Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,584,1890CT41.2% 18.5 / 31.6 34L508L (TTG→TTA) USA300HOU_RS07765hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (15/5);  new base T (5/9);  total (20/14)
Fisher's exact test for biased strand distribution p-value = 3.51e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCCTTGTCTTGTTTCTTCCG  >  USA300TCH1516_ALE/1584056‑1584319
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tGTTTCCTTCACCACTATCAGAAACAACTTTATTCATAATGTCTGTGTATGTGTTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGaa                                                                                                                             >  1:232854/1‑141 (MQ=255)
tGTTTCCTTCACCACTATCAGAAACAACTTTATTCATAATGTCTGTGTATGTGTTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGaa                                                                                                                             >  1:253945/1‑141 (MQ=255)
tGTTTCCTTCACCACTATCAGAAACAACTTTATTCATAATGTCTGTGTATGTGTTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGaa                                                                                                                             >  1:83767/1‑141 (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                                                                                                >  2:40682/1‑141 (MQ=255)
                             ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                                                >  2:309259/1‑141 (MQ=255)
                             ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                                                >  2:228163/1‑141 (MQ=255)
                                     aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                                                        >  1:131217/1‑141 (MQ=255)
                                     aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                                                        >  2:202909/1‑141 (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                                             <  2:138770/141‑1 (MQ=255)
                                                                                ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc                                             <  1:128263/141‑1 (MQ=255)
                                                                                ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc                                             <  1:263281/141‑1 (MQ=255)
                                                                                ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc                                             <  2:186492/141‑1 (MQ=255)
                                                                                ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc                                             <  1:398780/141‑1 (MQ=255)
                                                                                   cGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTCagt                                          <  2:26792/141‑3 (MQ=255)
                                                                                             tttgcttAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCa                                >  1:338446/1‑141 (MQ=255)
                                                                                             tttgcttAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCa                                >  1:338461/1‑141 (MQ=255)
                                                                                             tttgcttAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCa                                >  2:379609/1‑141 (MQ=255)
                                                                                                             ccAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCcttg                <  1:228163/141‑1 (MQ=255)
                                                                                                             ccAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCcttg                <  1:40682/141‑1 (MQ=255)
                                                                                                                           tGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTCAGTGCTGGACTTAAAGTCAAAGCCCCTTGTCTTGTttcttctg  >  1:64113/1‑139 (MQ=255)
                                                                                                                           tGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTCAGTGCTGGACTTAAAGTCAAAGCCCCTTGTCTTGTttcttctg  >  2:359502/1‑139 (MQ=255)
                                                                                                                                     |                                                                                                                                  
TGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCCTTGTCTTGTTTCTTCCG  >  USA300TCH1516_ALE/1584056‑1584319

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: ‑