Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE386,7620TA36.5% 54.9 / 41.8 53intergenic (‑152/‑60)licR/slyA_1putative licABCH operon regulator/Transcriptional regulator SlyA
Reads supporting (aligned to +/- strand):  ref base T (9/24);  new base A (7/12);  total (16/37)
Fisher's exact test for biased strand distribution p-value = 5.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TAATTGTAAGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGCTGATCAAAAGTTAGAGCAATT  >  USA300TCH1516_ALE/386630‑386901
                                                                                                                                    |                                                                                                                                           
taattgtaaGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTaa                                                                                                                                     >  1:135227/1‑141 (MQ=255)
taattgtaaGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTaa                                                                                                                                     <  1:96610/141‑1 (MQ=255)
     gtaaGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATg                                                                                                                                <  1:309019/141‑1 (MQ=255)
     gtaaGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATg                                                                                                                                >  1:272312/1‑141 (MQ=255)
     gtaaGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTATTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATg                                                                                                                                >  2:86701/1‑141 (MQ=255)
     gtaaGCGATTTCTTAAAAACGTAGATATGAAATCTCTGTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATg                                                                                                                                >  1:323357/1‑141 (MQ=255)
        aGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTACTCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGCCAATTTAAAAATGTCg                                                                                                                             <  1:146446/141‑1 (MQ=255)
        aGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCg                                                                                                                             <  1:324752/141‑1 (MQ=255)
            aTTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGt                                                                                                                         <  1:129035/141‑1 (MQ=255)
              ttcatAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGTGCAAGATTTTATAGAAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGtat                                                                                                                       <  1:391861/137‑1 (MQ=255)
              ttcatAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGTGCAAGATTTTATAGAAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGtat                                                                                                                       <  2:220187/137‑1 (MQ=255)
              ttcatAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGTGCAAGATTTTATAGAAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGtat                                                                                                                       <  1:174414/137‑1 (MQ=255)
                 ttAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATAtt                                                                                                                    >  2:130592/1‑141 (MQ=255)
                 ttAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATAtt                                                                                                                    >  2:72549/1‑141 (MQ=255)
                  tAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGACATTCATGTTGTCAATTTAAAAATGTCGCAGTATAttt                                                                                                                   >  2:227957/1‑141 (MQ=255)
                     aaaCGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATttagt                                                                                                                <  2:178288/141‑1 (MQ=255)
                     aaaCGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGAATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTAAATTTAAAAATGTCGCAGTATATttagt                                                                                                                <  2:103449/141‑1 (MQ=255)
                           aGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACa                                                                                                          <  2:202124/141‑1 (MQ=255)
                           aGATATGCAATCTCTTTCATATTTTAATCAGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAACATAAATTCGATATTAATGATAAAAATAAAAAAATGTCGCAGTATATTTAGTTAGACa                                                                                                          <  2:39780/141‑1 (MQ=255)
                              tatGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCt                                                                                                       >  1:281946/1‑141 (MQ=255)
                               atGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTa                                                                                                      <  1:152804/141‑1 (MQ=255)
                                 gCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAAc                                                                                                    <  2:243968/141‑1 (MQ=255)
                                 gCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAAc                                                                                                    <  2:412003/141‑1 (MQ=255)
                                 gCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAAc                                                                                                    <  2:62419/141‑1 (MQ=255)
                                 gCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAAc                                                                                                    <  2:255196/141‑1 (MQ=255)
                                                ttttAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCaa                                                                                     >  1:79913/1‑141 (MQ=255)
                                                ttttAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCaa                                                                                     >  2:250315/1‑141 (MQ=255)
                                                ttttAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCaa                                                                                     >  2:19416/1‑141 (MQ=255)
                                                ttttAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCaa                                                                                     >  1:294151/1‑141 (MQ=255)
                                                  ttAATCCGAAAAATTGTATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATa                                                                                   <  1:260553/141‑1 (MQ=255)
                                                  ttAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATa                                                                                   >  2:140099/1‑141 (MQ=255)
                                                     aTCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAAt                                                                                <  1:159363/141‑1 (MQ=255)
                                                     aTCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAAt                                                                                <  1:224210/141‑1 (MQ=255)
                                                                   atatCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTAtt                                                                  >  1:325384/1‑141 (MQ=255)
                                                                     atCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCg                                                                <  2:158995/141‑1 (MQ=255)
                                                                     atCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCg                                                                <  2:26604/141‑1 (MQ=255)
                                                                     atCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCg                                                                <  1:408913/141‑1 (MQ=255)
                                                                     atCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGATAAAAATAAAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCg                                                                <  2:396758/141‑1 (MQ=255)
                                                                          aaTGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAATATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGtagtt                                                           <  2:19441/141‑1 (MQ=255)
                                                                            tGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGtatttat                                                         >  1:123850/1‑141 (MQ=255)
                                                                               ttATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTAtttattta                                                      <  2:275259/141‑1 (MQ=255)
                                                                                  tGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGaa                                                   <  1:343367/141‑1 (MQ=255)
                                                                                                  aGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGAt                                   <  2:407790/141‑1 (MQ=255)
                                                                                                   ggAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATg                                  >  2:188759/1‑141 (MQ=255)
                                                                                                   ggAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATg                                  <  2:35549/141‑1 (MQ=255)
                                                                                                   ggAACTATTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCCATAAATGGAATTAACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATg                                  <  2:397571/141‑1 (MQ=255)
                                                                                                        ttttAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACa                             <  1:406923/141‑1 (MQ=255)
                                                                                                        ttttAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACa                             <  1:208998/141‑1 (MQ=255)
                                                                                                              aataaatTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGc                       <  2:294151/141‑1 (MQ=255)
                                                                                                              aataaatTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGc                       <  1:19416/141‑1 (MQ=255)
                                                                                                              aataaatTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGc                       <  1:250315/141‑1 (MQ=255)
                                                                                                              aataaatTAGATATTCATGTTGACAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTAACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGc                       <  2:79913/141‑1 (MQ=255)
                                                                                                                           ttCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGCTGATCAAAAGTTa          <  1:188759/141‑1 (MQ=255)
                                                                                                                                   gtCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGCTGATCAAAAGTTAGAGCAAtt  >  2:404938/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                           
TAATTGTAAGCGATTTCTTAAAAACGTAGATATGCAATCTCTTTCATATTTTAATCCGAAAAATTGCATATCAAAATGTTTATGGCGCAAGATTTTATAGGAACTTTTAAAATAAATTAGATATTCATGTTGTCAATTTAAAAATGTCGCAGTATATTTAGTTAGACATCTAACGAAATGGTGGTGCAATAAATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGCTGATCAAAAGTTAGAGCAATT  >  USA300TCH1516_ALE/386630‑386901

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑