Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE620,2230CT31.2% 38.7 / 19.3 33N262N (AAC→AAT) sdrESerine‑aspartate repeat‑containing protein E
Reads supporting (aligned to +/- strand):  ref base C (15/7);  new base T (5/5);  total (20/13)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CAGTAAATGTGTCAAAAGAAGAACTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGATGGTAAAGATAATGTGGCAGCAGCGCATGACGGTAA  >  USA300TCH1516_ALE/620087‑620357
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cAGTAAATGTGTCAAAAGAAGAACTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCaa                                                                                                                                    >  2:267473/1‑141 (MQ=255)
cAGTAAATGTGTCAAAAGAAGAACTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCaa                                                                                                                                    >  2:224417/1‑141 (MQ=255)
  gTAAATGTGTCAAAAGAAGAACTTAAAAATAATCCTGAGAAATTAAAAGAATTAGTTAGAAATGATAACAATACAGATCGTTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCgaaa                                                                                                                                  >  1:229774/1‑141 (MQ=255)
                  aagaaCTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTg                                                                                                                  <  1:372159/141‑1 (MQ=255)
                     aaCTTAAAAATAATCCTGAGAAATTAAAAGAATTAGTTAGAAATGATAACAATACAGATCGTTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGcac                                                                                                               <  2:229774/141‑1 (MQ=255)
                      aCTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGcaca                                                                                                              >  1:279411/1‑141 (MQ=255)
                       cTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACaa                                                                                                             >  2:440/1‑141 (MQ=255)
                       cTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACaa                                                                                                             >  2:1783/1‑141 (MQ=255)
                         tAAAAATAATCCTGAGAAATTAAAAGAATTAGTTAGAAATGATAACAATACAGATCGTTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAAcc                                                                                                           <  1:16647/141‑1 (MQ=255)
                             aataatCCTGAGAAACTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTAGCTACAGCTCCAACAAGTGTTGCACCAAAACGTAAAAAAGAAAAAATGCGCTTTGCAGTTGCACAACcagca                                                                                                       <  2:293967/141‑1 (MQ=255)
                               taatCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACcagcagc                                                                                                     <  1:406159/141‑1 (MQ=255)
                               taatCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAACGCGCTTTGCAGTTGCACAACcagcagc                                                                                                     <  1:303125/141‑1 (MQ=255)
                                  tCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGt                                                                                                  <  2:242202/141‑1 (MQ=255)
                                              aaaaGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACaa                                                                                      >  1:125084/1‑141 (MQ=255)
                                              aaaaGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACaa                                                                                      >  1:116937/1‑141 (MQ=255)
                                              aaaaGAATTAGTTAGAAATGATAACAATACAGATCGTTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCaaataa                                                                                      >  2:275803/1‑138 (MQ=255)
                                              aaaaGAATTAGTTAGAAATGATAACAATACAGATCGTTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAATaa                                                                                      >  2:224085/1‑141 (MQ=255)
                                              aaaaGAATTAGTTAGAAATGATAACAATACAGATCGTTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAACAAGCAGCAGTTGCTTCaaataa                                                                                      >  1:293531/1‑138 (MQ=255)
                                                  gAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTa                                                                                  >  2:302059/1‑141 (MQ=255)
                                                                   tAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGt                                                                 <  1:84399/141‑1 (MQ=255)
                                                                     gCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGa                                                               >  1:222445/1‑141 (MQ=255)
                                                                             gATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCaa                                                       >  2:335811/1‑141 (MQ=255)
                                                                                       cTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAATAATGTAAATGACTTAATTACAGTTACGAAACAGACGATCAAAg                                             >  1:408176/1‑141 (MQ=255)
                                                                                          aaCCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGAAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTg                                          <  2:214170/141‑1 (MQ=255)
                                                                                              aGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAATAATGTAAATGACTTAATTACAGTTACGAAACAGACGATCAAAGTTGGCGa                                      <  1:275803/141‑1 (MQ=255)
                                                                                              aGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAATAATGTAAATGACTTAATTACAGTTACGAAACAGACGATCAAAGTTGGCGa                                      <  1:224085/141‑1 (MQ=255)
                                                                                              aGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGATTAAATGCGAAAATGCGTTTTGCAGTTGCACAACAAGCAGCAGTTGCTTCAAATAATGTAAATGACTTAATTACAGTTACGAAACAGACGATCAAAGTTGGCGa                                      <  2:293531/141‑1 (MQ=255)
                                                                                               gTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGAt                                     >  2:141270/1‑141 (MQ=255)
                                                                                                      cAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGATGGTAAAg                              >  1:330022/1‑141 (MQ=255)
                                                                                                                aaGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGATGGTAAAGATAATGTGgc                    >  2:188714/1‑141 (MQ=255)
                                                                                                                aaGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGATGGTAAAGATAATGTGgc                    >  1:288113/1‑141 (MQ=255)
                                                                                                                       gCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGATGGTAAAGATAATGTGGCAGCAgcg             >  2:108194/1‑141 (MQ=255)
                                                                                                                                  tgtAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGATGGTAAAGATAATGTGGCAGCAGCGCATGACGGTaa  <  2:222445/141‑1 (MQ=255)
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CAGTAAATGTGTCAAAAGAAGAACTTAAAAATAATCCTGAGAAATTAAAAGAATTGGTTAGAAATGATAGCAATACAGATCATTCAACTAAACCAGTTGCTACAGCTCCAACAAGTGTTGCACCAAAACGTGTAAACGCAAAAATGCGCTTTGCAGTTGCACAACCAGCAGCAGTTGCTTCAAACAATGTAAATGATTTAATTAAAGTGACGAAGCAAACAATCAAAGTTGGCGATGGTAAAGATAATGTGGCAGCAGCGCATGACGGTAA  >  USA300TCH1516_ALE/620087‑620357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑