Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,759,201 T→A 20.9% L31F (TTA→TTT USA300HOU_1650 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,759,2010TA20.9% 110.2 / 26.8 53L31F (TTA→TTTUSA300HOU_1650hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (23/17);  new base A (5/6);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 5.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTACATTCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATCTAATTATATATTTTATTATGTATAT  >  CP000730/1759062‑1759341
                                                                                                                                            |                                                                                                                                            
gTACATTCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTa                                                                                                                                             >  1:517160/1‑141 (MQ=255)
gTACATTCGTTATTAAATCATTTTCTTTTAGTGAATATCTCTCTCCACTAACATAAACATGTTGGGAGTCATTAGTGGGTTGCGTAACTTGATTCATTTAATCCTTATCGTGGTTTACAGGATTCCCCGCTTGTTCTTTTa                                                                                                                                             <  2:727415/141‑1 (MQ=255)
   cATTCTTTATTAAGTCATTTTCTTTTATTGAGTATTTCTCTACTCTTCCAGAAACATGTTTCGCATCACCACTGCATTTCGGAACTTGATACATTTGAACATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTaaaa                                                                                                                                          <  2:264147/141‑1 (MQ=255)
     ttCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTaaaaaa                                                                                                                                        >  1:226064/1‑141 (MQ=255)
      tCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAg                                                                                                                                       >  2:399451/1‑141 (MQ=255)
       cgcttttaAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACGTGTTGGGCATCATTAGTGGGTTTCGTAACTTGATTCATTTGATCATTACCGTGATTTACAGGGTTCCTATCTTGTTCTTTTAAAAAAgt                                                                                                                                      >  2:613890/6‑140 (MQ=255)
           attaAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCg                                                                                                                                  <  1:68857/141‑1 (MQ=255)
             taAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCTAATCTTGTTCTTTTAAAAAAGGTGCGTa                                                                                                                                <  1:508220/141‑1 (MQ=255)
              aaaTCCTTTTCTTTTAATGAATATTTCTCACCACTTACATAAAAATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAt                                                                                                                               <  1:389410/141‑1 (MQ=255)
               aaTCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAtt                                                                                                                              <  1:142756/141‑1 (MQ=255)
               aaTCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAtt                                                                                                                              <  1:364728/141‑1 (MQ=255)
               aaTCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAtt                                                                                                                              <  1:559458/141‑1 (MQ=255)
                attaTTTTCTTTTAATGAATACTTCTCACCCATTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGACTCATTTGATCATGATCGTGATTTACAGGATTCCAATCTTGTTCTTTGAAAAAAGGTGCGTAttt                                                                                                                             <  1:239404/138‑1 (MQ=255)
                     tttCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAgg                                                                                                                        >  2:424820/1‑141 (MQ=255)
                       tCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCg                                                                                                                      >  1:634224/1‑141 (MQ=255)
                       tCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCg                                                                                                                      >  1:7000/1‑141 (MQ=255)
                        cTTTTAATGAATATTTCTCCCCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGa                                                                                                                     <  1:691940/141‑1 (MQ=255)
                                       tctcACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATca                                                                                                      >  2:774642/1‑141 (MQ=255)
                                         tcACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATcaca                                                                                                    >  2:482888/1‑141 (MQ=255)
                                          caccacTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGAGATATAAACAATTATCACaa                                                                                                   >  2:229090/1‑141 (MQ=255)
                                          caccacTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACaa                                                                                                   >  2:781547/1‑141 (MQ=255)
                                          cacaacTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACaa                                                                                                   >  2:93794/1‑141 (MQ=255)
                                               cTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCt                                                                                              <  2:244540/141‑1 (MQ=255)
                                                 tACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTAt                                                                                            >  1:207897/1‑141 (MQ=255)
                                                         atggTTGTGCATCATTAGTGCGTTGCGTAATTTGATTCATTTCATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAATAATTATCACAATTGCTATTACTGCta                                                                                    <  1:429814/138‑1 (MQ=255)
                                                             ttGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATACACAATTATCACAATTGCTATTACTGCTATAAt                                                                                >  2:120797/1‑141 (MQ=255)
                                                             ttGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAAt                                                                                >  1:80642/1‑141 (MQ=255)
                                                              tGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGCTTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATGATCACAATTGCTATTACTCCTATAATg                                                                               >  2:373011/1‑141 (MQ=255)
                                                               gggTATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGt                                                                              <  2:717639/141‑1 (MQ=255)
                                                                ggCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACACTCATCAAAATTGCTATTAGTGGTATAATGtt                                                                             >  2:306894/1‑141 (MQ=255)
                                                                ggCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGtt                                                                             >  2:150283/1‑141 (MQ=255)
                                                                ggCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCCTTAATGtt                                                                             >  2:138244/1‑141 (MQ=255)
                                                                     catTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAATGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTaa                                                                        >  1:532386/1‑141 (MQ=255)
                                                                     catTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTaa                                                                        >  1:682795/1‑141 (MQ=255)
                                                                                tGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTCGATAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAat                                                             <  1:774642/141‑1 (MQ=255)
                                                                                   gTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGTCGATATAAACAATTATCACAATTGCTATTACTGCTATTATGTTTTTAATCATTCTAAatagc                                                          >  1:618117/1‑139 (MQ=255)
                                                                                   gTAACTTGATTCATTTGATATAACTTATGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATc                                                          >  1:580595/1‑141 (MQ=255)
                                                                                          gATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCa                                                   <  1:320555/141‑1 (MQ=255)
                                                                                           aTTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCAt                                                  <  1:332745/141‑1 (MQ=255)
                                                                                                   gATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTACCCTGACTAAATATCAATCTCATAGTTCGcc                                          <  1:781547/141‑1 (MQ=255)
                                                                                                   gATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGcc                                          <  1:93794/141‑1 (MQ=255)
                                                                                                    aTCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCt                                         >  1:286709/1‑141 (MQ=255)
                                                                                                      cATTATCGTGATTTATAGGATTCCAATCATGTTCATTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTcc                                       <  2:190291/141‑1 (MQ=255)
                                                                                                      cATTATCCTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTTCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTcc                                       <  2:187696/141‑1 (MQ=255)
                                                                                                        ttATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCaa                                     >  1:703926/1‑141 (MQ=255)
                                                                                                          aTCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATg                                   <  1:675090/141‑1 (MQ=255)
                                                                                                          aTCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATCATATTCTTCAATCTCATAGTTCGCCTCCAATg                                   <  2:760650/141‑1 (MQ=255)
                                                                                                           ttCGTGATTTACAGGATTCCAATTGTGTGCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATg                                   <  1:204272/140‑1 (MQ=255)
                                                                                                             cGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGCTATAAACAATTATCACAATTGCTATTACTGCTATAATGGTTTTAATCATACTAAGTATCAATCTGATGGTTCGCCTCCAATGTc                                 >  1:224994/1‑141 (MQ=255)
                                                                                                                  tttACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATTTCTTCAt                            >  2:79640/1‑141 (MQ=255)
                                                                                                                   ttACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATc                           <  2:407976/141‑1 (MQ=255)
                                                                                                                                     gTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATCTAATTATATATTttatta         <  1:26365/141‑1 (MQ=255)
                                                                                                                                      ttCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATCTAATTATATATTTtattat        >  2:67024/1‑141 (MQ=255)
                                                                                                                                            tAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATCTAATTATATATTTTATTATGTatat  >  1:228176/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
GTACATTCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTATCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATCTAATTATATATTTTATTATGTATAT  >  CP000730/1759062‑1759341

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: