Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,929,928 T→A 58.0% intergenic (‑1011/‑157) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,929,9280TA58.0% 25.1 / 56.9 51intergenic (‑1011/‑157)USA300HOU_1794/USA300HOU_1796hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (8/13);  new base A (15/14);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 3.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

TATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  CP000730/1929792‑1930068
                                                                                                                                                |                                                                                                                                                   
tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTT‑‑TGCTAATGGTTACTTATCACATCATAGCACCAGTCATCAGGGGCTGGGCTGTTGCGTATTATACtt                                                                                                                                                >  1:99374/9‑141 (MQ=255)
    cacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTg                                                                                                                                            >  2:197643/5‑141 (MQ=255)
     acagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTTTTGCGTATTATACTTATTgg                                                                                                                                           <  1:217272/138‑1 (MQ=255)
      ccGATGATATAATAGTAGAGGCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCCGTTATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTgg                                                                                                                                           <  2:58816/141‑1 (MQ=255)
      cagatggtATAATAATAGAGGCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                                                                          <  1:175042/139‑1 (MQ=255)
      cagagggtataATAATAGAGTCGCCTATCTCTCCGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                                                                          <  2:357515/134‑1 (MQ=255)
       cGAGGATATAATAGGAGAGTCGCCGATGTCTCAGGCGGCAATGTAGGCGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCAGAGCACCAGTCATCAGTGGCTGTGCCACTGCGTTTTTTTCTTATTGGc                                                                                                                                          <  1:270609/141‑1 (MQ=255)
       agatggtATAATAAAAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCt                                                                                                                                         >  2:243199/2‑141 (MQ=255)
        gatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt                                                                                                                                        >  1:87064/1‑140 (MQ=255)
         atggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtta                                                                                                                                       >  1:38217/5‑139 (MQ=255)
          tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                                      >  1:285321/4‑138 (MQ=255)
          tggtagaataagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTGCGTTCACAGCATAGCACCAGTCATCAGGGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAg                                                                                                                                      <  2:305221/129‑1 (MQ=255)
          tggcataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                                      <  2:241046/137‑4 (MQ=255)
           ggtataATAATAAAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTGTACTTATTGGCTTAgg                                                                                                                                     >  2:209550/3‑140 (MQ=255)
             tataATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTa                                                                                                                                    >  1:336584/1‑141 (MQ=255)
             tataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaa                                                                                                                                   <  2:173789/141‑2 (MQ=255)
             taaaataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCGCATCATAGCACCAGTCATCAGTGGCTGTGCCGTTGCGTTTTTTTCTTCATGGCTAAGTa                                                                                                                                    >  2:24364/4‑141 (MQ=255)
              ataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa                                                                                                                                  <  2:56056/141‑3 (MQ=255)
                 ataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTGTCCTGTCAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                                                                                               <  1:82463/141‑1 (MQ=255)
                 ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATCGCGTTTTTTTGTTATTGGCTCCGTAGACg                                                                                                                                >  1:294474/1‑141 (MQ=255)
                  tagtagAGTCGCCTATCTCTCCGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc                                                                                                                               <  2:282721/141‑1 (MQ=255)
                  tagtagAGTCGCCTATCTCTCAGGCGTCAATTTAGTCGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTTCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGc                                                                                                                               <  2:268317/141‑1 (MQ=255)
                  taatagAGTCGCCTATCTCTCAGGCGTCGATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                              <  1:249006/138‑1 (MQ=255)
                  aaagagagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                              <  1:37940/137‑1 (MQ=255)
                      agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGGGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                                          >  1:159474/1‑138 (MQ=255)
                      agagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTGTTATACTTATTGGCTTAGTGAACGCaacaa                                                                                                                          >  1:33425/1‑138 (MQ=255)
                      agagTCGCCTATCTCTCAGGCGTCAATT‑‑CACGAAGAGAGGAGGTGCATTACTTTACTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAAGGCaacaa                                                                                                                          >  1:231223/1‑138 (MQ=255)
                      agagTCGCCTAGCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaa                                                                                                                          <  1:63764/141‑4 (MQ=255)
                       gagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaa                                                                                                                         >  1:270385/1‑137 (MQ=255)
                             ccTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGATGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                                   >  1:172911/1‑131 (MQ=255)
                             ccTATCTCTCAGGCGTCAA‑‑TAGACGAAGGGAGGAGGTGCATTACTTTGCTAATCTT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatta                                                                                                                   >  1:232189/1‑131 (MQ=255)
                               tATCTCTCAGGCGGCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                                 <  1:222125/141‑13 (MQ=255)
                               tATCTCTAAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                                                                                 <  2:94746/141‑13 (MQ=255)
                                ttctctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATTGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGt                                                                                                             <  2:313064/140‑1 (MQ=255)
                                aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                >  1:221566/1‑128 (MQ=255)
                                aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                >  1:32157/1‑128 (MQ=255)
                                aTCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAT‑‑TTTCGTTCACATCATAGCACCAGTCAGCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaata                                                                                                                <  1:346969/141‑14 (MQ=255)
                                   tctcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTCGCTAAGTGGACGCACT‑‑CCAC‑‑AATAGGCGAc                                                                                                          >  2:230209/1‑141 (MQ=255)
                                          cGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGTCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGc                                                                                                 >  2:347322/1‑141 (MQ=255)
                                              aaTTTAGACGCAGAAAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCCTTCACATCAAAAAAAAAAAAAAAAGTGGCTGGGACAGTGCGTTTTTTTCTTACTGGCTACGTAGAAAAAAT‑‑ACAA‑‑AGCCGGTTTCATATAgaaaaa                                                                                             <  2:155225/141‑6 (MQ=255)
                                                                        taAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGc                                                                   <  2:212254/141‑1 (MQ=255)
                                                                                        tAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAggg                                                       <  1:249357/141‑1 (MQ=255)
                                                                                          t‑‑tttCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGa                                                     <  1:171248/141‑1 (MQ=255)
                                                                                          t‑‑tttCGTTCACACCCTCGCACCAGTCATCAGTGGCTGTGCCATTGCGTTCTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGa                                                     <  1:24364/141‑1 (MQ=255)
                                                                                                          catAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGt                                        >  1:194722/1‑141 (MQ=255)
                                                                                                          catAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGGGAGGGGGTTGGTGTATAAGt                                        >  1:91724/1‑141 (MQ=255)
                                                                                                           atAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCAACAAATAATTAATAGGCGACTTTATAAGCCAGCAACGAAAAAATCCCCACACTACTGCAATAGTGAGGGGATGGGTGcat                                            >  2:125072/1‑141 (MQ=255)
                                                                                                               cACCAGTCATCAGGGGCTGTGCCATTGCGTTTTTTTCTTAGTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATa                                   <  2:241423/141‑1 (MQ=255)
                                                                                                                           gTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGtt                       >  2:309151/1‑141 (MQ=255)
                                                                                                                               cTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCt                   <  1:148616/141‑1 (MQ=255)
                                                                                                                                      aTTGCGTTTTTTTCTTCTTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATCAGTCATTTCGTAGTTTCGTTGTCTTAATtat            <  2:254164/141‑1 (MQ=255)
                                                                                                                                              tttttCTTTTTTGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGAACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATCCTTATTTTCGTTGTCTTAAtttaccttctaa    >  2:16784/1‑131 (MQ=255)
                                                                                                                                                tttCGTATTGGCTAAGGAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt  <  2:336584/141‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                                   
TATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAT‑‑TTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAT‑‑ACAA‑‑AATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  CP000730/1929792‑1930068

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: