Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000731 25,669 (A)7→6 coding (322/333 nt) USA300HOU_pUSA300HOUMR0031 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073125,6630A.97.8% 194.8 / ‑3.2 45coding (316/333 nt)USA300HOU_pUSA300HOUMR0031hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (25/19);  total (25/20)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAACA  >  CP000731/25526‑25797
                                                                                                                                         |                                                                                                                                      
gtatGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTACTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaa                                                                                                                                     <  1:163466/141‑1 (MQ=255)
   tGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATTCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTCCTATACTACAAATaaaaaat                                                                                                                                  >  2:59472/1‑140 (MQ=255)
     ttATGTACACTAGCGCGTAAATGTACAGGTTTGACATCAAGTATTGAAGGATCTTGGTTGTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaaaatat                                                                                                                                <  2:25511/141‑4 (MQ=255)
      tATTTAAAATAGTGCTTAAATTTAGAGGTTTGTCAACAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaaaatata                                                                                                                               <  2:147926/141‑5 (MQ=255)
                aGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAgg                                                                                                                    <  1:213404/141‑1 (MQ=255)
                aGTGCTTAAATTTACAGGTTTGTCACAAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAgg                                                                                                                    <  1:51124/141‑1 (MQ=255)
                 gTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGt                                                                                                                   >  1:2151/1‑141 (MQ=255)
                     ttAAATTTATAGATTTGTAACTAAATATTAAAGGATCTTAGTTCTCTCAATATACAGAAATTTACTTTATAATCGTAGCACTATTTCTTATGCTGTTTAAATAATATAATAAAAAT‑AAAAAATATACATCTAAAGGTTaaa                                                                                                               <  2:17065/141‑1 (MQ=255)
                      tAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAAt                                                                                                              >  1:234882/1‑141 (MQ=255)
                      tAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAAt                                                                                                              >  1:199407/1‑141 (MQ=255)
                       aaaTTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAAtt                                                                                                             >  1:167952/1‑141 (MQ=255)
                        aaTTTACAGGTTTGTCACCAAGTATTGAAGGATATTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTATATTa                                                                                                            >  2:200596/1‑141 (MQ=255)
                          tttACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTCCAAAT‑AAAAAATATACATCTAAAGGTTAAATTAAt                                                                                                          <  1:224637/141‑1 (MQ=255)
                          tttACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAAt                                                                                                          >  1:176192/1‑141 (MQ=255)
                          tttACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAAt                                                                                                          <  1:36490/141‑1 (MQ=255)
                          tttACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAAt                                                                                                          >  2:201001/1‑141 (MQ=255)
                          tttACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAAGATACATCTAAAGATTAACTTAAt                                                                                                          >  2:215806/1‑141 (MQ=255)
                            tACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGa                                                                                                        <  1:195509/141‑1 (MQ=255)
                            tACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATAATACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGa                                                                                                        <  2:135297/141‑1 (MQ=255)
                             aCAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaa                                                                                                       >  2:164343/1‑141 (MQ=255)
                              cAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaaa                                                                                                      >  2:60962/1‑141 (MQ=255)
                                ggctggTCACCAAGTATAGAAGGATCTTGGCAGTCTCAAGAACCAGAAATGTTCTGAATAATTGTAGCAATAGAACATATGCCCGTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGCTTACATTAATCaagaa                                                                                                    >  2:59342/6‑141 (MQ=255)
                                ggTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaaaaa                                                                                                    <  1:233873/141‑1 (MQ=255)
                                   ttGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAATTTTAAATTAATGAAAAAtca                                                                                                 >  2:225845/1‑139 (MQ=255)
                                                   aaGGATCTTGGTTTTCTTAATATACAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAAATACTATACAAAAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGa                                                                                 <  2:146432/141‑1 (MQ=255)
                                                    aGGATCTTGGTTTTCTCAATATCCAGAAATTTTCATTATAATTGTAGCAATAAATAATATGCAGTTTAATTACTATAATACAAAT‑AAAAAATATACATCTAAAGGTAAAATTAATGAAAAATAGAATTAGAGaaaaaaaaa                                                                                <  2:132671/141‑8 (MQ=255)
                                                           tGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTCATTACTATACTACAAAT‑AAAAAATATAAATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACaaaa                                                                         >  1:4217/1‑141 (MQ=255)
                                                           tGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATAAAGAAAACaaaa                                                                         >  2:200601/1‑141 (MQ=255)
                                                            ggTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTCATTACTATACTACAAAT‑AAAAAATATACATCTAAAGATTAAATTAATGAAAAATAGAATAAGCGAAGAGAGAGAACaaaaa                                                                        >  2:175269/1‑141 (MQ=255)
                                                            ggTTTTCTCAATATCCAGAAATTTTCTTTATAATGGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACaaaaa                                                                        >  2:79149/1‑141 (MQ=255)
                                                                ttCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGaa                                                                    >  1:93142/1‑141 (MQ=255)
                                                                   tcAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAAttt                                                                 >  1:141598/1‑141 (MQ=255)
                                                                      atatCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTtctc                                                              >  1:22856/1‑141 (MQ=255)
                                                                         tgcAGAAATTTTCTTTATCCTTGTAGGAATATTTCTAATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACAGCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAg                                                           <  2:141511/139‑1 (MQ=255)
                                                                           cAGAAATTTTCTTTATAATTGTAGCACTATTGCTTAGGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGaa                                                         >  1:124019/1‑141 (MQ=255)
                                                                                  tttCTTTATAATTGTCGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAACGGTTACATTAATGAAAAATAGAATTACAGAATATAGAAAAAAAAAAGGAAAATCTCAAGAAACTTTaa                                                  >  2:69015/1‑141 (MQ=255)
                                                                                           aaTTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAAt                                         <  1:228919/141‑1 (MQ=255)
                                                                                           aaTTGGAGCATTATGTCTTATGCTGTTTAATTACTAGACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAAt                                         <  1:227893/141‑1 (MQ=255)
                                                                                           aaTAGTAGCACTATATCTTATGATGTTTAATTACTATAATAAAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAAt                                         <  2:10661/141‑1 (MQ=255)
                                                                                                   cACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAgtg                                 >  1:134412/1‑141 (MQ=255)
                                                                                                    aCTATTTATTATGCTGTTTAATGACTATAATAAAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAgtgt                                <  2:24349/141‑1 (MQ=255)
                                                                                                                actgataaaTTAATATACTACAAA‑AAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGACTTAAACGTGTCTAGGCAAACTa                    <  2:86551/134‑1 (MQ=255)
                                                                                                                  tGTTTAATTAATATAAAACAAAT‑AAAAAATAAACATCTAAAAGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTAtt                  <  2:216838/141‑1 (MQ=255)
                                                                                                                       aaatactaaaataAAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGc             <  2:185390/138‑1 (MQ=255)
                                                                                                                           actatactaCAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATa         >  1:13686/1‑141 (MQ=255)
                                                                                                                           actatactaCAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGACAAACTATTAATGCAATa         >  1:107707/1‑141 (MQ=255)
                                                                                                                                  tacAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTAtt                  <  2:124455/125‑1 (MQ=255)
                                                                                                                                  tacAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTAtt                  >  1:124455/1‑125 (MQ=255)
                                                                                                                                  aacAAAT‑AAAAAATATACAACTAAAGGATAAATTAATGAAAAATAGAATTAGAGAAAATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGattgcc  <  1:56222/140‑6 (MQ=255)
                                                                                                                                         |                                                                                                                                      
GTATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAACA  >  CP000731/25526‑25797

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: ‑