Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA33.3% 37.0 / 13.9 30Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (10/10);  new base A (5/5);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACA‑AATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATT  >  USA300TCH1516_ALE/111378‑111653
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gAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCaa                                                                                                                                          >  1:29665/1‑141 (MQ=255)
 aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGAGAAGTGCGCAATAGAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCGCAat                                                                                                                                         <  1:84175/141‑1 (MQ=25)
 aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTAAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                         <  2:185791/141‑1 (MQ=255)
        tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                                  <  1:274010/141‑1 (MQ=255)
              agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGTATATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTaa                                                                                                                            <  1:5600/141‑1 (MQ=255)
                aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCACCTCAATATCAATTAACTAatg                                                                                                                          >  2:220890/1‑141 (MQ=255)
                   aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                       >  1:24280/1‑141 (MQ=255)
                   aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgatg                                                                                                                       >  1:95973/1‑141 (MQ=255)
                     aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATgatgat                                                                                                                     >  1:200477/1‑141 (MQ=255)
                      tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                                    >  1:250887/1‑141 (MQ=255)
                      aaaaaaaaGAAATCGAAAAATTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAtt                                                                                                                    <  2:275488/140‑1 (MQ=255)
                            aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATCTCATAAAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATg                                                                                                              <  1:116317/141‑1 (MQ=255)
                               aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                           <  2:252591/141‑1 (MQ=255)
                               aaaTCGAAAACTTTAAGTTTTGTCCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                           <  2:56468/141‑1 (MQ=255)
                                  tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATACAGATGGAGATATATCATATCATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGGaaaaa                                                                                                        >  1:102877/1‑140 (MQ=255)
                                   cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                       >  2:266148/1‑141 (MQ=255)
                                         cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGAAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTAca                                                                                                 >  2:84998/1‑140 (MQ=255)
                                                     tGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGa                                                                                     <  1:162624/141‑1 (MQ=255)
                                                             ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaa                                                                             <  1:25070/141‑1 (MQ=255)
                                                             ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACcaa                                                                             <  1:120071/141‑1 (MQ=255)
                                                               aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacg                                                                           <  2:229957/141‑5 (MQ=11)
                                                               aGCAATTTAAAAGATCTAATGAATTATAAAGATGGAGATATATCAAAAAAAAAAAAAGTAGCTAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacg                                                                           <  1:207939/141‑5 (MQ=2)
                                                                   aTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacgagta                                                                       >  2:11434/1‑136 (MQ=11)
                                                                      ttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACA‑AATAAAg                                                                   <  1:136821/141‑1 (MQ=255)
                                                                           gATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACTAACA‑AATAAAGCGCCg                                                              >  1:45481/1‑141 (MQ=255)
                                                                                         taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACA‑AATAAAGCGCCGAAGCTGTTGTTGaa                                                <  1:288930/141‑1 (MQ=255)
                                                                                                 gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACC‑AATAAACCGCCGAAGCTCTTGTTGAAAGGTACaa                                        >  2:114570/1‑140 (MQ=255)
                                                                                                           atatAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACA‑AATAAAGAGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaa                              >  2:113495/1‑141 (MQ=255)
                                                                                                                aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATA‑AAACACAATTTGACTCTTAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                         >  2:293110/1‑141 (MQ=17)
                                                                                                                                       gCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACA‑AATAAAGCGACGAAGCTGTTGTTGAAAGGTACAGAGAATTTAAAAGATTCATCAGATGAATATAAAAAAAtt  >  2:154671/1‑141 (MQ=17)
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GAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACA‑AATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATT  >  USA300TCH1516_ALE/111378‑111653

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: ‑