Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,847,204 A→G 7.4% H10R (CAC→CGC)  yceI → Protein YceI

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,847,2040AG 7.4% 145.0 / 4.3 54H10R (CAC→CGC) yceIProtein YceI
Reads supporting (aligned to +/- strand):  ref base A (24/26);  new base G (2/2);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.71e-01

TATTCGAATTCGAAATAAAATGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTACTGCAACAATTATTCCAAGCTC  >  USA300TCH1516_ALE/2847067‑2847342
                                                                                                                                          |                                                                                                                                          
tatTCGAATTCGAAATAAAATGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGGGTGAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACAAag                                                                                                                                         >  1:153288/1‑141 (MQ=255)
tatTCGAATTCGAAATAAAATGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACag                                                                                                                                         >  1:449316/1‑141 (MQ=255)
    cgaattcgaaATAAAATGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACagtagt                                                                                                                                     >  1:652646/1‑141 (MQ=255)
     gaattcgaaATAAAATGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTGTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGtt                                                                                                                                    >  1:380200/1‑141 (MQ=255)
          cgaaATAAAATGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACGCAGTAGTTTAGaa                                                                                                                               <  1:628880/141‑1 (MQ=255)
                 aaaTGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCaaa                                                                                                                        >  1:164647/1‑141 (MQ=255)
                 aaaTGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCaaa                                                                                                                        <  2:467465/141‑1 (MQ=255)
                 aaaTGCTTGCATCTTTGTTTTTTAGGTGGTATTGAATGTATATAAATTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACCTTCCTTTTGATGGTGCCCACAGTAGTTTAGACTTCCaca                                                                                                                        <  2:467432/141‑3 (MQ=255)
                        tGCAGCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATAGCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGCGGACGCACTATGTTAGAATTCCAAATTAAACa                                                                                                                 <  1:322170/141‑1 (MQ=255)
                          cATCTTTGTTTTTTAGGAGGTCTTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGTGATAAAAATATGGAGAGTTTATATAACGAATAACTTTACTCTTAATGGAGCAAACACTCGTCTAGAATTTCGATTTAAACAtt                                                                                                               >  2:539926/1‑141 (MQ=255)
                               ttGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATg                                                                                                          <  1:477268/141‑1 (MQ=255)
                                   tttttAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGttt                                                                                                      <  1:399918/141‑1 (MQ=255)
                                   tttttAGGTGGTATTGGATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGttt                                                                                                      <  2:262477/141‑1 (MQ=255)
                                    ttttAGGTTGTATTGTATGTATATCAAGTATAAAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGttt                                                                                                      <  2:262640/141‑1 (MQ=255)
                                          gtggtATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTGCATATTAAACATTTAATGGTTTCTAAAGt                                                                                               <  2:113586/141‑1 (MQ=255)
                                                tttgatgtatACTAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATTGTTTCTAAAGTGAAAgg                                                                                         <  1:394253/137‑1 (MQ=255)
                                                ttGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAgg                                                                                         <  1:365935/141‑1 (MQ=255)
                                                    atgtatATCAAGTAG‑AAAAAATATATCTACGAGATACAAATATGGATGGTGTATATTATGACTAACTTTACTTTTGGTGGTGCAAAGAGTAGTTTAGAATTCGAAATTAAACATTTAATGGTTTCTTAAGTGAAAGGTTct                                                                                     >  2:116045/1‑140 (MQ=255)
                                                      gtatATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGCTTCTAAAGTGAAAGGTTCAtt                                                                                   >  2:484939/1‑141 (MQ=255)
                                                             aaGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCaa                                                                            <  2:314935/141‑1 (MQ=255)
                                                                 at‑aAAAAATATATTTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTg                                                                        <  2:328206/141‑1 (MQ=255)
                                                                 at‑aAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTg                                                                        >  2:312558/1‑141 (MQ=255)
                                                                     aaaaaTATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATg                                                                     >  1:260542/1‑141 (MQ=255)
                                                                      aaaaTATATCTAATAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGACAGGTTCATTTGATCAATTTGATGt                                                                    <  1:323400/141‑1 (MQ=255)
                                                                      aaaaTATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGt                                                                    <  1:121579/141‑1 (MQ=255)
                                                                           atatCTAAGGGATAAAAATATGGAGGTTTTATATTATGACTAACTTTAATTTTGACGGTGCGCACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTg                                                               <  2:167607/141‑1 (MQ=255)
                                                                           atatCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTg                                                               <  2:332931/141‑1 (MQ=255)
                                                                            tatCTAAGAGATAAAAATAGGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGt                                                              >  2:610666/1‑141 (MQ=255)
                                                                              tCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTg                                                            >  2:208152/1‑141 (MQ=255)
                                                                              tCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTg                                                            >  1:407284/1‑141 (MQ=255)
                                                                                tAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGaa                                                          >  1:24641/1‑141 (MQ=255)
                                                                                 aaGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAg                                                         <  1:572590/141‑1 (MQ=255)
                                                                                  acagaTAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAgg                                                        <  1:326033/139‑1 (MQ=255)
                                                                                     gaTAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGgaga                                                     >  1:663710/1‑141 (MQ=255)
                                                                                     gaTAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGgaga                                                     >  1:384739/1‑141 (MQ=255)
                                                                                       tAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTGGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGata                                                   >  2:366723/1‑141 (MQ=255)
                                                                                        aaaaaTATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGatat                                                  <  2:612686/141‑1 (MQ=255)
                                                                                        aaaaaTATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGCAGacat                                                  <  2:645934/141‑1 (MQ=255)
                                                                                         aaaaTATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATAtt                                                 >  1:122294/1‑141 (MQ=255)
                                                                                         aaaaTATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATAtt                                                 >  1:629126/1‑141 (MQ=255)
                                                                                          aaaTATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTa                                                <  2:666760/141‑1 (MQ=255)
                                                                                                ggAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACt                                          >  1:277929/1‑141 (MQ=255)
                                                                                                 gAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACtt                                         >  2:92510/1‑141 (MQ=255)
                                                                                                  aGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTc                                        >  2:176601/1‑141 (MQ=255)
                                                                                                   ggTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCa                                       <  1:280642/141‑1 (MQ=255)
                                                                                                      tttATATTATGACTAACTTTACTTTTGATGGTGCACGCAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTa                                    >  2:186168/1‑141 (MQ=255)
                                                                                                      tttATATTATGACTAACTTTACTTTTGATGGTGCACGCAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTa                                    >  2:385820/1‑141 (MQ=255)
                                                                                                            ttatGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGa                              <  1:622796/141‑1 (MQ=255)
                                                                                                                gACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGc                          <  1:227479/141‑1 (MQ=255)
                                                                                                                   tAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTAc                       <  2:57523/141‑1 (MQ=255)
                                                                                                                   tAACTTTACTTTGGATGGTTCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTAc                       <  2:594926/141‑1 (MQ=255)
                                                                                                                        ttactttTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGAGGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTACGGcaa                  >  1:235173/1‑141 (MQ=255)
                                                                                                                                gATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCGTTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTACTGCAACAattatt          >  1:93634/1‑141 (MQ=255)
                                                                                                                                     tGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTACTGCAACAATTATTCCAAg     <  1:610666/141‑1 (MQ=255)
                                                                                                                                        acacaGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTACTGCAACAATTATTCCAAGCTc  >  1:409476/1‑141 (MQ=255)
                                                                                                                                        acacaGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTACTGCAACAATTATTCCAAGCTc  >  2:256768/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                          
TATTCGAATTCGAAATAAAATGCTTGCATCTTTGTTTTTTAGGTGGTATTGTATGTATATCAAGTAT‑AAAAAATATATCTAAGAGATAAAAATATGGAGGTTTTATATTATGACTAACTTTACTTTTGATGGTGCACACAGTAGTTTAGAATTCCAAATTAAACATTTAATGGTTTCTAAAGTGAAAGGTTCATTTGATCAATTTGATGTAGCTGTTGAAGGAGATATTAATGACTTCAGTACTTTGAAAGCTACTGCAACAATTATTCCAAGCTC  >  USA300TCH1516_ALE/2847067‑2847342

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑