Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA35.7% 25.4 / 14.8 29Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (11/7);  new base A (5/5);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 6.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTG  >  USA300TCH1516_ALE/111390‑111639
                                                                                                                              |                                                                                                                           
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)
                                                                                                                              |                                                                                                                           
GAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTG  >  USA300TCH1516_ALE/111390‑111639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑