Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,679,725 G→A W70* (TGG→TAG)  ssaA2_4 → Staphylococcal secretory antigen ssaA2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,679,7250GA77.6% 117.2 / 31.1 58W70* (TGG→TAG) ssaA2_4Staphylococcal secretory antigen ssaA2
Reads supporting (aligned to +/- strand):  ref base G (7/6);  new base A (26/19);  total (33/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

TCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAA  >  USA300TCH1516_ALE/2679588‑2679858
                                                                                                                                         |                                                                                                                                     
tCAATCCGTCGAACACACGCATCAATCGCATGCCGCAGTTAATTATTATAGTCAAAACCAATGTAAATGGTGGGAATTTAAACGTCGAGCACTAGTCGGTGAAACTATTTCTAATAGATGGCGCAATGCTAAAAATTGGTa                                                                                                                                    <  1:391543/141‑1 (MQ=255)
    tCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTAc                                                                                                                                >  1:959173/1‑141 (MQ=255)
      cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACaa                                                                                                                              >  1:361227/1‑141 (MQ=255)
      cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACaa                                                                                                                              >  1:911962/1‑141 (MQ=255)
      cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACaa                                                                                                                              >  1:284944/1‑141 (MQ=255)
        tCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATg                                                                                                                            >  1:782843/1‑141 (MQ=255)
        tCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATg                                                                                                                            >  2:352923/1‑141 (MQ=255)
            aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACg                                                                                                                        <  1:461797/141‑1 (MQ=255)
            aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACg                                                                                                                        >  2:12305/1‑141 (MQ=255)
            aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACg                                                                                                                        <  1:298526/141‑1 (MQ=255)
              aaaCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTa                                                                                                                      <  1:179846/141‑1 (MQ=255)
                aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAAACAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTaaa                                                                                                                    >  1:515040/1‑141 (MQ=255)
                 cGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAAt                                                                                                                   >  1:896536/1‑141 (MQ=255)
                  gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATc                                                                                                                  <  2:34437/141‑1 (MQ=255)
                    aTCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCaa                                                                                                                <  2:228773/141‑1 (MQ=255)
                         tCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAatat                                                                                                           >  2:46987/1‑141 (MQ=255)
                         tCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAatat                                                                                                           >  1:742383/1‑141 (MQ=255)
                         tCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAatat                                                                                                           <  2:65969/141‑1 (MQ=255)
                              tGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGAc                                                                                                      >  2:314855/1‑141 (MQ=255)
                                  gCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGt                                                                                                  >  1:416148/1‑141 (MQ=255)
                                  gCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGt                                                                                                  >  2:233955/1‑141 (MQ=255)
                                   cAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTc                                                                                                 <  1:914420/141‑1 (MQ=255)
                                            attatAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCaa                                                                                        <  1:277820/141‑1 (MQ=255)
                                                taGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGaaa                                                                                    <  1:535540/141‑1 (MQ=255)
                                                            aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCAt                                                                        >  1:888870/1‑141 (MQ=255)
                                                            aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCAt                                                                        >  1:854800/1‑141 (MQ=255)
                                                                aCATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCaa                                                                    >  1:468295/1‑141 (MQ=255)
                                                                aCATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCaa                                                                    <  1:704362/141‑1 (MQ=255)
                                                                   tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                                 >  1:546153/1‑141 (MQ=255)
                                                                   tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                                 <  2:327397/141‑1 (MQ=255)
                                                                   tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                                 >  2:91836/1‑141 (MQ=255)
                                                                     gtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAAc                                                               <  1:724431/141‑1 (MQ=255)
                                                                       gggCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTg                                                             >  1:505428/1‑141 (MQ=255)
                                                                        ggCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGc                                                            >  1:194659/1‑141 (MQ=255)
                                                                           aTTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAgg                                                         >  1:614727/1‑141 (MQ=255)
                                                                            tttAAACGGCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGa                                                        <  1:849268/141‑1 (MQ=255)
                                                                               aaaCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGatat                                                     >  1:43894/1‑141 (MQ=255)
                                                                                  cGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGAtattat                                                  <  1:675545/141‑1 (MQ=255)
                                                                                   gTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATg                                                 <  1:795388/141‑1 (MQ=255)
                                                                                      gcgcACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGAc                                              >  1:890993/1‑141 (MQ=255)
                                                                                          acaAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGt                                          <  1:110025/141‑1 (MQ=255)
                                                                                             aGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGc                                       >  2:18108/1‑141 (MQ=255)
                                                                                                 ggTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgtt                                   <  1:344977/141‑1 (MQ=255)
                                                                                                     aaCCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGttgttg                               <  1:119664/141‑1 (MQ=255)
                                                                                                     aaCCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGttgttg                               <  1:19496/141‑1 (MQ=255)
                                                                                                       ccTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGaa                             >  1:418631/1‑141 (MQ=255)
                                                                                                            ttCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGt                        >  1:781735/1‑141 (MQ=255)
                                                                                                              cTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGtat                      <  1:856905/141‑1 (MQ=255)
                                                                                                                        gggCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg            <  1:198757/141‑1 (MQ=255)
                                                                                                                        gggCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg            >  1:629092/1‑141 (MQ=255)
                                                                                                                         ggCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCCTGAAATCAACTGCAGGATATTATGGCCATGTCGCCATTGTTGAAAAAGTATATAAAAACGgt           >  2:335882/1‑141 (MQ=255)
                                                                                                                          gCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTTATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgta          >  1:741093/1‑141 (MQ=255)
                                                                                                                             aTGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgtagta       >  1:591840/1‑141 (MQ=255)
                                                                                                                             aTGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgtagta       >  1:147579/1‑141 (MQ=255)
                                                                                                                              tGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAt      <  2:41185/141‑1 (MQ=255)
                                                                                                                              tGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAt      <  1:14117/141‑1 (MQ=255)
                                                                                                                               gCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAtt     <  1:923624/141‑1 (MQ=255)
                                                                                                                                  aaaaaTTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTaaa  >  1:228413/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                     
TCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAA  >  USA300TCH1516_ALE/2679588‑2679858

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑