Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 678,888 G→T 11.2% intergenic (+91/+160) USA300HOU_0621 → / ← sarA hydrolase/staphylococcal accessory regulator A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730678,8880GT11.2% 173.1 / 3.4 62intergenic (+91/+160)USA300HOU_0621/sarAhydrolase/staphylococcal accessory regulator A
Reads supporting (aligned to +/- strand):  ref base G (25/29);  new base T (6/2);  total (31/31)
Fisher's exact test for biased strand distribution p-value = 2.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAAGCATTTATGAATTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAATGTATCATCTATCAAACTTCA  >  CP000730/678749‑679027
                                                                                                                                           |                                                                                                                                           
aGAAGCATTTATGAATTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGa                                                                                                                                            <  1:336513/141‑1 (MQ=255)
 gAAGCATTTATGAATTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGaa                                                                                                                                           >  2:296044/1‑141 (MQ=255)
     cATTTATGAATTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGCTATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGt                                                                                                                                       >  1:65097/1‑141 (MQ=255)
     cATTTATGAATTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGt                                                                                                                                       >  1:574445/1‑141 (MQ=255)
     cATTTATGAAATATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGt                                                                                                                                       <  2:448973/141‑1 (MQ=255)
      aTTAATGAATTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAGAGTCCTTAGGCCATGTGAAAAGGCGGATGACTATTCCTTATTGGATAGAAATCAGCGTTCTTTGcaagcta                                                                                                                                      >  2:223072/1‑137 (MQ=255)
             aaTTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGata                                                                                                                               <  2:51638/141‑1 (MQ=255)
             aaTTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGata                                                                                                                               <  2:746756/141‑1 (MQ=255)
              attattattTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTGTTGAAATGTATTTGctat                                                                                                                              >  1:277149/1‑141 (MQ=255)
                tattattTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGttatat                                                                                                                            >  2:714525/1‑141 (MQ=255)
                  ttattTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATAc                                                                                                                          <  1:267203/141‑1 (MQ=255)
                   tattTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACt                                                                                                                         >  1:428057/1‑141 (MQ=255)
                       tAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGGAATCAGCTTTTTTTGAAAGGTATTTGATATATACTGCTc                                                                                                                     >  2:573229/1‑141 (MQ=255)
                         aaaTTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGTTTTTTTTGAAATGTATTTGATATATACTGCTCGt                                                                                                                   <  2:124990/141‑1 (MQ=255)
                           aTTTTTAAAAAGCGCAACATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGATTTTTTTGAAATGTATTTGATATATACTGCTCGTTa                                                                                                                 >  1:421512/1‑141 (MQ=255)
                                 aaaaaGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGc                                                                                                           <  1:438496/141‑1 (MQ=255)
                                      gCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCt                                                                                                      >  2:715334/1‑141 (MQ=255)
                                         aaTCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTcc                                                                                                   <  2:580451/140‑1 (MQ=255)
                                          aTCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCt                                                                                                  >  2:510876/1‑141 (MQ=255)
                                             ttaaaaagtgATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTtat                                                                                               <  2:113949/134‑1 (MQ=255)
                                                atatGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTGATGCGGCTATCTTCCTTATAtt                                                                                            >  1:525653/1‑141 (MQ=255)
                                                    gtgATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGt                                                                                        <  2:691165/141‑1 (MQ=255)
                                                    gtgATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGt                                                                                        >  1:431219/1‑141 (MQ=255)
                                                      gATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTCTTCATTATTTGATAGAAATCAGCTGTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGc                                                                                      <  1:471385/141‑1 (MQ=255)
                                                      gATAAATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATACGGATATCTTCCTTTTATTAAGttc                                                                                      >  1:516134/1‑139 (MQ=255)
                                                              aaCCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGGAATGTGTTTGATATGTACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCTTTAGTg                                                                              >  2:103930/1‑141 (MQ=255)
                                                              aaCCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTg                                                                              <  1:111200/141‑1 (MQ=255)
                                                              aaCCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTg                                                                              <  2:517897/141‑1 (MQ=255)
                                                              aaCCTAGGGCATAAAGACCTTAGGCAATGTGAAAAAGCTGATTACTATTCAATATTTGATAGAAATCAGCTTATTTTGAAATGTATTTGATATATACTGCACGTTATGCGGCACTCTTCCTTATATTAAGTGCCATTAgag                                                                              >  2:456752/1‑139 (MQ=25)
                                                               aCCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGc                                                                             <  2:312528/141‑1 (MQ=255)
                                                               aCCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGc                                                                             <  2:714779/141‑1 (MQ=255)
                                                                     ggCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTGTTGCAAAAcc                                                                       >  2:64169/1‑141 (MQ=255)
                                                                        aTAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAACTCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACctct                                                                    <  1:424406/141‑1 (MQ=255)
                                                                         tAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCtt                                                                   <  1:61120/141‑1 (MQ=255)
                                                                                cTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAAtt                                                            >  1:622787/1‑141 (MQ=255)
                                                                                cTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAAtt                                                            >  1:566179/1‑141 (MQ=255)
                                                                                  tAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAg                                                          <  1:262570/141‑1 (MQ=255)
                                                                                  tAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAg                                                          <  1:87385/141‑1 (MQ=255)
                                                                                      cAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTaa                                                      >  1:265452/1‑141 (MQ=255)
                                                                                        aTGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTTTAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAACCCTCTTAACCATTCGATaaaa                                                    >  2:677776/1‑141 (MQ=25)
                                                                                        aTGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTaaaa                                                    >  1:81830/1‑141 (MQ=255)
                                                                                            gAAAAAGCTTATTACTAATCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGACCAAagag                                                <  2:464916/141‑1 (MQ=25)
                                                                                            aaaacaGCTGATTACTATTCTTTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGAGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAagag                                                <  2:645929/140‑1 (MQ=255)
                                                                                              aaaaGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCa                                              <  1:320121/141‑1 (MQ=255)
                                                                                               aaaGCTGATTACTATTCATTATTTGATAGAAACCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCAt                                             <  1:52246/141‑1 (MQ=255)
                                                                                                aaGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTTTTTTTTTTTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAATTGCCATTAGTGCAACACCTCTTAACAATTAGGTAAAAAGAGCATa                                            >  2:47199/1‑141 (MQ=25)
                                                                                                    tGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTTTTTTTTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATaaaaa                                        >  2:623731/1‑141 (MQ=37)
                                                                                                    tGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTTTATTGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTTACAATTAGGTGAAAagataacattaa                                        >  2:154387/1‑132 (MQ=25)
                                                                                                      aTTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATaaaaaaa                                      <  1:600549/141‑1 (MQ=255)
                                                                                                       ttACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAACTAGGTAAAAAGAGCATAAAAAAAg                                     <  1:646470/141‑1 (MQ=255)
                                                                                                       ttACTATTAATTATTTGATAGAAATCAGCTTTTTGTGAAGTGAATGTGAGTTATACTATTAGTTATGCGGCTATCTTCCTTATATTAAGTGTCATTTGTGCAAAACCTCTCAACAATTAGAGAAAAAGAGCATAAAAAAAg                                     <  2:155825/141‑1 (MQ=25)
                                                                                                       ttACGATTCATAACTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCACAACCTCTTAACAATTAGGTAAAAAGAGCATaaaaaaca                                     >  2:542442/1‑139 (MQ=255)
                                                                                                              tCATTATTTGATAGAAATCAGCTTTTTTTTTTTTTTTTTTGATATATACTGCTCCTTATGCATCTATCTTCCTTATCTTAAGTGCCATTTGTGCTATTCCTCTTCACAATTATTTTAAAATATCATAAAAAAAGGAAGttt                              >  2:552176/1‑141 (MQ=255)
                                                                                                                      tGATAGAAATCAGCTTTTTTTTTTTTTTTTTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATTTTAAGTGCCATTAGTGCAAAACCTCTTAACTATTTTGTAAAAAGAGCATAAAAAATGGTAGTTTAAtttaat                      >  2:750076/1‑136 (MQ=25)
                                                                                                                      tGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAAt                      >  1:695894/1‑141 (MQ=255)
                                                                                                                      tGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAAAAt                      >  2:751728/1‑141 (MQ=255)
                                                                                                                            aaaTCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAATGTatca                <  2:702829/141‑1 (MQ=255)
                                                                                                                            aaaTCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAATGTatca                <  1:223072/141‑1 (MQ=255)
                                                                                                                                     ttttttGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAATGTATCATCTATCaaa       >  2:49187/1‑141 (MQ=255)
                                                                                                                                       ttttTAAATTTATTTAATATATACTGCACGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACATATTAACAATTAGGTAAAAAAAAAAAAAAAAAAGGAAGTTTAATAGAATGTATCATCTATCAAACt     <  2:633673/141‑1 (MQ=255)
                                                                                                                                       ttttTAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAATGTATCATCTATCAAACt     <  1:339130/141‑1 (MQ=255)
                                                                                                                                          tGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGCGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAATGTATCATCTATCAAACTTCa  <  1:510876/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                           
AGAAGCATTTATGAATTATTATTTAAAATTTTTAAAAAGCGTATCATAATATGTGATATATAAACCTAGGGCATAAAGTCCTTAGGCAATGTGAAAAAGCTGATTACTATTCATTATTTGATAGAAATCAGCTTTTTTTGAAATGTATTTGATATATACTGCTCGTTATGCGGCTATCTTCCTTATATTAAGTGCCATTAGTGCAAAACCTCTTAACAATTAGGTAAAAAGAGCATAAAAAAAGGAAGTTTAATAGAATGTATCATCTATCAAACTTCA  >  CP000730/678749‑679027

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: ‑