Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA25.8% 46.4 / 11.6 32Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (9/14);  new base A (1/7);  total (10/22)
Fisher's exact test for biased strand distribution p-value = 2.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.81e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111380‑111652
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ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                       <  1:247079/140‑1 (MQ=255)
ggAAGTTAAAGAAGAAAACAGAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                       <  2:202296/140‑1 (MQ=255)
 gAAGTTAAAGGAGCAAACATAGATAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                                                                      <  2:64674/140‑1 (MQ=18)
  aaGTTAAAGAAGAAAACATAAAAAAAGAAATTGAAAACTTTAAGTTTTTTGCGCAATATAACAATTTAAAAGATTTATTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAatat                                                                                                                                     >  2:4808/1‑140 (MQ=18)
         agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATATCAATTTTAAAGATTTAATGAATCATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                              <  1:147738/140‑1 (MQ=255)
          gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAc                                                                                                                             >  1:158088/1‑140 (MQ=255)
          gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAc                                                                                                                             >  1:208888/1‑140 (MQ=255)
           aagaaAAAATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                            <  2:249883/140‑1 (MQ=255)
            agaaAACAGGAAAAAAGAAGTCGAAAAGGTTAAGTTTGTGGCGCAATATAGCAATTGTAAAGATTGAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTa                                                                                                                           <  1:1030/140‑1 (MQ=21)
              aaaaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                                                         <  1:126723/140‑1 (MQ=255)
                aagaaaaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATATCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCAGATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                                                                       <  2:123780/135‑1 (MQ=17)
                 aCATAAAAAAAGAAATCGAAAACTTTAAGAATTTTGAGCAAAATAGCAATTATAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCAAGAGGAGCCAAGTTATTGAGATCAATATGAATTAACTAatgat                                                                                                                      >  2:121900/1‑140 (MQ=18)
                    tAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGTGATAACAAACAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATgatgat                                                                                                                   >  1:264319/1‑140 (MQ=21)
                       aaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                <  1:198098/140‑1 (MQ=255)
                                               tttttGCGCAATATAGCAATTTTAAATATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                        <  1:255163/140‑1 (MQ=255)
                                                                       aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                <  2:208888/140‑1 (MQ=255)
                                                                       aaGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                                <  2:158088/140‑1 (MQ=255)
                                                                         gATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGcc                                                              <  2:191892/140‑1 (MQ=255)
                                                                            ttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATGATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGaa                                                           <  2:45016/140‑1 (MQ=255)
                                                                                      ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGttgttg                                                 <  1:253911/140‑1 (MQ=255)
                                                                                            aTGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAAGATCAATTAACTAAGGATGATTATAATGTAAACCAATTACGTTTAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                           <  2:3880/140‑1 (MQ=17)
                                                                                                 gaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                      >  2:56899/1‑140 (MQ=255)
                                                                                                              aTCTAGAGGTGCCGAGTTATTAAGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGTCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                         <  2:39584/140‑1 (MQ=255)
                                                                                                              aTCCAGAGGAGCCGAGTTATTCAGCTCAATATCAATTAACTAATAATAATTATAATGTAAAACAAATACGTAAAAGATATTACACACCAACAAAAAAAACACCGCAGATGTTATTAAAAGATACAGGAAAATTAAAAggg                         >  2:153587/1‑139 (MQ=255)
                                                                                                               tCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAAAAAGTAAATTGCGTAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                        >  1:181686/1‑140 (MQ=17)
                                                                                                                ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtc                       <  1:253104/140‑1 (MQ=255)
                                                                                                                  agagGTGCCGAGTTATTCAGCTTAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcat                     <  2:112062/140‑1 (MQ=255)
                                                                                                                  agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcat                     <  1:31095/140‑1 (MQ=255)
                                                                                                                   gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                    <  1:95522/140‑1 (MQ=255)
                                                                                                                       tGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCAGTTGTTGAAAGGTACAGGGAATTTAAAAGATTCATCAGtt                >  2:91584/1‑140 (MQ=255)
                                                                                                                                aTTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaa       <  1:255871/140‑1 (MQ=255)
                                                                                                                                     gCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCAGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGAAATAAAAAAAt  >  2:20742/1‑140 (MQ=255)
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GGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111380‑111652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑