Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,584,1530CT37.5% 26.1 / 24.9 32K520K (AAG→AAA) USA300HOU_RS07765hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (16/4);  new base T (3/9);  total (19/13)
Fisher's exact test for biased strand distribution p-value = 3.51e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CACCTCCTTAACGCATTATATCTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCA  >  USA300TCH1516_ALE/1584014‑1584289
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cACCTCCTTAACGCATTATATCTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCtgctttgct                                                                                                                                         >  2:51585/1‑141 (MQ=255)
cACCTCCTTAACGCATTATATCTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCtgctttgct                                                                                                                                         >  2:411450/1‑141 (MQ=255)
                   atCTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTcc                                                                                                                      <  1:171899/141‑1 (MQ=255)
                     cTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGt                                                                                                                    >  2:1671/1‑141 (MQ=255)
                     cTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGt                                                                                                                    >  1:41421/1‑141 (MQ=255)
                         aaTACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCt                                                                                                                >  1:34373/1‑141 (MQ=255)
                         aaTACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCt                                                                                                                >  1:400138/1‑141 (MQ=255)
                                          tGTTTCCTTCACCACTATCAGAAACAACTTTATTCATAATGTCTGTGTATGTGTTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGaa                                                                                               >  1:83767/1‑141 (MQ=255)
                                          tGTTTCCTTCACCACTATCAGAAACAACTTTATTCATAATGTCTGTGTATGTGTTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGaa                                                                                               >  1:232854/1‑141 (MQ=255)
                                          tGTTTCCTTCACCACTATCAGAAACAACTTTATTCATAATGTCTGTGTATGTGTTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGaa                                                                                               >  1:253945/1‑141 (MQ=255)
                                              tCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACatt                                                                                           >  1:47079/1‑141 (MQ=255)
                                                 ttCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACattatt                                                                                        >  2:191405/1‑141 (MQ=255)
                                                         tGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAATCAGTTTCCGTTTCTTTCTAGTTTCAACTGAACATTATTGATATAcc                                                                                >  1:157600/1‑141 (MQ=255)
                                                                       ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                  >  2:61169/1‑141 (MQ=255)
                                                                       ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                  >  2:228163/1‑141 (MQ=255)
                                                                       ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                  >  2:309259/1‑141 (MQ=255)
                                                                       ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                  >  2:40682/1‑141 (MQ=255)
                                                                               aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                          >  2:202909/1‑141 (MQ=255)
                                                                               aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                          >  1:131217/1‑141 (MQ=255)
                                                                               aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                          >  2:151365/1‑141 (MQ=255)
                                                                                              gtTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTAttttgcc                                           <  2:83767/141‑4 (MQ=255)
                                                                                              gtTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTAttttgcc                                           <  2:253945/141‑4 (MQ=255)
                                                                                              gtTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTAttttgcc                                           <  2:232854/141‑4 (MQ=255)
                                                                                                        gctgcAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAAc                                 >  1:59921/1‑141 (MQ=255)
                                                                                                          tgcAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACAt                               >  1:230603/1‑141 (MQ=255)
                                                                                                           gcAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACAtt                              <  2:284560/141‑1 (MQ=255)
                                                                                                                         tttACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCtt                <  1:61169/141‑1 (MQ=255)
                                                                                                                         tttACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCCTTTAAATCCtt                <  1:309259/141‑1 (MQ=255)
                                                                                                                          ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc               <  1:398780/141‑1 (MQ=255)
                                                                                                                          ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc               <  1:263281/141‑1 (MQ=255)
                                                                                                                          ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc               <  2:186492/141‑1 (MQ=255)
                                                                                                                          ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc               <  1:128263/141‑1 (MQ=255)
                                                                                                                          ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc               <  2:138770/141‑1 (MQ=255)
                                                                                                                             cGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTCagt            <  2:26792/141‑3 (MQ=255)
                                                                                                                                       tttgcttAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCa  >  1:338461/1‑141 (MQ=255)
                                                                                                                                       tttgcttAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCa  >  1:338446/1‑141 (MQ=255)
                                                                                                                                       tttgcttAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCa  >  2:379609/1‑141 (MQ=255)
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CACCTCCTTAACGCATTATATCTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCA  >  USA300TCH1516_ALE/1584014‑1584289

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑