Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 677,166 T→G 13.8% Y15D (TAC→GAC)  USA300HOU_RS03265 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE677,1660TG13.8% 111.9 / 5.4 53Y15D (TAC→GAC) USA300HOU_RS03265hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (32/13);  new base G (2/6);  total (34/19)
Fisher's exact test for biased strand distribution p-value = 1.92e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGGCATAATACAGTGAATATTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCA  >  USA300TCH1516_ALE/677026‑677298
                                                                                                                                            |                                                                                                                                    
aTGGCATAATACAGTGAATATTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGAtt                                                                                                                                      <  2:82679/141‑1 (MQ=255)
       aataCAGTGAATATTAATTCTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTaa                                                                                                                               >  1:419427/1‑141 (MQ=255)
        ataCAGTGAATATTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAAt                                                                                                                              >  2:216842/1‑141 (MQ=255)
          aCATTGAATATTATTTTATATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATGACTTTAATCa                                                                                                                            <  1:74743/141‑1 (MQ=255)
          aCAGTGAATATTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCa                                                                                                                            >  1:618005/1‑141 (MQ=255)
               gAATATTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAg                                                                                                                       <  2:585890/141‑1 (MQ=255)
                  tatTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAGTCATACAGGtt                                                                                                                    >  1:157719/1‑141 (MQ=255)
                   atTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGttt                                                                                                                   >  1:271325/1‑141 (MQ=255)
                    ttAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGtttt                                                                                                                  >  1:721784/1‑140 (MQ=255)
                    ttAATTTTTATGATTTGCGAAGGGGAAATTAAACAAATACAATAAATAAAGATGTTTCATGTTAAAGGAGAACTACCAATGCGTATTAACGATAAAATTTTACGAGAAAATATAGAAGATTACTTTAATCAAAAAGGTTTa                                                                                                                  >  2:677999/1‑141 (MQ=255)
                     tAATTTTTATGATTTTCGAAGGGGACATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTAt                                                                                                                 >  1:396974/1‑141 (MQ=255)
                     tAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACAACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATAATAAAGGTTTAt                                                                                                                 >  2:686720/1‑141 (MQ=255)
                        tttttATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATGACTTTAATCATAAAGGTTTATCAc                                                                                                              <  2:530992/141‑1 (MQ=255)
                             aTGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGACTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATGACTTTAATCATAAAGGTTTATCACCGCAt                                                                                                         <  2:565628/141‑1 (MQ=255)
                               gATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCAatt                                                                                                       >  1:199099/1‑141 (MQ=255)
                                  ttGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACTGAATttgat                                                                                                    >  1:752815/1‑141 (MQ=255)
                                   tGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATttgatt                                                                                                   <  2:127510/141‑1 (MQ=255)
                                        aGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCAGttgcttagtgt                                                                                              >  2:33733/1‑136 (MQ=255)
                                        aGGGGAAAATAAACCAATAAAATAAACAAAGATGTTTCATTATAAAGGATTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATtgatga                                                                                              <  1:419295/141‑1 (MQ=255)
                                         ggggAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTgatgat                                                                                             >  1:740943/1‑141 (MQ=255)
                                              aaTTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATGACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTaa                                                                                        >  2:709028/1‑141 (MQ=255)
                                                  aaaCCAATACAATAAATAAAAATGTTTCATTATATAGGAGTACTACCAATGCGTATTACCGATAAAATGTTGCTAGAAAGTATAGAAGACGATTTTAATTTTAAATGTTTGTTACCGCATTTGATTGATGATATTAAagag                                                                                    >  2:391591/1‑141 (MQ=255)
                                                     ccAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATAATAAAGGTTTATCACCGCCTTTGATTCATGATATTAAAGAGaaa                                                                                 >  2:349591/1‑141 (MQ=255)
                                                                aataaaGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGa                                                                      >  1:536634/1‑141 (MQ=255)
                                                                 ataaaGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGat                                                                     >  1:160171/1‑141 (MQ=255)
                                                                    aaGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACAGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGAaata                                                                  >  2:473024/1‑141 (MQ=255)
                                                                      taTGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATaaa                                                                <  2:253070/140‑1 (MQ=255)
                                                                         gTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATaaaaaa                                                             >  2:330563/1‑141 (MQ=255)
                                                                            tCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAAttt                                                          >  1:408747/1‑140 (MQ=255)
                                                                            tCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACAGATATAAAAAATTc                                                          >  1:544161/1‑141 (MQ=255)
                                                                             cATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATCACTGATATAAAAAATTCt                                                         >  2:176649/1‑141 (MQ=255)
                                                                               ttttAAAGGAGTACTACCAATTCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGa                                                       <  1:113634/141‑1 (MQ=255)
                                                                               ttttAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGa                                                       <  1:767187/141‑1 (MQ=255)
                                                                                tttAAAGTATTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGaa                                                      <  1:604677/141‑1 (MQ=255)
                                                                                  tAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGaaaa                                                    >  1:674029/1‑141 (MQ=255)
                                                                                     aGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAaaagaa                                                 >  2:74267/1‑141 (MQ=255)
                                                                                      ggAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAaaagaaa                                                <  2:707241/141‑1 (MQ=255)
                                                                                        aGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAaagaaaga                                              <  2:776937/141‑1 (MQ=255)
                                                                                         gTACTACCACTGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATGACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAATATTCTGAAAAGAAAGAt                                             <  2:735403/141‑1 (MQ=255)
                                                                                         gTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGAt                                             >  1:630747/1‑141 (MQ=255)
                                                                                                cAATGCGTATTCACGATAAAATTTTACTAGAAAATATAGACGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAACAATTCTGAAAAGAAAGCTCAAGAtt                                      >  1:748403/1‑141 (MQ=255)
                                                                                                  aTGGGTATTAAAGATAAAATTTTACTAGAAAATATAGAAGATGACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATtat                                    <  2:146348/141‑1 (MQ=255)
                                                                                                  aTGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAGGTAATGAATGATATAACAACCACTAAAAAGAAAGATCAAGATtat                                    >  2:197271/1‑141 (MQ=255)
                                                                                                       tATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGa                               <  2:618005/141‑1 (MQ=255)
                                                                                                             cGATAAAATTTTACTAGAAAATATAGAAGATGACTTTAATCATAAAGGTTTATCACCGCATTTGAGTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATaa                         <  2:437279/141‑1 (MQ=255)
                                                                                                                    aTTTTACTAGAAAATATAGAAGATTACTTTAATCATCGAGGTATATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGaaaa                  <  2:357913/141‑1 (MQ=255)
                                                                                                                    aTTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGaaaa                  >  2:80868/1‑141 (MQ=255)
                                                                                                                     ttttACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAAt                 >  1:595635/1‑141 (MQ=255)
                                                                                                                     ttttACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAAt                 >  2:484324/1‑141 (MQ=255)
                                                                                                                     ttttACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATCGAATATaaaaaagaac                 >  2:530087/1‑135 (MQ=255)
                                                                                                                       ttACTAGAAAATATAGAAGCTTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAATATCATGATTATATTGAATATAAAAGAAAAtcc               >  1:181553/1‑140 (MQ=255)
                                                                                                                           tAGTAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATTAAAGAAAAtctcagc           <  2:638114/141‑4 (MQ=255)
                                                                                                                           tAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAg           <  1:71703/141‑1 (MQ=255)
                                                                                                                                    taGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTATGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCa  >  1:611820/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                    
ATGGCATAATACAGTGAATATTAATTTTTATGATTTGCGAAGGGGAAATTAAACCAATACAATAAATAAAGATGTTTCATTTTAAAGGAGTACTACCAATGCGTATTAACGATAAAATTTTACTAGAAAATATAGAAGATTACTTTAATCATAAAGGTTTATCACCGCATTTGATTGATGATATTAAAGAGAAAGTAATTACTGATATAAAAAATTCTGAAAAGAAAGATCAAGATTATATTGAATATAAAAGAAAATCTCCAGCACAAATCA  >  USA300TCH1516_ALE/677026‑677298

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: ‑