Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,759,201 T→A 20.9% L31F (TTA→TTT)  USA300HOU_RS08780 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,759,2010TA20.9% 111.0 / 27.3 53L31F (TTA→TTT) USA300HOU_RS08780hypothetical 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

GTACATTCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATCTAATTATATATTTTATTATGTATAT  >  USA300TCH1516_ALE/1759062‑1759341
                                                                                                                                            |                                                                                                                                            
gTACATTCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTa                                                                                                                                             >  1:517160/1‑141 (MQ=255)
gTACATTCGTTATTAAATCATTTTCTTTTAGTGAATATCTCTCTCCACTAACATAAACATGTTGGGAGTCATTAGTGGGTTGCGTAACTTGATTCATTTAATCCTTA‑TCGTGGTTTACAGGATTCCCCGCTTGTTCTTTTa                                                                                                                                             <  2:727415/141‑1 (MQ=255)
   cATTCTTTATTAAGTCATTTTCTTTTATTGAGTATTTCTCTACTCTTCCAGAAACATGTTTCGCATCACCACTGCATTTCGGAACTTGATACATTTGAACATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTaaaa                                                                                                                                          <  2:264147/141‑1 (MQ=255)
     ttCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTaaaaaa                                                                                                                                        >  1:226064/1‑141 (MQ=255)
      tCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAg                                                                                                                                       >  2:399451/1‑141 (MQ=255)
       cgcttttaAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACGTGTTGGGCATCATTAGTGGGTTTCGTAACTTGATTCATTTGATCATTA‑CCGTGATTTACAGGGTTCCTATCTTGTTCTTTTAAAAAAgt                                                                                                                                      >  2:613890/6‑140 (MQ=255)
           attaAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCg                                                                                                                                  <  1:68857/141‑1 (MQ=255)
             taAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCTAATCTTGTTCTTTTAAAAAAGGTGCGTa                                                                                                                                <  1:508220/141‑1 (MQ=255)
              aaaTCCTTTTCTTTTAATGAATATTTCTCACCACTTACATAAAAATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAt                                                                                                                               <  1:389410/141‑1 (MQ=255)
               aaTCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAtt                                                                                                                              <  1:364728/141‑1 (MQ=255)
               aaTCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAtt                                                                                                                              <  1:142756/141‑1 (MQ=255)
               aaTCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTAtt                                                                                                                              <  1:559458/141‑1 (MQ=255)
                attaTTTTCTTTTAATGAATACTTCTCACCCATTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGACTCATTTGATCATGA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTGAAAAAAGGTGCGTAttt                                                                                                                             <  1:239404/138‑1 (MQ=255)
                     tttCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAgg                                                                                                                        >  2:424820/1‑141 (MQ=255)
                       tCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCg                                                                                                                      >  1:7000/1‑141 (MQ=255)
                       tCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCg                                                                                                                      >  1:634224/1‑141 (MQ=255)
                        cTTTTAATGAATATTTCTCCCCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGa                                                                                                                     <  1:691940/141‑1 (MQ=255)
                                       tctcACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATca                                                                                                      >  2:774642/1‑141 (MQ=255)
                                         tcACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATcaca                                                                                                    >  2:482888/1‑141 (MQ=255)
                                          caccacTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGAGATATAAACAATTATCACaa                                                                                                   >  2:229090/1‑141 (MQ=255)
                                          caccacTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACaa                                                                                                   >  2:781547/1‑141 (MQ=255)
                                          cacaacTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACaa                                                                                                   >  2:93794/1‑141 (MQ=255)
                                               cTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCt                                                                                              <  2:244540/141‑1 (MQ=255)
                                                 tACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTAt                                                                                            >  1:207897/1‑141 (MQ=255)
                                                         atggTTGTGCATCATTAGTGCGTTGCGTAATTTGATTCATTTCATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAATAATTATCACAATTGCTATTACTGCta                                                                                    <  1:429814/138‑1 (MQ=255)
                                                             ttGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATACACAATTATCACAATTGCTATTACTGCTATAAt                                                                                >  2:120797/1‑141 (MQ=255)
                                                             ttGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAAt                                                                                >  1:80642/1‑141 (MQ=255)
                                                              tGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGCTTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATGATCACAATTGCTATTACTCCTATAATg                                                                               >  2:373011/1‑141 (MQ=255)
                                                               gggTATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGt                                                                              <  2:717639/141‑1 (MQ=255)
                                                                ggCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACACTCATCAAAATTGCTATTAGTGGTATAATGtt                                                                             >  2:306894/1‑141 (MQ=255)
                                                                ggCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGtt                                                                             >  2:150283/1‑141 (MQ=255)
                                                                ggCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCCTTAATGtt                                                                             >  2:138244/1‑141 (MQ=255)
                                                                     catTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAATGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTaa                                                                        >  1:532386/1‑141 (MQ=255)
                                                                     catTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTaa                                                                        >  1:682795/1‑141 (MQ=255)
                                                                                tGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTCGATAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAat                                                             <  1:774642/141‑1 (MQ=255)
                                                                                   gTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGTCGATATAAACAATTATCACAATTGCTATTACTGCTATTATGTTTTTAATCATTCTAAatagc                                                          >  1:618117/1‑139 (MQ=255)
                                                                                   gTAACTTGATTCATTTGAT‑ATAACTTATGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATc                                                          >  1:580595/1‑141 (MQ=255)
                                                                                          gATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCa                                                   <  1:320555/141‑1 (MQ=255)
                                                                                           aTTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCAt                                                  <  1:332745/141‑1 (MQ=255)
                                                                                                   gATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTACCCTGACTAAATATCAATCTCATAGTTCGcc                                          <  1:781547/141‑1 (MQ=255)
                                                                                                   gATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGcc                                          <  1:93794/141‑1 (MQ=255)
                                                                                                    aTCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCt                                         >  1:286709/1‑141 (MQ=255)
                                                                                                      cATTA‑TCGTGATTTATAGGATTCCAATCATGTTCATTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTcc                                       <  2:190291/141‑1 (MQ=255)
                                                                                                      cATTA‑TCCTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTTCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTcc                                       <  2:187696/141‑1 (MQ=255)
                                                                                                        ttA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCaa                                     >  1:703926/1‑141 (MQ=255)
                                                                                                          a‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATg                                   <  1:675090/141‑1 (MQ=255)
                                                                                                          a‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTAAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATCATATTCTTCAATCTCATAGTTCGCCTCCAATg                                   <  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)
                                                                                                                                            |                                                                                                                                            
GTACATTCTTTATTAAATCATTTTCTTTTAATGAATATTTCTCACCACTTACATAAACATGTTGGGCATCATTAGTGGGTTGCGTAACTTGATTCATTTGATCATTA‑TCGTGATTTACAGGATTCCAATCTTGTTCTTTTAAAAAAGGTGCGTATTTCAAGGCGATATAAACAATTATCACAATTGCTATTACTGCTATAATGTTTTTAATCATACTAAATATCAATCTCATAGTTCGCCTCCAATGTCTTCATCTAATTATATATTTTATTATGTATAT  >  USA300TCH1516_ALE/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: ‑