Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,490,0740AC22.2% 36.2 / 16.8 27V120V (GTT→GTG) USA300HOU_RS12815putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (10/11);  new base C (3/3);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.20e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGG  >  USA300TCH1516_ALE/2489936‑2490212
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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                                  <  2:31733/140‑1 (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)
                                                                                                                                          |                                                                                                                                          
AGAATAATCATTATACACTTTATTATTACTACCAAATTTATTTGCTTCATTATTAGCCGCATTTAAAGCTGTTTGGAAATTTGGCAATTGCTGTAAAGCTTGATTTTTATTTCCATTAAACGGATAAATTTGACGTGCAACCGGCGCGGCATTTTGTCCATAATATGGTGCAACGTAACTTGATTTTTGATTATTATTCGCTTGGTTATTACTTGATTGGTTATTATTTGTTTGGTTTTGGTCATTGTTTGTTGCATTTGAATTAGATTGTTGCTGG  >  USA300TCH1516_ALE/2489936‑2490212

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: ‑