Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,929,930 T→A 56.3% intergenic (‑1013/‑155) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,929,9300TA56.3% 17.9 / 51.6 46intergenic (‑1013/‑155)USA300HOU_1794/USA300HOU_1796hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (10/10);  new base A (16/9);  total (27/19)
Fisher's exact test for biased strand distribution p-value = 3.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.64e-01

TATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  CP000730/1929792‑1930068
                                                                                                                                              |                                                                                                                                          
tattcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACtt                                                                                                                                         >  2:79705/9‑141 (MQ=255)
 tttcggcGATGATATATTAGTAGAGGCGCCTATCTGTCAGGCGTCAACTTAGACGCAGAGAGGATGTGTATAAGGTGATGCTTATTTTCGTTCACATCGTAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCtt                                                                                                                                         <  1:85934/135‑1 (MQ=255)
 atTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCTTTTTTTTCtt                                                                                                                                         <  1:288682/141‑1 (MQ=255)
   ttGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTAt                                                                                                                                       <  2:18332/141‑1 (MQ=255)
   tcacagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTAtt                                                                                                                                      >  1:37368/6‑141 (MQ=255)
      cagacggtataATTATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCAATTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                                                                   <  1:87477/134‑1 (MQ=255)
       cGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGCGAGGAGGTGTATAAGGCGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGc                                                                                                                                   <  1:260833/141‑1 (MQ=255)
         agcatatAATAGGAGAGTCGCCTATCTCTCAGGCGTCAATTTAGCCGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTa                                                                                                                                 <  2:215536/138‑1 (MQ=255)
          tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATCCTTATTGGCTTAg                                                                                                                               >  1:220004/4‑141 (MQ=255)
          tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCttag                                                                                                                               <  1:141444/138‑4 (MQ=255)
          tggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTACTCATTTTCGTTCACGTCATAGCACCTGTCATCAGTGGCTGTGCTGCTGCGTATTATACTTATTGGCTTAg                                                                                                                               <  2:275815/138‑1 (MQ=255)
          tgatATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCACCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTaa                                                                                                                                >  2:238635/1‑141 (MQ=255)
           ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAgg                                                                                                                              >  2:291720/3‑140 (MQ=255)
           ggtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGt                                                                                                                              >  2:319625/3‑141 (MQ=255)
              ataataataGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaa                                                                                                                           >  1:313259/1‑139 (MQ=255)
               taataaTAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAAGATCGGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTaaac                                                                                                                          <  1:30533/141‑4 (MQ=255)
               gaataatAGGGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGCGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTCTTGGCTTAGTaaac                                                                                                                          <  2:272455/140‑4 (MQ=255)
                 ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTATTAAACGc                                                                                                                        >  2:159873/5‑141 (MQ=255)
                 ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACg                                                                                                                         >  1:335014/1‑141 (MQ=255)
                 ataGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCCCTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACg                                                                                                                         >  1:290362/1‑141 (MQ=255)
                  taatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                       <  1:297687/138‑1 (MQ=255)
                  caatatagTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCa                                                                                                                       <  2:196202/135‑1 (MQ=255)
                    atagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GAGGAAGAGAGGAGGTGCATTACTGTGCTAATCATTTTCGTTCGCATCATAGCACCAGTCATCAGTCGCTGTGCTGTGGCGTCTTATACTTATTGGCTTAGTCAACGCaac                                                                                                                     >  2:301096/2‑140 (MQ=255)
                         gTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACaa                                                                                                                 <  1:24325/141‑1 (MQ=255)
                         gTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacgaata                                                                                                                >  1:12308/1‑135 (MQ=255)
                         gTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaata                                                                                                                >  2:286085/1‑135 (MQ=255)
                          tCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataa                                                                                                               >  2:314126/1‑134 (MQ=255)
                            gcctttccgtcAGGCTTCAATTTAAGCGCAGAGGGGAGGTGTATAAGGTGATGCTTATGTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTGTTTCTTATTGGCTAAGTAGACGCAATACAAAAt                                                                                                              <  2:77131/132‑1 (MQ=255)
                            gCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAATCATCAGTGGCTTTGCTGTTGCGTATCATACTTATTGGCTTAGTAAACGCaacaaatgatt                                                                                                             >  2:102184/1‑132 (MQ=255)
                            gCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt                                                                                                             >  1:21717/1‑132 (MQ=255)
                            gCCTATCTCGCAGGCGTCAAGT‑‑GGCGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTGCGTTCACATCATAGCACCAGTCATCCGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataatt                                                                                                             <  1:76933/141‑10 (MQ=255)
                              cTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaa                                                                                                           <  1:312343/141‑12 (MQ=255)
                              cTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTCAATGGCTTAGTAAACGCaacaaataattaa                                                                                                           >  1:187558/1‑130 (MQ=255)
                               tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTAATTGGCTTAGTAAACGCaacaaataattaaa                                                                                                          >  2:105831/1‑129 (MQ=255)
                               tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGCAGGTGCATTACTTGGCTAATCATTTTCACTCACAACATAGCACAAGTCATGAGTGGCTGTGCTGATGCGTATTATACTTATTGGCTTAGTAAACGCaacaactaattaat                                                                                                          >  2:149117/1‑129 (MQ=255)
                                 tctctcAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaatag                                                                                                        >  2:295300/1‑127 (MQ=255)
                                     tcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCCTTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATaacatacct                                                                                                     >  2:278132/1‑133 (MQ=255)
                                     tcAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACat                                                                                                     <  1:93331/141‑1 (MQ=255)
                                             cAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGc                                                                                             >  2:352045/1‑141 (MQ=255)
                                                               gaggTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAAGACAAAATAGGTGCCATATAGCCGCACCAATAAAAATcccccc                                                                           >  2:28321/1‑139 (MQ=255)
                                                                                     cTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCCCACTACCGCAAATAGTGAg                                                         <  1:211986/141‑1 (MQ=255)
                                                                                      ttATATTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGACTAAGTAGACGCAATAAAAAATAGGTGAAATATAGCCGCACCAATAAAAATCACCTCACTACAGAAAATAATGAgg                                                        >  1:167631/1‑141 (MQ=255)
                                                                                                       atAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTa                                       >  1:102260/1‑141 (MQ=255)
                                                                                                                  catcaGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAACTAGTGAGGGGCTTGGTGTATAAGTAAATACTAAttt                            >  2:152766/1‑141 (MQ=255)
                                                                                                                     caGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGAGTGGTGTATAAGTAAACACTTATTTTCg                         >  2:156389/1‑141 (MQ=255)
                                                                                                                                 cagtGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATta             <  1:51878/138‑1 (MQ=255)
                                                                                                                                            tttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTCAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt  <  2:44754/141‑1 (MQ=255)
                                                                                                                                            tttCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt  <  1:160986/141‑1 (MQ=255)
                                                                                                                                            tgtCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATAGAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAAtt  <  2:177470/139‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                          
TATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGTATAAGTAAATACTTATTTTCGTTGTCTTAATTATACTGCTAATT  >  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: