Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,581 C→T 41.1% 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
*CP00073036,5810CT41.1% 41.7 / 57.0 56intergenic (‑30/‑493)USA300HOU_0026/USA300HOU_0028IS431mec transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (18/15);  new base T (14/9);  total (32/24)
Fisher's exact test for biased strand distribution p-value = 7.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.01e-01

CTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTAGT  >  CP000730/36445‑36721
                                                                                                                                        |                                                                                                                                            
cTTAATATTCCAGATATATCACGATAACTCAATGTATATCTTAGATAGCAGCCAACGGCTACAGTGATAACATCCTTGTCAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACtata                                                                                                                                          <  1:261740/141‑1 (MQ=12)
     tttgtCAGATATATCACGATAGCTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTc                                                                                                                                     <  2:256962/137‑1 (MQ=255)
         tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCaaat                                                                                                                                 >  1:311228/1‑139 (MQ=21)
         tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACt                                                                                                                                 >  1:143815/1‑141 (MQ=35)
         tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTCCATACAGAAGACTCCTTTTTGTTAAAATTATACTCTAAATTCAACt                                                                                                                                 >  1:164453/1‑141 (MQ=21)
             atatatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAATGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTGAAAATTATACTATAAATTCAACTTTGc                                                                                                                             >  1:49910/1‑141 (MQ=25)
                tatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGCATACAGTGATAACATCCTTGTTAAATTGCTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTCCaaa                                                                                                                          >  2:172205/1‑140 (MQ=255)
                   cACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGa                                                                                                                       >  1:92812/1‑141 (MQ=35)
                       aTAACTCAATGTATTTCTTAGATAGTAGCCAACGGCGACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCg                                                                                                                   <  2:98122/141‑1 (MQ=25)
                         agcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGCTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGta                                                                                                                 <  2:1101/139‑1 (MQ=255)
                           cTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGtatt                                                                                                               >  1:324118/1‑141 (MQ=40)
                            tCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattt                                                                                                              >  1:83529/1‑140 (MQ=16)
                            tCAATGCATATCTTAGATAGTAGCCAAAGGCTAAAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGAATCCTTTTTGTTAAAATTATATTATAAATTCAACTTTTCAGCGGCACCGtattt                                                                                                              >  1:85105/1‑140 (MQ=11)
                             cAATGCATATTTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt                                                                                                             <  2:85732/141‑3 (MQ=255)
                             cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt                                                                                                             >  1:348519/1‑139 (MQ=255)
                             cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt                                                                                                             >  1:348638/1‑139 (MQ=16)
                              aaTGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGCTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATg                                                                                                            >  1:318484/1‑141 (MQ=255)
                               atgcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttat                                                                                                           <  1:103994/137‑5 (MQ=255)
                                 gtattgcTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGaa                                                                                                         <  1:161356/135‑1 (MQ=255)
                                 gcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatga                                                                                                         >  2:106375/3‑135 (MQ=255)
                                 gTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGaa                                                                                                         >  1:236359/1‑141 (MQ=255)
                                   atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACCTAACCGtattttatgagt                                                                                                       >  2:66204/1‑133 (MQ=11)
                                   atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTAACAGTGGTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgatt                                                                                                       >  1:279805/1‑133 (MQ=11)
                                   atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCGTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGAGTCCTTTTTGTTAAAATTATATTATAAATTCAGCTTTGCAACAGAAcctgctagctgtgtt                                                                                                       >  2:90272/1‑128 (MQ=11)
                                    tatCTTAGGTAGGAGCCAACGGCTGCAGTGATAACTTCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATag                                                                                                      <  2:12583/141‑1 (MQ=255)
                                    tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATTCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGTAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATag                                                                                                      <  2:12579/141‑1 (MQ=255)
                                    tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagta                                                                                                      >  2:190438/1‑132 (MQ=255)
                                    tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagta                                                                                                      >  2:25369/1‑132 (MQ=255)
                                    tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACAGtattttatgagta                                                                                                      >  1:219265/1‑132 (MQ=11)
                                    tatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAATATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactatatg                                                                                                      >  2:209405/1‑127 (MQ=11)
                                    tatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactatatg                                                                                                      >  1:163126/1‑127 (MQ=11)
                                    tatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTCCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactatatg                                                                                                      >  1:229665/1‑127 (MQ=11)
                                      tCTTAGATAGTAGCGAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgactaca                                                                                                    <  2:280799/141‑12 (MQ=11)
                                      tCTTAGATAGTAGCCAACGGCTACAGTGATAACATCTTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtaca                                                                                                    <  2:336791/141‑12 (MQ=11)
                                        ttAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacact                                                                                                  <  1:87727/141‑14 (MQ=11)
                                        ttAGATAGTAGCCAACGGATAACGTGATCACATCTTTGTTAACTTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacact                                                                                                  <  1:74039/141‑14 (MQ=11)
                                         tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTTTTTTTTTTTTATTATAAATTCAACTTTGCAACAGAACCGtattttatgggtatactt                                                                                                 >  2:1906/1‑127 (MQ=11)
                                         tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                                 >  2:181306/1‑127 (MQ=11)
                                         tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                                 <  2:343227/141‑15 (MQ=11)
                                         tAGATAGTAGCCAACGGATACAGTCAAAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc                                                                                                 >  1:263805/1‑127 (MQ=11)
                                              agtagCCAACGGCTACAGTAAATTCATCCTTTTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGt                                                                                            <  1:332157/141‑1 (MQ=17)
                                               gtagCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTa                                                                                           >  1:210084/1‑141 (MQ=255)
                                                  gCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACa                                                                                        <  2:170544/141‑1 (MQ=255)
                                                   ccAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACAt                                                                                       <  1:285829/141‑1 (MQ=255)
                                                     aaCGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATCATGGAATAGAGATGTTGGTAACAttt                                                                                     >  2:181968/1‑141 (MQ=255)
                                                       cGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTCACATTtat                                                                                   >  1:122784/1‑141 (MQ=255)
                                                        ggCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGCAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTtata                                                                                  >  1:11054/1‑141 (MQ=255)
                                                               gTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATc                                                                           >  2:26280/1‑141 (MQ=255)
                                                                           ttGTTAAATTGTTTATATCTGTAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGTACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAg                                                               <  1:193245/141‑1 (MQ=255)
                                                                             gTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATCATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGtt                                                             <  1:181968/141‑1 (MQ=255)
                                                                                      tttATATCTGAAATAGTTCATACAGAAGACTCCTTGTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGt                                                    <  2:107537/141‑1 (MQ=255)
                                                                                       ttATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAGCTTTAATTTCGtt                                                   <  2:92812/141‑1 (MQ=255)
                                                                                               gAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGa                                           >  1:286457/1‑141 (MQ=255)
                                                                                                        taTACGGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACAt                                  <  2:31410/140‑1 (MQ=255)
                                                                                                                agaCTCCTTATTGTTAAAATTATACTATAAATTCCACTTTGCAACAGAACCGGATTATGGAATAGAGATGTTGGTAACATATATACAGTATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCa                          <  2:47035/141‑1 (MQ=255)
                                                                                                                           tGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGt               <  2:159770/141‑1 (MQ=255)
                                                                                                                                        cTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTAGt  >  1:284792/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                            
CTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACATTTATACAGGATCATTATACTTAAGTTTAATTTCGTTATTACAGAACCACACATTCCAACCAGAAGAGAAAGTATGTCTATTTAGT  >  CP000730/36445‑36721

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: ‑