Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730111,5120AG35.9% 57.1 / 43.1 53S194S (TCA→TCG) USA300HOU_0110possible staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (17/17);  new base G (12/7);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 4.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  CP000730/111374‑111651
                                                                                                                                          |                                                                                                                                           
tACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGc                                                                                                                                           <  2:130253/141‑1 (MQ=255)
tACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGc                                                                                                                                           <  2:156585/141‑1 (MQ=255)
     aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                      <  2:81297/141‑1 (MQ=255)
     aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                      >  1:81297/1‑141 (MQ=255)
      ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGGAATATGGCATTGTTATTCATTTAATTAAGGAGAAAGTGGTAGAGATATCATAGAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                     >  1:180892/1‑141 (MQ=12)
        aaGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                                                                   >  1:207081/1‑141 (MQ=255)
         aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                  >  2:73301/1‑141 (MQ=255)
         aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGATGCCAAGTTATTCGGCTAAATAACa                                                                                                                                  >  1:140953/1‑141 (MQ=18)
          gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                                                                 >  1:301255/1‑141 (MQ=255)
          gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCaa                                                                                                                                 <  2:19941/141‑1 (MQ=255)
          gTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATATTAAAGAATAAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                                                                 >  1:4830/1‑141 (MQ=18)
            tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                               <  2:231485/141‑1 (MQ=255)
              aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                             >  1:32402/1‑141 (MQ=255)
               agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                            <  2:130264/141‑1 (MQ=255)
                gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTCTTAATATTGTAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATAGCATATAATCCATAGGTGTCGAGTAATTCGGCTAAATATCAAATaaac                                                                                                                           >  2:176449/1‑139 (MQ=17)
                gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGGTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACt                                                                                                                           >  2:55365/1‑141 (MQ=255)
                gaagaaAACATAAAAAAAGAAATCGAAAACTATAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTAAAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                           >  2:57157/1‑141 (MQ=255)
                 aagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                          <  1:96432/141‑1 (MQ=255)
                   gaaAACATAAAAAAAGAAATCGAAAACTTCAAGTTTTTTGCGCAATATAACAATTTCAAAAATTTAATGAATTATAAAGTTGGAGATCTATCATATAATCCAAAGGTGCCTAGTTATTCAGCTAAATATCAATTAACTAat                                                                                                                        >  2:271315/1‑141 (MQ=18)
                     aaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatga                                                                                                                      >  1:270299/1‑141 (MQ=255)
                      aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                     <  1:236821/141‑1 (MQ=255)
                          tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTTTTTAATATTGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATAAATTAACTAATGATGAtt                                                                                                                 >  2:282366/1‑141 (MQ=14)
                             aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtata                                                                                                              >  2:111228/1‑141 (MQ=255)
                                   aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                        <  1:303911/141‑1 (MQ=255)
                                      tCGAAAACTTTAAGTTTTTTGCGCAATATAGTAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                                                                     <  1:282684/141‑1 (MQ=255)
                                          aaaCTTTAAGTTTTTTTCGCATTATAGCAATATTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAtt                                                                                                 >  2:301401/1‑141 (MQ=255)
                                            aCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                                                               <  1:73301/141‑1 (MQ=255)
                                             cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                              <  1:183083/141‑1 (MQ=255)
                                              tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                             <  2:189401/141‑2 (MQ=255)
                                                 aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaa                                                                                          >  1:159806/1‑141 (MQ=255)
                                                  aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaaaa                                                                                         >  1:112836/1‑141 (MQ=255)
                                                    ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGa                                                                                       <  2:266642/141‑1 (MQ=255)
                                                       tttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGatat                                                                                    >  1:123310/1‑141 (MQ=255)
                                                         tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGa                                                                                  >  2:238400/1‑141 (MQ=255)
                                                            gcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATGTATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACAt                                                                               >  1:247633/1‑141 (MQ=255)
                                                              aaTATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAc                                                                             <  2:159806/141‑1 (MQ=255)
                                                               atatAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAcc                                                                            <  2:79931/141‑1 (MQ=255)
                                                                 ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccga                                                                          <  1:140026/141‑3 (MQ=14)
                                                                       aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATa                                                                    >  1:268204/1‑141 (MQ=255)
                                                                              aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatga                                                                                                                      <  2:66152/84‑1 (MQ=255)
                                                                              aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatga                                                                                                                      >  1:66152/1‑84 (MQ=255)
                                                                               gATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCg                                                            <  1:261683/141‑1 (MQ=255)
                                                                                    aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                       <  1:182795/141‑1 (MQ=255)
                                                                                             taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaa                                              <  2:216563/141‑1 (MQ=255)
                                                                                               aaGATGGAGATATATCATATAATCGAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATACAGCGGAAAAGCTGTTGTTGAAAg                                            >  1:2512/1‑141 (MQ=17)
                                                                                                   tGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAt                                                                     >  1:73549/1‑112 (MQ=255)
                                                                                                   tGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAt                                                                     <  2:73549/112‑1 (MQ=255)
                                                                                                      agaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                     >  2:203277/1‑141 (MQ=255)
                                                                                                      agaTATAACATATAATCCAGAGGTGCCGAGTAATTCAACTGAATATCGATTAAATAATGATGATTATAATGTAAAACAATTACGTAAAAGAGATGACATACCAACAAAAAAAACGCCGAAGCTGTTGTTGAAAGGTACatg                                     >  2:145816/1‑139 (MQ=14)
                                                                                                            atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                               <  1:301401/141‑1 (MQ=255)
                                                                                                            atCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAttt                               >  2:164890/1‑141 (MQ=255)
                                                                                                                    aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                       >  2:296307/1‑141 (MQ=255)
                                                                                                                                         cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa  <  1:132445/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                           
TACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  CP000730/111374‑111651

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: ‑