Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5160CA28.1% 87.9 / 30.9 59Q196K (CAA→AAA) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (19/22);  new base A (5/11);  total (24/35)
Fisher's exact test for biased strand distribution p-value = 3.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.46e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTG  >  USA300TCH1516_ALE/111376‑111654
                                                                                                                                            |                                                                                                                                          
aagaagAAGTTAAAGAGGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTc                                                                                                                                            <  2:20333/136‑1 (MQ=255)
 tGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCa                                                                                                                                           >  2:209512/1‑141 (MQ=255)
   aGGAAGTTAAAGAATAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAat                                                                                                                                         <  2:126315/141‑1 (MQ=255)
     gAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAatat                                                                                                                                       <  2:8721/141‑1 (MQ=255)
       aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                     >  2:3223/1‑141 (MQ=255)
           aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTa                                                                                                                                 >  1:262179/1‑141 (MQ=255)
             ataagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                               <  1:421552/139‑1 (MQ=255)
             agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATCAAGATGGAGATATATCATATAATCCCAAAGTCCCGAGTTATTCAGCTCAATAACAATTAAc                                                                                                                               >  2:306358/1‑141 (MQ=21)
             agaagaAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAc                                                                                                                               <  1:171301/141‑1 (MQ=255)
              gaagaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                              <  2:204954/141‑1 (MQ=255)
                    aaCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                        >  2:272336/1‑141 (MQ=255)
                    aaCATAAAAAAAGAAATCGAAAACTTTAAGTTGTTTGCGCAATATAGCAATTTTAACGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                                                                        >  2:335897/1‑141 (MQ=255)
                     aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATCTAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAatgatg                                                                                                                       >  1:416442/1‑141 (MQ=255)
                     aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTACCTAatgatg                                                                                                                       >  2:349908/1‑141 (MQ=255)
                       aTAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATACAGAAGTGACGAATTATTAAGATAAATATAAATTAACTAAtaatgaa                                                                                                                     >  2:335435/1‑140 (MQ=17)
                            aaaaGAAATCGAAAACTTTAAGTTTTATGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGAAAGGCCATCTTTTAACTAATGATGATTATaa                                                                                                                <  2:246765/141‑1 (MQ=18)
                               aGAAATCGAAAACTTTAAGTTTTGTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                                             <  2:197386/141‑1 (MQ=255)
                               aGAAATAGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTCAATATCAATTAACTAATGATGATTATAATGt                                                                                                             <  2:383338/141‑1 (MQ=255)
                                aaaaTCGAAAACTTTAAGTTTTTTGCGTAATTTAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTa                                                                                                            <  2:295217/140‑1 (MQ=17)
                                 aaaTTGAAAATTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                           <  1:32786/141‑1 (MQ=255)
                                 aaaTCAAAAATTTTAAGGTTTTTGATTAATATAGAAATTTTAAAGATTTAATGAATTATAAAGATGGATATATATCATATAATCCATAGGTGTCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                           <  2:382429/141‑1 (MQ=14)
                                       aaaaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAAt                                                                                                     <  1:134493/141‑1 (MQ=255)
                                         aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGATTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                   >  1:260175/1‑141 (MQ=255)
                                         aaCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                   >  1:51043/1‑141 (MQ=255)
                                          aCTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTGTAAAGATGGAGCTATATCATATAATCCAGAGGTGCCGAGTTATTCGGTGCAATATCAATTAACTAATGGTGATTATAATGTAAAACGATTAc                                                                                                  >  1:40794/1‑141 (MQ=18)
                                            tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAATATGGAGATATATCATATAATCCAGAGGTGTCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGt                                                                                                <  2:207713/141‑1 (MQ=255)
                                            tttAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACgc                                                                                                <  1:203321/141‑2 (MQ=255)
                                              tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                              <  2:188472/141‑1 (MQ=255)
                                               aaGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGAATATAATGTAAAACAATTACGCaaa                                                                                             >  1:109713/1‑141 (MQ=255)
                                               aaGTTTTGTGAGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCaaa                                                                                             <  2:286827/141‑1 (MQ=14)
                                                  ttttttGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                          >  1:105778/1‑141 (MQ=255)
                                                  tatgttGCGCAATATAGCAATTTTAAAGATTTAATTAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGa                                                                                          <  1:433622/137‑1 (MQ=255)
                                                         cgcAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACa                                                                                   <  1:361736/141‑1 (MQ=255)
                                                               ataGCAATTTTAAAGAATTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccga                                                                             <  2:119380/141‑3 (MQ=11)
                                                                 aGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATTATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacg                                                                           <  2:368525/141‑5 (MQ=11)
                                                                    aaTTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAAt                                                                        >  2:239667/1‑141 (MQ=255)
                                                                      ttttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTTAAAGACTTCTAACAACAAATGATCAGCTTGTTTATCAATTACGTAAAAGATATGACATACCAACAAATaa                                                                      <  1:209512/141‑1 (MQ=12)
                                                                       tttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATaaa                                                                     <  1:221202/141‑1 (MQ=255)
                                                                            aGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAACGcc                                                                >  2:132553/1‑141 (MQ=255)
                                                                                  aaTGAATTATAAAGATGGAGGTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                          <  1:29105/141‑1 (MQ=255)
                                                                                  aaTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAACACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCt                                                          <  1:217093/141‑1 (MQ=255)
                                                                                      aaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttg                                                      <  1:3223/141‑1 (MQ=255)
                                                                                                gtGGAGATATATCATATAATACAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTa                                            <  2:112207/140‑1 (MQ=255)
                                                                                                   gagaTATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTCATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAg                                         >  1:224332/1‑141 (MQ=255)
                                                                                                         tatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAAtt                                   <  1:303576/141‑1 (MQ=255)
                                                                                                             atatAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTaaa                               <  1:319586/141‑1 (MQ=255)
                                                                                                                   accAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtc                         <  2:300995/140‑1 (MQ=255)
                                                                                                                     cAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcat                       <  1:353082/141‑1 (MQ=255)
                                                                                                                        agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                    >  2:381478/1‑141 (MQ=255)
                                                                                                                        agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                    <  1:56009/141‑1 (MQ=255)
                                                                                                                        agGTGCCGAGTTATTCAGCAAAATATCAATTTACTAATTATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                    >  1:420015/1‑141 (MQ=255)
                                                                                                                             ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATGAGTTGGa               >  1:271532/1‑141 (MQ=255)
                                                                                                                             ccGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTggg               >  1:116435/1‑140 (MQ=255)
                                                                                                                              cGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGat              >  1:27633/1‑141 (MQ=255)
                                                                                                                              agAGTTATTCAGCTCAATATCAATTAACGAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATAGCAACAAATAAAGCGTCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGat              <  2:185785/140‑1 (MQ=255)
                                                                                                                              aaaGTTAATCAGCTAAAAATCAATTAACTAATGATGATTATAATGTAAAACAATTACGAAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTAAAGGGAATTTAAAAGGTTCATCAGTTGGat              <  2:151671/139‑1 (MQ=14)
                                                                                                                                aGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGatat            <  1:308883/141‑1 (MQ=255)
                                                                                                                                       cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa     >  2:172189/1‑141 (MQ=255)
                                                                                                                                       cAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATaaaaaaa     >  2:63178/1‑141 (MQ=255)
                                                                                                                                          cTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTg  <  1:294549/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                          
CTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAATTG  >  USA300TCH1516_ALE/111376‑111654

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑