Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,231,470 A→C 43.9% M39L (ATG→CTG)  USA300HOU_1156 → possible PP2C protein phosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,231,4700AC43.9% 15.7 / 66.3 59M39L (ATG→CTG) USA300HOU_1156possible PP2C protein phosphatase
Reads supporting (aligned to +/- strand):  ref base A (18/15);  new base C (16/10);  total (34/25)
Fisher's exact test for biased strand distribution p-value = 6.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAATTTTC  >  CP000730/1231332‑1231608
                                                                                                                                           |                                                                                                                                          
cAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATg                                                                                                                                          >  2:538330/1‑141 (MQ=255)
    tAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCCAACTAATCAACAACTTTTAGTTGTGAGTGATGGTCTGGTTg                                                                                                                                      >  2:419225/1‑141 (MQ=255)
       aacgggcgtaattaCAAATGCTCGAAGTAGAATTGATGACGGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGcc                                                                                                                                   <  1:288494/128‑1 (MQ=255)
       aaaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGcc                                                                                                                                   >  2:213863/1‑141 (MQ=255)
       aaaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGcc                                                                                                                                   <  2:257942/141‑1 (MQ=255)
        aaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGTACTACATATGTATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCa                                                                                                                                  <  2:208390/141‑1 (MQ=255)
        aaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTAATGATACGGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCCAACTAATCAACACCTTTTAGTTCTGTGTGATGGTCTGGGTgtcaa                                                                                                                                  >  2:251376/1‑137 (MQ=255)
         aCGAGGAAAAGAAAAATGCAAGAGGGACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCAt                                                                                                                                 <  2:560114/141‑1 (MQ=255)
                aaaaACAAATGCTAGAGGCACAATTTTTTACTGAGACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTGTTTATAATCAACCTAATCAACGACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAg                                                                                                                          <  1:564085/141‑1 (MQ=255)
                 aaGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACCACCTTTAATTACATTTAATGGTATGGGTGGCCATAAAGCacg                                                                                                                         >  2:126067/1‑139 (MQ=255)
                  aGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGga                                                                                                                        >  1:489215/1‑141 (MQ=255)
                        aTGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGAGGGTATGGGTGGCCATAAAGCAGGAGAAGtt                                                                                                                  <  2:602739/141‑1 (MQ=255)
                            tAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGCAGTTGCaa                                                                                                              >  1:11398/1‑141 (MQ=255)
                            tAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAAGCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCaa                                                                                                              >  1:201616/1‑141 (MQ=255)
                            tAGAGGCACAATTTTTTACGGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCaa                                                                                                              >  1:335907/1‑141 (MQ=255)
                            tAGAGGCACAATTTGTTACAGATACTGGACAACATAGAGATAAGCATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCaa                                                                                                              >  1:335721/1‑141 (MQ=255)
                               agGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTa                                                                                                           <  2:381393/141‑1 (MQ=255)
                                      aTTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTgg                                                                                                    >  1:508322/1‑140 (MQ=255)
                                          tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACa                                                                                                >  1:540952/1‑141 (MQ=255)
                                          tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTCTTGTGAGCATGGAGTGGCGGAAATAAACCAGGAGAAGTTGCAAGTAAATTTGTTACa                                                                                                >  1:138541/1‑141 (MQ=255)
                                          tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTGTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGCGAAGTTGCAAGTAAATTTGTTACa                                                                                                >  1:387365/1‑141 (MQ=255)
                                           ttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAg                                                                                               <  1:343061/141‑1 (MQ=255)
                                             aCTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGAt                                                                                             <  2:284696/141‑1 (MQ=255)
                                                    cTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCTAGTAAATTTCTTACAGATGAGTTGa                                                                                      <  1:307788/141‑1 (MQ=255)
                                                    cTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGa                                                                                      <  1:482276/141‑1 (MQ=255)
                                                          aacaTAGAGGTAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTGGTTCTGTGTGATGGTATCGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccg                                                                                >  2:403740/1‑140 (MQ=255)
                                                          aacaTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccc                                                                                <  2:219975/141‑1 (MQ=255)
                                                          aacaTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccc                                                                                >  1:436638/1‑141 (MQ=255)
                                                            caTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGt                                                                              >  1:218369/1‑141 (MQ=255)
                                                             aTAGAGATAAGAATGAGGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGtt                                                                             >  1:304925/1‑141 (MQ=255)
                                                                    tAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGc                                                                      <  1:213863/141‑1 (MQ=255)
                                                                    tAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAGAtacgctggaggacg                                                                      >  2:426243/1‑128 (MQ=255)
                                                                      aGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCgg                                                                    >  2:50281/1‑141 (MQ=255)
                                                                      aGAATGAAGATGCGGGTGGTAGTTTTTATAATCAAACTAATCAACAACTTTTAGTTATGTGTGATGGTCTGGGTCGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGCAGCgg                                                                    <  1:450231/141‑1 (MQ=255)
                                                                         aTGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGGGTTGAAATCCCGTTTTGACGCGGaaa                                                                 >  1:260771/1‑141 (MQ=255)
                                                                         aTGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGaaa                                                                 >  1:504331/1‑141 (MQ=255)
                                                                          tggagagtcGGGTTGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGaaaa                                                                <  2:471251/133‑1 (MQ=255)
                                                                           gAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCACCAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAAt                                                               <  2:64568/141‑1 (MQ=255)
                                                                              gATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCtt                                                            >  1:479998/1‑141 (MQ=255)
                                                                              gATGCGGGTGATATTTTTTATAATCATACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTAGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAATTTTGTTACAGATGAGTTGAAGTCCGGTTTTGAAACGGAAAATcat                                                            >  2:374415/1‑139 (MQ=255)
                                                                               aTGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTta                                                           <  2:99368/141‑1 (MQ=255)
                                                                                 gCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTtata                                                         >  2:244276/1‑141 (MQ=255)
                                                                                   gggTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGGTGAGTTGAAATCCCGTGTTGAAGCGGAAAATCTTATAGa                                                       >  2:420483/1‑141 (MQ=255)
                                                                                       ggtATTTTTTGTAATCCACCTAATCAACACCTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGaacaa                                                   <  2:201616/141‑1 (MQ=255)
                                                                                        gtATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGaacaac                                                  >  1:154749/1‑141 (MQ=255)
                                                                                            tttttATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCa                                              <  1:280796/141‑1 (MQ=255)
                                                                                               ttATAATCAAACTAATCAACAACTTTTAGTTATGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGc                                           >  2:325933/1‑141 (MQ=255)
                                                                                                 acaaccacaccaaTCAACAACTGTTAGTTCTGTGTGATGGTATGGGTGGCCATAAACCACCAGAAGCTCCAAGTAAATTTTTTCCAGATGAGTTGAAATCCCGCTTTGAATCGGAAAATCTTATAGAACAACATCCAGCtc                                         <  2:185600/130‑2 (MQ=255)
                                                                                                  taATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGa                                        >  1:89913/1‑141 (MQ=255)
                                                                                                  taATCAAACTAATCAAAAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGa                                        <  2:129013/141‑1 (MQ=255)
                                                                                                      cAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAAt                                    >  1:258064/1‑141 (MQ=255)
                                                                                                           tAATCAACAACTTTTAGTTTCGTGTGATGGTATCGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAACTGGtt                               <  2:342559/141‑1 (MQ=255)
                                                                                                                  caacTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGtaat                        <  1:50281/141‑1 (MQ=255)
                                                                                                                    acTTTTAGTTCTGTGTGATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGtaataa                      <  1:217259/141‑1 (MQ=255)
                                                                                                                     cTTTTAGATCTGTGTGATGGCCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTaataat                     >  1:385094/1‑141 (MQ=255)
                                                                                                                       tttAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAatat                   >  1:540520/1‑141 (MQ=255)
                                                                                                                                gtgtgATGGTATGGGTGGCCATAAAGCAGGAGATGTTGCAAGTAAATTTGATACAGATGAGTTGAACTCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAatatat          <  1:416106/141‑1 (MQ=255)
                                                                                                                                    gATGGTCTGGGTGGCCATAAAGAAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAAt      >  2:492974/1‑141 (MQ=255)
                                                                                                                                         gTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATAAAAATTTTc  >  2:104620/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                          
CAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTGATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAATTTTC  >  CP000730/1231332‑1231608

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: