Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,909,4861.T70.8% 125.3 / 50.0 48coding (293/303 nt)USA300HOU_1771hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base . (8/6);  new base T (14/20);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 3.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACT  >  CP000730/1909350‑1909617
                                                                                                                                         |                                                                                                                                   
tCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑tttt                                                                                                                                 >  1:8662/1‑141 (MQ=255)
 cTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑Tttta                                                                                                                                >  1:183811/1‑141 (MQ=255)
  tataATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑ttttta                                                                                                                               >  1:242187/1‑139 (MQ=255)
  tataATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑ttttta                                                                                                                               <  1:218308/141‑3 (MQ=255)
         tttGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTaaaa                                                                                                                         >  1:293239/1‑141 (MQ=255)
            ttttttttttCAATTAAAAAACTAAAGCCTGATGAAGATTGGATTAGTATGGCGAGTAAGAGTTTGCCTTCGATTATTCTAATTGTTATTTTAGTATATATCTTTTGAATTGTTCGTACATTCGGTTTTTATTTaaataaa                                                                                                                      >  2:299163/9‑140 (MQ=255)
                aTCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTaa                                                                                                                  >  1:360882/1‑141 (MQ=255)
                aTCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAat                                                                                                                 >  1:198269/1‑141 (MQ=255)
                      cAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTc                                                                                                            <  1:187657/141‑1 (MQ=255)
                       aaTTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCAt                                                                                                          <  2:368243/141‑1 (MQ=255)
                        aTTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCAt                                                                                                          <  2:8662/141‑1 (MQ=255)
                               cACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGcc                                                                                                   <  1:118417/141‑1 (MQ=255)
                                aCTAAAGGCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCtt                                                                                                 >  1:331432/1‑141 (MQ=255)
                                      gCCTGATGCAGATTGGATTAGAATTGCGAGTAAACGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATAc                                                                                            >  1:114777/1‑141 (MQ=255)
                                         tGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACaaa                                                                                         <  1:131102/141‑1 (MQ=255)
                                          gATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACaaaa                                                                                        <  2:273838/141‑1 (MQ=255)
                                                gATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaatac                                                                                  >  1:391850/1‑141 (MQ=255)
                                                gATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaataca                                                                                 >  2:6205/1‑141 (MQ=255)
                                                        tAGAATTGCGAGTAAAAGATTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCa                                                                         <  1:76611/141‑1 (MQ=255)
                                                           aaTTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATg                                                                       <  1:28256/141‑1 (MQ=255)
                                                           aaTTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATg                                                                       <  1:299163/141‑1 (MQ=255)
                                                            aTTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGc                                                                      <  2:82083/141‑1 (MQ=255)
                                                             ttGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCt                                                                     <  2:242187/141‑1 (MQ=255)
                                                                       aaGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTa                                                           <  1:345728/141‑1 (MQ=255)
                                                                        aGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAAAAATACAATGTATCATGCTATAATGAGTaa                                                          <  1:378168/141‑1 (MQ=255)
                                                                          tatGCCTAGGATTATTCTAATGGTTATTTTAGTACATAACTTTTCAATTGTTCGTACATTCGA‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGACTTAATACAAAACAATACAATGTATCATGCTATAAAGAGTATAAc                                                       >  2:186596/3‑141 (MQ=255)
                                                                            tGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACaa                                                     <  2:291008/141‑1 (MQ=255)
                                                                             gCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACaa                                                     <  2:160857/141‑1 (MQ=255)
                                                                             gCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACaa                                                     <  1:75705/141‑1 (MQ=255)
                                                                                ttGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAAttt                                                  >  1:234851/1‑141 (MQ=255)
                                                                                  ggATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGAt                                               <  2:89355/141‑1 (MQ=255)
                                                                                        ttCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACgt                                          >  1:18738/1‑141 (MQ=255)
                                                                                        ttCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACgtt                                         >  2:288094/1‑141 (MQ=255)
                                                                                         tCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACgtt                                         <  1:269789/141‑1 (MQ=255)
                                                                                               tGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACgtaaaaacg                                   <  2:197018/141‑8 (MQ=255)
                                                                                                          tACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAatat                       <  2:379636/141‑1 (MQ=255)
                                                                                                           aCATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAatat                       <  1:87470/141‑1 (MQ=255)
                                                                                                             atatCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTa                     >  1:125380/1‑141 (MQ=255)
                                                                                                             atatCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTa                     <  2:219878/141‑1 (MQ=255)
                                                                                                              tatCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACATTACTATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAg                    >  1:356204/1‑141 (MQ=255)
                                                                                                               atCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGa                   <  1:401949/141‑1 (MQ=255)
                                                                                                                tCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGAtt                 <  2:336973/141‑1 (MQ=255)
                                                                                                                    ttCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTc              >  1:28513/1‑141 (MQ=255)
                                                                                                                      cAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGa            >  1:390229/1‑141 (MQ=255)
                                                                                                                       aaTTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGaa           <  1:306442/141‑1 (MQ=255)
                                                                                                                        aTTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGaaa          >  1:384392/1‑141 (MQ=255)
                                                                                                                         ttGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAAt         >  1:111474/1‑141 (MQ=255)
                                                                                                                            tttgTACAATCGG‑ATTTATTTAAAAAAGTTAATATGTCATTGTAGGTTTAATACAAAACAATACAATGTATCATGCTATAATTAGTAAAACAATTTGATAACGTTGTTGCGTATATAAAATATTAGATTTTCGAAATCAtc     >  2:371971/4‑140 (MQ=255)
                                                                                                                             tCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATaa    >  1:300154/1‑141 (MQ=255)
                                                                                                                              cGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATaa    <  2:172419/141‑1 (MQ=255)
                                                                                                                                tACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACt  >  1:229727/1‑141 (MQ=255)
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TCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACT  >  CP000730/1909350‑1909617

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