Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,679,462 (A)8→7 intergenic (+334/‑55) USA300HOU_RS13790 → / → ssaA2_4 hypothetical protein/Staphylococcal secretory antigen ssaA2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,679,4550A.97.1% 154.1 / ‑1.6 35intergenic (+327/‑62)USA300HOU_RS13790/ssaA2_4hypothetical protein/Staphylococcal secretory antigen ssaA2
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (12/22);  total (12/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

TGACATCCTTGTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCA  >  USA300TCH1516_ALE/2679308‑2679583
                                                                                                                                                   |                                                                                                                                
tGACATCCTTGTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTa                                                                                                                                  >  4:335978/1‑148 (MQ=255)
  aCATCCTTGTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTaaa                                                                                                                                >  4:326692/1‑148 (MQ=255)
  aCATCCTTGTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTaaa                                                                                                                                >  4:326705/1‑148 (MQ=255)
        ttGTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTaaaaaaatt                                                                                                                          >  3:59593/1‑146 (MQ=255)
         tGTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTaaaaaaattt                                                                                                                         <  4:271971/148‑4 (MQ=255)
            aTCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTTTTTTTTTACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGtt                                                                                                                     >  4:386193/1‑148 (MQ=255)
                 tATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTATTTTTTTTTTCTTTATATTATAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAATAATTTGTTATCAt                                                                                                                >  4:179893/1‑148 (MQ=255)
                  aTGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGt                                                                                                                      <  2:12493/141‑1 (MQ=255)
                  aTGAAAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGt                                                                                                                      <  2:50509/141‑1 (MQ=255)
                       aattaattGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTaa                                                                                                          >  3:128654/1‑148 (MQ=255)
                               gTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAAt                                                                                                  >  4:71006/1‑148 (MQ=255)
                                 tAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATaa                                                                                                <  4:62268/148‑1 (MQ=255)
                                 tAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATaa                                                                                                >  3:375689/1‑148 (MQ=255)
                                       cATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTCCTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGaaaa                                                                                          >  4:394421/1‑148 (MQ=255)
                                        aTGAATTTATACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATaa                                                                                                <  1:22471/141‑1 (MQ=255)
                                          gAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGaaaaaaa                                                                                       <  3:273362/148‑1 (MQ=255)
                                            aTTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAAtt                                                                                     >  3:326527/1‑148 (MQ=255)
                                                  aCATTTTATGAAAATATCCATTTTTATTACAATTAAACAATTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACATTAAAAAAAAAAAAAAATTAACTTg                                                                               <  4:188415/148‑1 (MQ=255)
                                                  aCATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAGATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTg                                                                               <  3:349806/148‑1 (MQ=255)
                                                  aCATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTg                                                                               <  4:45523/148‑1 (MQ=255)
                                                                aaTCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATgg                                                                 <  4:1961/148‑1 (MQ=255)
                                                                aaTCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATgg                                                                 <  4:130017/148‑1 (MQ=255)
                                                                aaTCCATTTTTATTACAAGTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATgg                                                                 <  3:335509/148‑1 (MQ=255)
                                                                aaTCCATTTTTAATACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCTTAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATgg                                                                 <  4:58198/148‑1 (MQ=255)
                                                                   ccATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAat                                                              <  4:95117/148‑1 (MQ=255)
                                                                   ccATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTAT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAat                                                              <  4:274905/148‑1 (MQ=255)
                                                                         ttattaCAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATaaaa                                                        <  3:13181/148‑1 (MQ=255)
                                                                              aCAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATa                                                   <  3:324668/148‑1 (MQ=255)
                                                                                         cTTTATATTACAAATTCATTACAGATACTACAAATATTGATTGCTTACAATGTATTCTAAAAAAAATTT‑TTATCATTATTAAAATAAAAAAAAAAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGttt                                        <  4:198157/148‑1 (MQ=255)
                                                                                           ttATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTttat                                      >  3:397706/1‑148 (MQ=255)
                                                                                                tGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAAtt                                 <  3:286766/148‑1 (MQ=255)
                                                                                                   cAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCt                              >  3:319856/1‑148 (MQ=255)
                                                                                                            tACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTa                     <  3:261903/148‑1 (MQ=255)
                                                                                                             aCAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTAc                    <  3:168446/148‑1 (MQ=255)
                                                                                                                 ttACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACGTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTCGCAGTACtttt                >  4:48860/1‑148 (MQ=255)
                                                                                                                           tgttgATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTTATTTTCTCAGCAGAt      >  3:127797/1‑148 (MQ=255)
                                                                                                                            gttgATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGAtt     >  3:5270/1‑148 (MQ=255)
                                                                                                                              tgATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTc   <  4:170073/148‑1 (MQ=255)
                                                                                                                              tgATTGCTTACATTAATTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTc   <  4:218950/148‑1 (MQ=255)
                                                                                                                               gATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCa  <  3:397394/148‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                
TGACATCCTTGTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCA  >  USA300TCH1516_ALE/2679308‑2679583

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: ‑