Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,490,0710TA22.2% 56.4 / 11.3 27A121A (GCA→GCT) USA300HOU_RS12815putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (11/10);  new base A (3/3);  total (14/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.27e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AATAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGC  >  USA300TCH1516_ALE/2489933‑2490209
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aaTAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGc                                                                                                                                          >  2:32225/1‑141 (MQ=255)
   aGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAAc                                                                                                                                       >  1:137638/1‑141 (MQ=255)
   aGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAAc                                                                                                                                       >  2:112184/1‑141 (MQ=255)
                     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                               <  2:145413/140‑1 (MQ=255)
                                                                                                           atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt                               <  2:175868/140‑1 (MQ=255)
                                                                                                           atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt                               <  2:31733/140‑1 (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)
                                                                                                                                          |                                                                                                                                          
AATAGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGC  >  USA300TCH1516_ALE/2489933‑2490209

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: ‑