Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,705,7420CT33.3% 35.6 / 24.9 36A31T (GCG→ACG) crtQ4,4'‑diaponeurosporenoate glycosyltransferase
Reads supporting (aligned to +/- strand):  ref base C (13/11);  new base T (6/6);  total (19/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GATCCGTCATTCATAACAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTGCGAC  >  USA300TCH1516_ALE/2705603‑2705882
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gATCCGTCCTTCATAACAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCATTTTTCTTCGTTTCTAGCCGGAATCATAATTATTAATGCTTTATGATTGAAGTTCAGCGTTTTCGcc                                                                                                                                             <  1:356934/141‑1 (MQ=255)
gATCCGTCATTCATAACAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGcc                                                                                                                                             <  1:92471/141‑1 (MQ=255)
      tcattcatAACAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGc                                                                                                                                       <  1:151413/141‑1 (MQ=255)
      tcattcatAACAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGc                                                                                                                                       <  2:119815/141‑1 (MQ=255)
      tcattcatAACAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGc                                                                                                                                       >  1:350271/1‑141 (MQ=255)
              aaCAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGtaa                                                                                                                               <  2:84642/141‑3 (MQ=255)
              aaCAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTCTCGCCTTTAGCTGATGtaa                                                                                                                               <  2:12199/141‑3 (MQ=255)
                     aCATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTa                                                                                                                        >  1:68209/1‑141 (MQ=255)
                     aCATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCATTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTa                                                                                                                        >  1:344574/1‑141 (MQ=255)
                     aCATCTACTGGAACTTGATGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCATTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTa                                                                                                                        >  1:413731/1‑141 (MQ=255)
                                aaCTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGc                                                                                                             >  2:191484/1‑141 (MQ=255)
                                 aCTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGca                                                                                                            <  2:72506/141‑1 (MQ=255)
                                                      tGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACAACACGCCATAGACATGGTc                                                                                       >  2:364700/1‑141 (MQ=255)
                                                                 aCCTATTCTTTTTTCTTCATTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGt                                                                            >  1:53051/1‑141 (MQ=255)
                                                                 aCCTATTCTTTTTTCTTCATTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGt                                                                            >  1:53055/1‑141 (MQ=255)
                                                                 aCCTATTCTTTTTTCTTCATTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGt                                                                            >  1:183507/1‑141 (MQ=255)
                                                                 aCCTATTCTTTTTTCTTCATTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGt                                                                            >  1:304901/1‑141 (MQ=255)
                                                                  ccTATTCTTTTTTTTTTTTTTTTAGCCGGAATAATAATTGTTAATGCTTTATGTTTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGtt                                                                           >  2:267274/1‑141 (MQ=255)
                                                                  ccTATTCTTTTTTTTTTTTTTTTAGCCGGAAAAATAATTGTTAACGCTTTATGTTTGAAGTTCAGCGTTTTCGCCTTTCGCTGATGTCTACGATTAAATATCAATGCATCTCTCTTTTTTTACATGGTTACTATTACTGtt                                                                           >  2:267165/1‑141 (MQ=255)
                                                                                ttcGTTTCTAGCCGGAATAATAATTGTTAATGCTTTAGTATTGAAGTTCAGCGTTTTCGCCTATAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATaa                                                             <  1:337824/141‑1 (MQ=255)
                                                                                  cGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTACTATTCGTGATAAcc                                                           >  2:246419/1‑141 (MQ=255)
                                                                                  cGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAAcc                                                           >  2:379121/1‑141 (MQ=255)
                                                                                  cGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAAcc                                                           >  1:136171/1‑141 (MQ=255)
                                                                                    tttCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCAt                                                         >  1:238165/1‑141 (MQ=255)
                                                                                             ggAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCAtcgtt                                                >  1:251327/1‑137 (MQ=255)
                                                                                             ggAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGat                                                <  1:308200/141‑1 (MQ=255)
                                                                                             ggAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGat                                                <  1:411136/141‑1 (MQ=255)
                                                                                               aataataatTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGatat                                              <  2:413731/141‑1 (MQ=255)
                                                                                               aataataatTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGatat                                              <  2:344574/141‑1 (MQ=255)
                                                                                                          ttAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTAtt                                   <  2:40120/141‑1 (MQ=255)
                                                                                                          ttAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTAtt                                   <  1:221441/141‑1 (MQ=255)
                                                                                                                        ttGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTcgcg                     >  2:350374/1‑141 (MQ=255)
                                                                                                                        ttGAAGTGCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAACTATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTcgcg                     <  2:231215/141‑1 (MQ=255)
                                                                                                                                       ttCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTg      <  2:304901/141‑1 (MQ=255)
                                                                                                                                       ttCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTg      <  2:53051/141‑1 (MQ=255)
                                                                                                                                       ttCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTg      <  2:53055/141‑1 (MQ=255)
                                                                                                                                       ttCGTCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTg      <  2:183507/141‑1 (MQ=255)
                                                                                                                                       ttCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTg      >  1:152794/1‑141 (MQ=255)
                                                                                                                                           ccTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTGCGAc  <  2:309786/141‑1 (MQ=255)
                                                                                                                                           ccTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTGCGAc  <  2:251677/141‑1 (MQ=255)
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GATCCGTCATTCATAACAATGACATCTACTGGAACTTGCTGTTGTATTATCGAATGTAGTAAATGACCTATTCTTTTTTCTTCGTTTCTAGCCGGAATAATAATTGTTAATGCTTTATGATTGAAGTTCAGCGTTTTCGCCTTTAGCTGATGTCTACGATTAAATATCAATGCACCACACGCCATAGACATGGTCACTATTACTGTTAATATTCGTGATAACCATTTCATAGATATCACTTCCTATTCTTCGCTTCTCGCGCGTTTATTTTGTCTGCGAC  >  USA300TCH1516_ALE/2705603‑2705882

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