Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 730,534 C→T 18.7% intergenic (+141/‑188) lipA → / → USA300HOU_0677 possible S9C family peptidase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730730,5340CT18.7% 78.8 / 10.8 38intergenic (+141/‑188)lipA/USA300HOU_0677possible S9C family peptidase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (18/12);  new base T (5/2);  total (23/15)
Fisher's exact test for biased strand distribution p-value = 6.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

GTAGTAATTTATTGCTTAAGCAACATTTAAGATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCAAAAGAAAAATT  >  CP000730/730403‑730672
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gtagtaATTTATTGCTTCAGCAACAACTACTATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGATCTTTATCATTTCTATCTCATTCTATTatg                                                                                                                                   >  1:343097/1‑141 (MQ=255)
 tagtaATTTATTGGTTAAGCAACATTTAAGATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTatga                                                                                                                                  <  2:53250/141‑1 (MQ=255)
      aTTTATTGCTTAAGCAACATTTAAGATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGa                                                                                                                             >  1:312493/1‑141 (MQ=255)
           ttGCTTAAGCAACATTTAAGATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACattt                                                                                                                        >  2:306888/1‑141 (MQ=255)
                  aGCAACATTTAAGATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTAc                                                                                                                 >  1:108431/1‑141 (MQ=255)
                   gCAACATTTAAGATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACa                                                                                                                >  1:185971/1‑141 (MQ=255)
                       cATTTAAGATTTTCAAATTAAAAATGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACt                                                                                                            >  1:221096/1‑141 (MQ=255)
                               aTTTTCAAAATAAGATCGAAGAATTTCAAAGATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGtt                                                                                                    <  1:76507/141‑1 (MQ=255)
                                           aaaaCGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGaaa                                                                                        >  1:156871/1‑141 (MQ=255)
                                            aaaCGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCATTCTATTATGATGTGACATTTATTTTACAAACTAATATGTTTTGACCCTGaaaa                                                                                       >  1:128543/1‑141 (MQ=255)
                                             aaCGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGGTCTTTATCATTTCTATCGCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGGTTTGAGCCTGAAAAt                                                                                      >  2:229577/1‑141 (MQ=255)
                                               cGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATaa                                                                                    >  2:205289/1‑141 (MQ=255)
                                                gaagaaTTTAAAACATGTGGTGCTAATGTTTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAAc                                                                                   <  2:216987/141‑1 (MQ=255)
                                                gaagaaTTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGCACCGGTAAATAAc                                                                                   <  2:246313/141‑1 (MQ=255)
                                                           aaCATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCATTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTAGAACCTGAAAATAACTTTTTACAACt                                                                        <  2:214529/141‑1 (MQ=255)
                                                             cATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTaa                                                                      <  1:163799/141‑1 (MQ=255)
                                                              aTGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCATTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTaaa                                                                     >  2:186630/1‑141 (MQ=255)
                                                                     gCTAATTTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGGGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGa                                                              <  1:34378/141‑1 (MQ=255)
                                                                         aTGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACATACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTTGaaaaa                                                          >  2:77642/1‑141 (MQ=255)
                                                                              tAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAgtg                                                     >  1:251675/1‑141 (MQ=255)
                                                                                             taatacATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTAAGATGTGACATTTATTTTACAACCTAATTTGTTTTGAACCTGACAATAACTTTTTACAACTAAATTGTCGAAAAACGGTGTGTACATGGTataaa                                      >  2:145146/1‑140 (MQ=255)
                                                                                             taataaATTGTTAGCGGGTCTTTATCCTTTCTAACACACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTCAATGCTataat                                      >  2:88830/1‑141 (MQ=255)
                                                                                                    ttGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAACAACCGCCTAACAGTGTGTACATGATATTATAAATTta                               <  1:253608/141‑1 (MQ=255)
                                                                                                        tAGCGGTTCTTTATCATTTCTATCTCATTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATaaa                           >  2:304984/1‑141 (MQ=255)
                                                                                                         aaatgtacTTTATAATTTCTAAATAAATCTATTAGGATGGGACATTTATTTTACAAACTAATTTTTTTTTAACCTGAAAATAACTTTTTACAACAAAAAAAAAAAAAAACAGTGTGTACATGATATAATAAATTTATAAAt                          <  2:171443/134‑1 (MQ=255)
                                                                                                           cGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAataaattgataaattg                        >  1:190386/1‑141 (MQ=255)
                                                                                                              ttCTTTTTCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGaaa                     <  2:253019/141‑1 (MQ=255)
                                                                                                               tCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTAGTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGataa                    >  2:87597/1‑141 (MQ=255)
                                                                                                                cTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTATAACCAAAATTTTGAAAAACAGTGTGTACATGATATAATAACTTTATAAATTGAAAAg                   <  2:332837/141‑1 (MQ=255)
                                                                                                                cTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACTACTTCAATGGCTAGTAACCGTGTGTACATGATATAATAAATTTATAAATTGAAAAg                   <  2:332845/141‑1 (MQ=255)
                                                                                                                   tATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAAAAt                >  2:35347/1‑141 (MQ=255)
                                                                                                                     tCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTc              >  1:152882/1‑141 (MQ=255)
                                                                                                                       aTTTCTCGCTCATTCTATTATGCTCTGACAGTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCaa            <  2:347429/141‑1 (MQ=255)
                                                                                                                          tCTATCTCACTCTATTATAATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCAAAAg         <  2:222071/141‑1 (MQ=255)
                                                                                                                             aTCTCATTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCAAAAGaaa      >  1:303421/1‑141 (MQ=255)
                                                                                                                              tctcACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCAAAAGaaaa     <  2:221096/141‑1 (MQ=255)
                                                                                                                              tctcACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCAAAAGaaaa     >  1:75847/1‑141 (MQ=255)
                                                                                                                                 cACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCAAAAGAAAAAtt  >  1:64355/1‑141 (MQ=255)
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GTAGTAATTTATTGCTTAAGCAACATTTAAGATTTTCAAATTAAAAACGAAGAATTTAAAACATGTGGTGCTAATGTGTAAGAGTCTGAGATATAATAAATTGTTAGCGGTTCTTTATCATTTCTATCTCACTCTATTATGATGTGACATTTATTTTACAAACTAATTTGTTTTGAACCTGAAAATAACTTTTTACAACTAAATTGTCGAAAAACAGTGTGTACATGATATAATAAATTTATAAATTGAAAAGAATTCAAAAGAAAAATT  >  CP000730/730403‑730672

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑