Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,581 C→T 36.6% 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
*CP00073036,5810CT36.6% 71.6 / 55.8 63intergenic (‑30/‑493)USA300HOU_0026/USA300HOU_0028IS431mec transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (19/21);  new base T (15/8);  total (34/29)
Fisher's exact test for biased strand distribution p-value = 1.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.09e-01

TCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATT  >  CP000730/36442‑36717
                                                                                                                                           |                                                                                                                                        
tCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATAc                                                                                                                                          <  1:132764/140‑1 (MQ=33)
       atatTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAAt                                                                                                                                   <  2:75347/140‑1 (MQ=35)
       atatTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAAt                                                                                                                                   <  1:12640/140‑1 (MQ=34)
                      cACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAg                                                                                                                    <  1:207486/140‑1 (MQ=35)
                       aCGATAGCTCAATGCATTTCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGa                                                                                                                   <  1:9725/140‑1 (MQ=255)
                           tAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACATGAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCg                                                                                                               <  1:61128/140‑1 (MQ=255)
                             gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGGTTGTATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGta                                                                                                             >  1:140894/2‑140 (MQ=11)
                             gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGta                                                                                                             >  2:218620/2‑140 (MQ=9)
                              cTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAAGAGCCGGTGTGAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGTACCGtat                                                                                                            >  1:168956/1‑140 (MQ=11)
                              cTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                                                                                                            >  1:77866/1‑140 (MQ=12)
                               tCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGGTCATACAGAAGACGCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatt                                                                                                           >  1:299583/1‑140 (MQ=11)
                               tCAATGCATATCGTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAGAATTATATTATAAATTCAACTTTGCAACAGAACCGtatt                                                                                                           >  1:226513/1‑140 (MQ=11)
                                cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattt                                                                                                          >  2:115346/1‑139 (MQ=255)
                                  atgcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttta                                                                                                        >  2:154754/5‑137 (MQ=255)
                                  aTGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttt                                                                                                        >  2:66915/1‑137 (MQ=255)
                                   tgcatttCTTAAATAGTAGCCAACGTCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttat                                                                                                       <  1:3994/134‑5 (MQ=11)
                                    gcatttCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGCTAATATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatg                                                                                                      <  2:291464/135‑6 (MQ=11)
                                    gcatatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttacta                                                                                                      <  2:113179/138‑11 (MQ=11)
                                     catatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTTTTTTTTTTACTATAAATTCAACTTTGCAACAGAAcctcatttactat                                                                                                     >  2:272284/2‑129 (MQ=11)
                                      atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAATTTGTTTAGATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtat                                                                                                    <  2:94594/140‑13 (MQ=11)
                                      atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgag                                                                                                    >  2:113924/1‑133 (MQ=255)
                                       tatCTTAGATAGTAGCCAACGGCTGCAGGGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatt                                                                                                   >  1:203328/1‑127 (MQ=11)
                                       tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatt                                                                                                   >  2:22239/1‑127 (MQ=11)
                                       tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatt                                                                                                   >  1:298721/1‑127 (MQ=11)
                                       tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatgttatgagt                                                                                                   >  1:5573/1‑131 (MQ=255)
                                       tatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTGAATTTCGAAACAGAActcaatttactatat                                                                                                   >  2:290199/1‑126 (MQ=11)
                                        atCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATag                                                                                                  >  1:119098/1‑140 (MQ=255)
                                         tCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtac                                                                                                 >  2:237468/1‑130 (MQ=11)
                                         tCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtac                                                                                                 <  2:230519/140‑11 (MQ=11)
                                          cTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATagag                                                                                                >  2:116202/1‑140 (MQ=255)
                                            tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacact                                                                                              <  2:299826/140‑14 (MQ=11)
                                             aGATAGTAGCCAACGGCTACAGTTATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                             <  1:20775/140‑15 (MQ=11)
                                             aGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                             <  1:145448/140‑15 (MQ=11)
                                                tagtagCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTg                                                                                          >  1:231866/1‑140 (MQ=255)
                                                   aagCCAACGGCTACAGTGATAACTTCCTTTTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTCTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTa                                                                                       <  1:320513/139‑1 (MQ=255)
                                                           ggCTACAGTGATCAACTCTTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACGCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTCTGGAATAGAGATGTTGGGAACCTTtat                                                                               >  1:63689/1‑140 (MQ=17)
                                                            gCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTtata                                                                              <  1:274268/140‑1 (MQ=255)
                                                             cTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATAc                                                                             >  1:91964/1‑140 (MQ=255)
                                                              tACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTACAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACa                                                                            <  1:10331/140‑1 (MQ=255)
                                                               aCAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAg                                                                           <  2:60004/140‑1 (MQ=255)
                                                                    gATAACATCCTTGTTAAATCGTTTAGATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCa                                                                      >  1:175485/1‑140 (MQ=255)
                                                                    gATAACATCCTTGATAAATTGTGTATATCTGGAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGAATCa                                                                      >  1:248189/1‑140 (MQ=255)
                                                                           cccTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTTCTTTTTTTTAAAATTATACTATAAATTCAACTTCGCAACACAGCCGTATGATGGAATAGAGATGTTGGTAACATTTATACACGATCATTATACt                                                               <  2:4373/139‑1 (MQ=21)
                                                                               tGTTTAATTGTTTATATCTGGAAAAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAAGTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAg                                                           <  1:52059/140‑1 (MQ=255)
                                                                               tGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAg                                                           <  1:137111/140‑1 (MQ=255)
                                                                               tGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAACGTACGAAGGAATAGAGATGTTGGTAACATTAATACAGGATCATtagaattcag                                                           >  1:299443/1‑132 (MQ=18)
                                                                                gTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGt                                                          <  2:91964/140‑1 (MQ=255)
                                                                                  tAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAACATTAGACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGttt                                                        <  1:42945/140‑1 (MQ=255)
                                                                                   aaaTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGAAACATTTATACAGGATCATTATACTTAAGTTTa                                                       >  2:83501/1‑140 (MQ=255)
                                                                                          ttATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGt                                                >  1:78843/1‑140 (MQ=255)
                                                                                             tatCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATCATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATCATTAAGTTTAATTTCGttat                                             <  2:3088/140‑1 (MQ=255)
                                                                                                    aaTAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGaa                                      <  1:66217/140‑1 (MQ=255)
                                                                                                    aaTAGGTCCTAATGAAGGCTCCTTTTTGTTAAAATTATACTATAAAATCAACGTTGCAACGGACGCGGTTTTTGGGATGGAGGTGTTGGTAACATTTATACAGTATCATTATACTTAAGTTTAATTTCGTTATTACAGaa                                      <  2:39651/140‑1 (MQ=25)
                                                                                                     aTAGTTCATACAGAAGACTCCTTTTTGTTAAAATTGTACTATAAAATCAAGGGTGCAGCAGAACAGTATTATGGAATAGAGATGTTGGTACCATTTATACAGGATCATTATACTTAAGTTTAGTTTCGTTATTCCGGaaa                                     >  1:140548/1‑139 (MQ=25)
                                                                                                        gTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACcac                                  <  1:275793/140‑1 (MQ=255)
                                                                                                         ttCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACcaca                                 <  1:205027/140‑1 (MQ=255)
                                                                                                              aCAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTc                            >  2:78198/1‑140 (MQ=255)
                                                                                                                   agaCTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAAAACCACACATTCCAAcc                       >  1:83662/1‑140 (MQ=255)
                                                                                                                          tttttGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACAAATTACAACCAGAagag                >  2:135450/1‑140 (MQ=255)
                                                                                                                             ttGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACAAGAAGAGaaa             >  2:297395/1‑140 (MQ=255)
                                                                                                                                  aaaaTTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAATTagc        >  1:103044/1‑138 (MQ=255)
                                                                                                                                        ataCTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTAtt  <  2:245500/140‑1 (MQ=255)
                                                                                                                                        ataCTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTAtt  >  2:270156/1‑140 (MQ=255)
                                                                                                                                        ataCTAAAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTAtt  <  2:292517/140‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                        
TCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATT  >  CP000730/36442‑36717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: