Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,584,1740GA33.3% 38.1 / 22.3 36N513N (AAC→AAT) USA300HOU_RS07765hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (19/5);  new base A (3/9);  total (22/14)
Fisher's exact test for biased strand distribution p-value = 3.17e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCCTTG  >  USA300TCH1516_ALE/1584035‑1584305
                                                                                                                                           |                                                                                                                                   
cTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGt                                                                                                                                    >  2:1671/1‑141 (MQ=255)
cTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGt                                                                                                                                    >  1:41421/1‑141 (MQ=255)
    aaTACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCt                                                                                                                                >  1:400138/1‑141 (MQ=255)
    aaTACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCt                                                                                                                                >  1:34373/1‑141 (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                                                                                  >  2:228163/1‑141 (MQ=255)
                                                  ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                                  >  2:309259/1‑141 (MQ=255)
                                                  ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                                  >  2:40682/1‑141 (MQ=255)
                                                  ttATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGa                                                                                  >  2:61169/1‑141 (MQ=255)
                                                          aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                                          >  2:202909/1‑141 (MQ=255)
                                                          aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                                          >  2:151365/1‑141 (MQ=255)
                                                          aataTCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGattattatt                                                                          >  1:131217/1‑141 (MQ=255)
                                                                         gtTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTAttttgcc                                                           <  2:83767/141‑4 (MQ=255)
                                                                         gtTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTAttttgcc                                                           <  2:232854/141‑4 (MQ=255)
                                                                         gtTTAAAAATGCTGCGAATCCATCTATTTTACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTAttttgcc                                                           <  2:253945/141‑4 (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                               <  2:186492/141‑1 (MQ=255)
                                                                                                     ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc                               <  1:398780/141‑1 (MQ=255)
                                                                                                     ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc                               <  1:263281/141‑1 (MQ=255)
                                                                                                     ttACGATACCTACTTTGTTTTGAAGGTAACCAGTTTCCATTTCTGTCCAGTTTTAACTGAACATTATTGATATACCATTTCATTAAAGGATTGTTATTAAATATTATTTTGCCGTCTAAAAACATCTCTTTTAGATCTTTc                               <  1:128263/141‑1 (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)
                                                                                                                                  ccAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCcttg  <  1:40682/141‑1 (MQ=255)
                                                                                                                                  ccAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCcttg  <  1:228163/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                   
CTTTAATACTAATAAATTCTATGTTTCCTTCACCCTTGTCAGAAACAACTTTATTCATAATATCTGTATATGTGTTTAAAAATGCTGCAAAGCCATCTATTTTACGATATCTGCTTTGCTTAGACGGCAACCAGTTTCCGTTTCTGTCTAGTTTCAACTGAACATTATTGATATACCATTTCATTAAAGGATTATTATTAAATATTATTTTCCCATCTAAAAACATTTCTTTTAAATCCTTCAATGCAGGGCTCAAGGTCAAAGCTCCTTG  >  USA300TCH1516_ALE/1584035‑1584305

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: ‑