Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,583,8170CA29.2% 25.8 / 13.5 24S67I (AGT→ATT) USA300HOU_RS07760hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (11/6);  new base A (4/3);  total (15/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.78e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTACCTTTTTCATTTCTGATTGTTTCAATTTGATTAATAAAATCAAAACTGCTCAGAGAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGCTGACTGATCAATCCAA  >  USA300TCH1516_ALE/1583679‑1583957
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ttACCTTTTTCATTTCTGATTGTTTCAATTTGATTAATAAAATCAAAACTGCTCAGAGAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTa                                                                                                                                            >  2:42094/1‑141 (MQ=255)
        ttCATTTCTGATTGTTTCAATTTGATTAATAAAATCAAAACTGCTCAGAGAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTATATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGa                                                                                                                                    >  1:40450/1‑141 (MQ=255)
           aTTTCTGATTGTTTCAATTTGATTAATAAAATCAAAACTGCTCAGAGAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAAtt                                                                                                                                 >  2:19775/1‑141 (MQ=255)
              tCTGATTGTTTCAATTTGATTAATAAAATCAAAACTGCTCAGAGAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGa                                                                                                                              <  1:197310/141‑1 (MQ=255)
                                aTTAATAAAATCAAAACTGCTCAGAAAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAAATAGCCATCGAATTAGATAACTTTGTAATAGCTGa                                                                                                            <  1:161794/141‑1 (MQ=255)
                                                 tacTCATAGAATTATTCGGTGACAATATAAGTAAATCAGATACTTCTGTATGAACTACTTTATAATCGTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAg                                                                                           <  2:112627/139‑1 (MQ=255)
                                                  gCTCAGAGAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAAATAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGt                                                                                          <  1:54949/141‑1 (MQ=255)
                                                    tCAGATCATTATTTGGTGAGATTGTAAGTAAATCAGATAATTCTGGATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGttt                                                                                        <  2:202185/141‑1 (MQ=255)
                                                                tCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAAATAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGtattat                                                                            >  2:178413/1‑141 (MQ=255)
                                                                                 aaaTCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATAAGATTCACGCGTATTATTAATTATACCCCaaaaa                                                           >  1:121911/1‑141 (MQ=255)
                                                                                           cTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTAtttt                                                 >  1:152962/1‑141 (MQ=255)
                                                                                            ttCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAAATAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTAttttt                                                >  1:15524/1‑141 (MQ=255)
                                                                                               tGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCa                                             <  2:203713/141‑1 (MQ=255)
                                                                                                      actactTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTa                                      >  1:27182/1‑141 (MQ=255)
                                                                                                      actactTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTa                                      >  1:197070/1‑141 (MQ=255)
                                                                                                       ctactTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTaa                                     >  1:21790/1‑141 (MQ=255)
                                                                                                       ctactTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTaa                                     <  1:203813/141‑1 (MQ=255)
                                                                                                                          cATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGGTTACACCCCAAAAAGATTTATTTTTTTATGGTCCAAAGTCATAAAGCTCAGAAGc                  >  1:90213/1‑141 (MQ=255)
                                                                                                                          cATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGc                  >  1:184941/1‑141 (MQ=255)
                                                                                                                             tttCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGctga               >  2:116727/1‑141 (MQ=255)
                                                                                                                               tCAAGGGCAAAATAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGctgact             <  1:178413/141‑1 (MQ=255)
                                                                                                                                cAAGGGCAAAATAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGctgactg            >  2:93065/1‑141 (MQ=255)
                                                                                                                                cAAGGGCAAAATAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGCCTAAAGTCATAAAGCTTAGAAGctgactc            >  2:211621/1‑140 (MQ=255)
                                                                                                                                      cAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGCTGACTGATCAAt      <  2:192937/141‑1 (MQ=255)
                                                                                                                                          cTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGCTGACTGATCAATCCaa  >  1:214025/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                            
TTACCTTTTTCATTTCTGATTGTTTCAATTTGATTAATAAAATCAAAACTGCTCAGAGAATTATTCGGTGACACTGTAAGTAAATCAGATACTTCTGTATTAACTACTTTATAATCTTCATACATTTTCAAGGGCAAACTAGCCATCGAATTAGATAACTTTGTAATAGCTGAAAATATCGTTTCATTAGTTTCAAGCGTATTATTGATTACACCCCAAAAAGATTTATTTTTCCATGGGCTAAAGTCATAAAGCTTAGAAGCTGACTGATCAATCCAA  >  USA300TCH1516_ALE/1583679‑1583957

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: ‑