Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5120AG24.1% 34.6 / 10.2 31S194S (TCA→TCG) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (12/10);  new base G (3/4);  total (16/15)
Fisher's exact test for biased strand distribution p-value = 6.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTG  >  USA300TCH1516_ALE/111379‑111639
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aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATTAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAg                                                                                                                                <  1:189051/135‑1 (MQ=255)
 ggAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGc                                                                                                                               <  1:139780/135‑1 (MQ=255)
           gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                                                     >  2:154346/1‑135 (MQ=255)
               aaaaCATAACAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                 >  1:28714/1‑135 (MQ=255)
                    aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAat                                                                                                            >  1:154807/1‑135 (MQ=255)
                      aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGTTATATTTTTTAATTCAGAGGTGCTTAGTTATTCAGCTCAATAGCAATTAACTAatga                                                                                                          <  1:73472/135‑1 (MQ=21)
                         agaaGAAATCGAAAACTTTAAGTTTTTTTATCAATATAGTAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                                       <  2:112646/133‑1 (MQ=14)
                               aaTCGAAAACTTTAAGTTTTTTGCGCTATATATCAATTTTAAAGATTTAATGAATTATAATGATGGATATATTTTTTATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATaa                                                                                                 <  1:87073/135‑1 (MQ=18)
                                  cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGt                                                                                              <  2:113563/135‑1 (MQ=255)
                                  cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGAAATAAAAAAATATAAAAAAGGAAATATATCATATAATCCAGAGGTGCAGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                              >  1:24123/1‑135 (MQ=17)
                                     aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTACCGAGTTATTCCGCTAAATATCAATTAACTACTACTAACTATAATGCaaa                                                                                           >  2:93574/1‑135 (MQ=18)
                                     aaaCGTTAATTTTTTTGCGTAATATAGCAATTTTAAAAATTTAATGAATTATAAAGATTGAGATATATCATATAATTTAGAGGTGCCGAGTTATTCTGCTAAATATCAATTAACTAATGATGATTATAATGTaaa                                                                                           <  1:216433/135‑1 (MQ=17)
                                          ttAAGTTTTTTGTGCAATATAGCAATTTTAAGGATTTAATGAATTATAAAGATGTAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAAccct                                                                                      <  2:36358/135‑4 (MQ=255)
                                          ttAAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                      <  2:149886/135‑1 (MQ=255)
                                            aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTTCCTAGTTATTCAGCTTAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                    <  1:217045/135‑1 (MQ=255)
                                            aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                    <  2:153704/135‑1 (MQ=255)
                                              gTTTTTTGCGCAATATCGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                  >  1:140680/1‑135 (MQ=255)
                                                    tGCGCAATATAGCAATTTTAAAGATTGAATGAGTCATTAATATTGAGATATATCATATAATCCAGATGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAg                                                                            <  2:218882/135‑1 (MQ=18)
                                                            ataGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGata                                                                    >  2:164051/1‑133 (MQ=255)
                                                                    tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacg                                                            <  1:33031/135‑2 (MQ=1)
                                                                             ttAATGAATTATAAAGATGGAGATATATCATATAATCCAAAGATGAAGAGATATACAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgcg                                                   >  1:60191/1‑135 (MQ=17)
                                                                                 tGAATTATAAAGATGGCGATATATCATATAATCCAGAGGTACCAAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGa                                               >  1:185173/1‑135 (MQ=255)
                                                                                               ggAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGaaa                                 >  1:37099/1‑135 (MQ=255)
                                                                                                          atatTATCCTGAGGTGTCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGTTATGACATACCAACAAATAAAGCTCCGAAGCTGTTTTTGAAAGGTACAGGGaa                      <  2:29434/135‑1 (MQ=14)
                                                                                                           tataATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCACCGAAGCTGTTGTTGAAAGGTACAGGGAAt                     >  2:224456/1‑135 (MQ=255)
                                                                                                             taATCCAGAGGTGACGAGTTATTAAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCAAAGCTGTTGTTGAAAGGTACAGGGAAttt                   >  2:80560/1‑135 (MQ=255)
                                                                                                                      ggTGCCGAGTTAGTCAGGTCAATAGCAATTAAGTAATGAGGATTATAATGTAAAACAATTACGTAAAAGACATCACATACCAACACATAAAGCGCAGACGCTGTTGATGAAAGGTATAAGGAATTTAAAAgttcc          >  2:227434/1‑131 (MQ=18)
                                                                                                                         gCCGAGTTATTCAGCTCAATATCAATTAACTAATAATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGAGAATTTAAAAGGTtcatc       >  1:120725/1‑135 (MQ=255)
                                                                                                                             aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATAACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATGTAAAAGGTTCATCAGtt   >  1:75553/1‑135 (MQ=255)
                                                                                                                              gTTATTTATATCAATATCTATTAACTAATTATGATTATATTGTAAAACAATTACGTAAAAGATATGACATACCAACTAATAAATCGCCGAAGCTGTTGTTGATAGGTACAGGGAATTTAAAAGGTTCATCAGTTg  <  2:84110/135‑1 (MQ=14)
                                                                                                                              gTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGAAAAACAAATACGAAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTg  >  1:140555/1‑135 (MQ=255)
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AGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTG  >  USA300TCH1516_ALE/111379‑111639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑