Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,490,0770CT24.0% 41.7 / 11.5 25P119P (CCG→CCA) USA300HOU_RS12815putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (8/11);  new base T (3/3);  total (11/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGG  >  USA300TCH1516_ALE/2489954‑2490212
                                                                                                                           |                                                                                                                                       
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                                  <  2:145413/140‑1 (MQ=255)
                                                                                      atttATTACCATTAAATGGATAAATTTGACGAGCCACTGGCGCTGCGTTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTGTTATTCGCTTGATTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCAt                                  <  2:175868/140‑1 (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)
                                                                                                                           |                                                                                                                                       
TTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGG  >  USA300TCH1516_ALE/2489954‑2490212

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: ‑