Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5120AG29.0% 88.5 / 35.7 62S194S (TCA→TCG) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (21/23);  new base G (5/13);  total (26/36)
Fisher's exact test for biased strand distribution p-value = 1.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111373‑111651
                                                                                                                                           |                                                                                                                                           
cTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAg                                                                                                                                            >  2:219869/1‑141 (MQ=255)
  aCTGAGGAAGTAAAAAAAAAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCt                                                                                                                                          <  1:202450/141‑1 (MQ=255)
   cTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCta                                                                                                                                         >  1:368525/1‑140 (MQ=255)
   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                 <  1:56009/141‑1 (MQ=255)
                                                                                                                           agGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAg                 >  2:381478/1‑141 (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)
                                                                                                                                           |                                                                                                                                           
CTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAA  >  USA300TCH1516_ALE/111373‑111651

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: ‑