Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730110,6510CT22.9% 67.5 / 16.0 35D170D (GAC→GAT) USA300HOU_0109staphylococcal tandem lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (16/11);  new base T (5/3);  total (21/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAG  >  CP000730/110512‑110787
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aaaGATATCCGGTTAAAATGATAAATAATAAAATCATACAAACAAAAGAAATTAAAAAAAAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACg                                                                                                                                         <  2:142505/141‑1 (MQ=18)
    atatCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGgaga                                                                                                                                     >  1:36707/1‑141 (MQ=255)
     tatCCGGGCAAAATGGACGACAATAAAATCATTCCAACAAAAGAAATTAACGATGAAAAAAT‑AAAAAACGAAATCGAAAACTTTAAGTTCATTGTTCAATATGGCGACTGTAATAATTTGAAAAATAATAAAGACGGAGat                                                                                                                                    >  2:307025/1‑141 (MQ=17)
      atCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATG‑AAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGatat                                                                                                                                  >  1:202384/1‑141 (MQ=255)
        ccGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATAtt                                                                                                                                 <  2:273121/141‑1 (MQ=255)
                   ggTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATcc                                                                                                                      <  1:116568/141‑1 (MQ=255)
                    gTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCataggatgtg                                                                                                                     >  2:155795/1‑134 (MQ=255)
                             aaaaTCATTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCg                                                                                                            >  2:163466/1‑141 (MQ=255)
                               aaTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGa                                                                                                           <  1:14614/141‑1 (MQ=255)
                                   aTTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTAt                                                                                                      >  2:163552/1‑141 (MQ=255)
                                       caacaaAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                                  <  2:176658/141‑1 (MQ=255)
                                       aaacaaAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                                  <  1:284001/140‑1 (MQ=255)
                                         acaaAAGAAATTAAAGATG‑AAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTa                                                                                               <  2:202384/141‑1 (MQ=255)
                                          caaAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTa                                                                                               >  1:341593/1‑141 (MQ=255)
                                              aGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                           <  2:138641/141‑1 (MQ=255)
                                               gAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAatat                                                                                          >  2:57098/1‑141 (MQ=255)
                                                   ttAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAACATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGGAGAGTTATTCGGCTAAATATTAAt                                                                                      >  1:312400/1‑141 (MQ=255)
                                                                aaT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                         <  1:152262/141‑1 (MQ=255)
                                                                  t‑AAAAAAAGAAATCGAAAACTTTAAGTTGTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCTGCTAAATATCAATTAACTAATGATGAtt                                                                       >  1:261628/1‑141 (MQ=255)
                                                                  t‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                       >  1:244844/1‑141 (MQ=255)
                                                                             aaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                             <  2:36707/141‑1 (MQ=255)
                                                                                cGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                          >  2:22242/1‑141 (MQ=255)
                                                                                     aCTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAc                                                     >  2:11699/1‑141 (MQ=255)
                                                                                                                     aaaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGCTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCt                     >  2:362337/1‑141 (MQ=255)
                                                                                                                       agatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTcc                   <  1:343202/131‑1 (MQ=14)
                                                                                                                        gatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCa                  <  2:291165/132‑1 (MQ=14)
                                                                                                                        gatttaatgaaTTATAAAGATGGAGATATATCATATAATCCAGAATTGCCAAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAACGATATGATAGAACAACGAGGAAAGcgaca                  >  2:69309/10‑137 (MQ=1)
                                                                                                                            taatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGt              >  1:310296/6‑141 (MQ=255)
                                                                                                                             gAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt             >  2:66916/1‑141 (MQ=255)
                                                                                                                                aaaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTAtt          >  1:288635/1‑141 (MQ=255)
                                                                                                                                  aTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGt        <  1:349720/141‑1 (MQ=255)
                                                                                                                                   ttATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGCTGATTATAATGTAAAACAAGTTCGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGtt       >  1:106081/1‑141 (MQ=18)
                                                                                                                                       aaaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaaa   >  1:282732/1‑141 (MQ=255)
                                                                                                                                        aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAg  <  1:181902/141‑1 (MQ=255)
                                                                                                                                        aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAg  >  1:285186/1‑141 (MQ=255)
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AAAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAAT‑AAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAG  >  CP000730/110512‑110787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑