Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,490,0860AG22.2% 46.1 / 12.2 27N116N (AAT→AAC) USA300HOU_RS12815putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (9/12);  new base G (3/3);  total (12/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGGTTATCGTTTGC  >  USA300TCH1516_ALE/2489954‑2490223
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tttATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTACATTAAACGGATATATTTGACGTGCAACCGGTGCGGCATTTTGTcc                                                                                                                                   >  2:125641/1‑141 (MQ=255)
            acCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGc                                                                                                                       >  1:132700/1‑141 (MQ=255)
                           ttCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGAttt                                                                                                        >  2:131536/1‑141 (MQ=255)
                               ttattaGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGa                                                                                                    <  2:35715/141‑1 (MQ=255)
                                  ttaGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCAGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGatta                                                                                                 <  1:57319/141‑1 (MQ=255)
                                    agctgCATTTAAAGCTGTTTGGAAATTAGGCAATTGTTGTAATGCTTGTGATTTATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGattgtt                                                                                               >  1:145413/5‑138 (MQ=255)
                                    agctgCATTTAAAGCTGTTTGGAAATTAGGCAATTGTTGTAATGCTTGTGATTTATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGattgtt                                                                                               >  1:175868/5‑138 (MQ=255)
                                    agctgCATTTAAAGCTGTTTGGAAATTAGGCAATTGTTGTAATGCTTGTGATTTATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGattgtt                                                                                               >  1:31733/5‑138 (MQ=255)
                                             tAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTg                                                                                      <  1:19250/141‑1 (MQ=255)
                                                 gCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGtta                                                                                  >  2:170529/1‑141 (MQ=255)
                                                 gCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGtta                                                                                  >  2:157253/1‑141 (MQ=255)
                                                    gTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTTCAACGTAACTTGATTTTTGATTATTATTCGCTTGGttatta                                                                               >  1:97345/1‑141 (MQ=255)
                                                                      tGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTAttt                                                             >  2:199980/1‑141 (MQ=255)
                                                                        cTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTAtttgt                                                           <  2:128256/141‑1 (MQ=255)
                                                                           tAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTAtttgtttg                                                        <  1:108529/141‑1 (MQ=255)
                                                                                      atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt                                             <  2:31733/140‑1 (MQ=255)
                                                                                      atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt                                             <  2:175868/140‑1 (MQ=255)
                                                                                      atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt                                             <  2:145413/140‑1 (MQ=255)
                                                                                                          tAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTTATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTa                         <  1:40662/141‑1 (MQ=255)
                                                                                                          tAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTa                         <  1:154095/141‑1 (MQ=255)
                                                                                                           aaaTTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAg                        <  2:40887/141‑1 (MQ=255)
                                                                                                                 gACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGAttgtt                  >  2:17726/1‑141 (MQ=255)
                                                                                                                 gACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGAttgtt                  <  1:125641/141‑1 (MQ=255)
                                                                                                                   cGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGc                <  2:132700/141‑1 (MQ=255)
                                                                                                                      gCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTgg             <  1:199980/141‑1 (MQ=255)
                                                                                                                              cgcgGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGGTTATCGtt     >  1:83682/1‑141 (MQ=255)
                                                                                                                                 ggCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTTATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGGTTATCGTTTGc  <  2:129756/141‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                         
TTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGGTTATCGTTTGC  >  USA300TCH1516_ALE/2489954‑2490223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑