                                                                                  >  1:103819/1‑127 (MQ=11)
                                tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagta                                                                                                  <  1:353390/141‑10 (MQ=255)
                                tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagta                                                                                                  <  2:286375/141‑10 (MQ=255)
                                tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATACAACTTTGCAACAGACCCGtattttatgagta                                                                                                  >  2:51169/1‑132 (MQ=11)
                                tatCTTAGATAGTAGCAAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACGGAACCgcctaactgtatta                                                                                                  >  1:236758/1‑128 (MQ=11)
                                 atCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtac                                                                                                 <  2:345371/141‑11 (MQ=255)
                                     tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                             <  1:364675/141‑15 (MQ=11)
                                      aGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGt                                                                                            >  1:69015/1‑141 (MQ=255)
                                         tagtagCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTgg                                                                                         >  2:327601/1‑141 (MQ=255)
                                         tagtagCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTgg                                                                                         >  2:354153/1‑141 (MQ=255)
                                             agCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAAc                                                                                     >  1:6773/1‑141 (MQ=255)
                                                  aCGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTTTTTTTTTTACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATATTGGTAACAtttt                                                                                >  2:45729/1‑140 (MQ=17)
                                                   cGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTtat                                                                               >  2:313451/1‑141 (MQ=255)
                                                     gCTACAGTGGTAACGTTCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGCCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATAc                                                                             <  2:186768/141‑1 (MQ=255)
                                                     gCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATAATATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATAc                                                                             <  2:84376/141‑1 (MQ=255)
                                                       tACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAg                                                                           >  1:62490/1‑141 (MQ=255)
                                                          aGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGAt                                                                        >  1:128947/1‑141 (MQ=255)
                                                             gATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCAt                                                                     <  2:134355/141‑1 (MQ=255)
                                                                       ttGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAg                                                           <  1:313451/141‑1 (MQ=255)
                                                                            aaaTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTaa                                                      >  1:48580/1‑141 (MQ=255)
                                                                              atagTTCATATCTCAAATAGCACAAACAGAAGACTCCTTCTTATTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAAtt                                                    <  1:231379/138‑1 (MQ=25)
                                                                              aTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAAtt                                                    <  1:148273/141‑1 (MQ=255)
                                                                               ttGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAAttt                                                   >  1:81264/1‑141 (MQ=255)
                                                                                        tCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCACCTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTAc                                          <  1:264159/141‑1 (MQ=255)
                                                                                           gAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACCGa                                       >  2:75197/1‑141 (MQ=255)
                                                                                              aTAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTATATTTTAGTTATTACACaagc                                    >  2:258090/1‑139 (MQ=255)
                                                                                                          gaagaCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACGGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAAc                        <  1:175813/141‑1 (MQ=255)
                                                                                                          gaagaCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAAc                        >  1:321041/1‑141 (MQ=255)
                                                                                                          gaagaCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAAc                        >  2:118144/1‑141 (MQ=255)
                                                                                                                tCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAAAACAACACATTCCAACGagaag                  >  1:138566/1‑141 (MQ=255)
                                                                                                                 ccTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGACGAGATATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCagaaga                 <  1:189242/141‑1 (MQ=255)
                                                                                                                  cTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAagag                <  2:118197/141‑1 (MQ=255)
                                                                                                                      ttGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAg            >  1:278205/1‑141 (MQ=255)
                                                                                                                                aataCAATAAATTCAACCTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTAtt  <  1:152181/140‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                        
ATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATT  >  CP000730/36449‑36717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑