Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA32.4% 47.8 / 20.5 37Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (14/11);  new base A (7/5);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGA  >  USA300TCH1516_ALE/111383‑111655
                                                                                                                                     |                                                                                                                                           
aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATc                                                                                                                                       >  1:306728/1‑140 (MQ=255)
      agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                                 >  1:14583/1‑140 (MQ=255)
      aaaaaaaaaaataaaaaaataAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                                 <  1:57470/135‑1 (MQ=17)
          gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAAATaa                                                                                                                             >  1:185282/1‑140 (MQ=255)
               cATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                        <  2:197865/140‑1 (MQ=255)
               cATAAAAAAAGAAATCGAAAACTTTAAGTTGTTTGCGCAATATAGCAATTTAAAAGACATAATGAATTCTAAAGATGGAGATATATCATATAATCCAGAGATGCCGAGTTATTCAACTAAAACTCACTTAACTAatgctc                                                                                                                        >  2:315257/1‑137 (MQ=18)
                aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGATCTAAGATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtgatga                                                                                                                       >  1:240040/1‑140 (MQ=18)
                  aaaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCAAATAATCAAGAAGTGCAGAGATATTCAGCACAAAAACAATTAACTAAtgatgaat                                                                                                                     >  1:16342/1‑138 (MQ=21)
                      aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAAtaatgaacaaaa                                                                                                                 >  1:151671/1‑134 (MQ=18)
                      aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATaa                                                                                                                 >  1:258998/1‑140 (MQ=255)
                      aaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCGCAATATCAATTAACTAATGATGATTATaa                                                                                                                 <  2:242312/140‑1 (MQ=255)
                       aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGATATATAACATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                <  1:170848/140‑1 (MQ=255)
                       aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAAt                                                                                                                <  1:270749/140‑1 (MQ=255)
                          aaaTCGAAAACTTTAAGTTTTTTGCGCAACATAGCAATTTTATTGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTa                                                                                                             <  1:89405/140‑1 (MQ=17)
                           aaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAATGTTGGTGATATATCATATAATCCAGAGGTGCCGAGTTAGTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                            <  1:112791/140‑1 (MQ=255)
                                 aaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                      <  2:205073/140‑1 (MQ=255)
                                      ttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGAAGGAGATATATCAAACAATCGTACACCACCAAGTTTTTCGGCTAACCAACAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                                 <  1:77438/140‑2 (MQ=12)
                                      gaaaGTTTTTTGAGCAATATAGCAATGTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATAGAATCCAGAGGTGCCGAATTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                                 <  2:34246/138‑1 (MQ=18)
                                         aGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                              >  1:76642/1‑140 (MQ=255)
                                                       tatattaaTTTTAAATATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAcc                                                                                <  2:262817/134‑1 (MQ=255)
                                                        ataGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccg                                                                               <  1:208885/140‑2 (MQ=11)
                                                                 ttAAAGATCAAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGATCAATATCAATTAACTAATGCTGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCACCAAATaca                                                                      >  2:288031/1‑138 (MQ=17)
                                                                  tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAg                                                                     >  1:311829/1‑140 (MQ=255)
                                                                      gATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAAATACCAACAAATaaaacccc                                                                 >  2:222341/1‑135 (MQ=255)
                                                                         ttAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGaa                                                              <  2:293263/140‑1 (MQ=255)
                                                                            attaaTTATAAAGATAGATATATATCATATAATCCAAAGGTGCCGAGTTATTCAGCTCAATATCAATTAAATAATGATAATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                           <  1:276410/137‑1 (MQ=17)
                                                                                              gaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgg                                         >  1:270942/1‑140 (MQ=255)
                                                                                               atatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAggg                                        <  1:180933/140‑1 (MQ=255)
                                                                                                           aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGAAGAAGATGTTGTTGAAAGGTACAGGGAATTTAAAAGGt                            >  1:273846/1‑140 (MQ=255)
                                                                                                                       cGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGa                >  2:311308/1‑140 (MQ=255)
                                                                                                                       cGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGAGAATTTAAAAGGTTCATCAGTTGGa                >  2:11060/1‑140 (MQ=255)
                                                                                                                        gAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGCTGGac               >  2:279662/1‑139 (MQ=255)
                                                                                                                         aGTTATTCATCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATAAGACATACCAACAAATAAAACGCCTAAGCTTTTCTTGATAGTTATAGGGCATTTAAAACATTCACTAGttctata              >  2:173969/1‑135 (MQ=17)
                                                                                                                          gTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACTTACCAACAAAAAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat             <  1:276602/140‑1 (MQ=255)
                                                                                                                          gTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGTatat             >  2:134844/1‑140 (MQ=255)
                                                                                                                               tCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAATCTGTTGTTTAAAGGTACAGGAAATTTAAAAGGTTCATCAGTTGGATATaaaaa        >  1:53966/1‑140 (MQ=255)
                                                                                                                                 aGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACAAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTAAAAAGGTTCATCAGTTGGATATaaaaaac      >  2:126213/1‑139 (MQ=255)
                                                                                                                                     cAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGCCGCTGTTGTAGAAATAGATAGGGCGTAAAAAAAAGGCACCAGTTGGATATAAAAAAATTGa  >  1:206414/1‑140 (MQ=17)
                                                                                                                                     |                                                                                                                                           
AGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTGA  >  USA300TCH1516_ALE/111383‑111655

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: ‑