Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913753,1250TA43.9% 55.3 / 16.2 41intergenic (‑330/+60)ybgD/gltAputative fimbrial‑like adhesin protein/citrate synthase
Reads supporting (aligned to +/- strand):  ref base T (18/5);  new base A (0/18);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 1.69e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGC  >  NC_000913/752977‑753272
                                                                                                                                                    |                                                                                                                                                     
aTTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCAtata                                                                                                                                                      >  1:334576/1‑150 (MQ=255)
   ttCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATaaaa                                                                                                                                                   >  1:305054/1‑150 (MQ=255)
    tCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATaaaaa                                                                                                                                                  <  2:159256/150‑1 (MQ=255)
     cATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAAt                                                                                                                                                 <  1:749952/150‑1 (MQ=255)
     cATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAAt                                                                                                                                                 <  1:592552/150‑1 (MQ=255)
                       aCTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAAcgg                                                                                                                              >  2:707197/1‑151 (MQ=255)
                                   tttttAATTGAAATTATTGGGTTGCTGATAATTTGAGCTGTTCTTTTTTTTTTAAATATTTATATAGGTCTTTTAATGGATTTTATTTTTAAAATTTTTTGTGTTTAGGCAAATAAAAATCAACCCGCCATATGAACGGCGGGTTaaaa                                                                                                                    <  2:277091/149‑1 (MQ=255)
                                     tttAATGAAAATTATTGGTTTAGTGATAATTGGGGTTGTTCTTTTTTTTTTAAATATCTATATGGGCCTGTTAATGTTTTTTTTTTTTACATTTTTTTGTTTTAAGGAATAAAAAAATCACACCGCCATATGAACGGCGGGTTAAAatat                                                                                                                 <  2:494702/150‑1 (MQ=255)
                                        aaTTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTTTTCTTTTTAAATATCTATATAGGTCTTTTAATGGATTTTATTTTTACAATTTTTTGTTTTTAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTAc                                                                                                             <  2:730894/151‑1 (MQ=255)
                                          ttaaaaTTATTGGGTTGTGTATAATTTGGGTTTTTTTTTTTTTTTTAAATATCTATATGGGTTTTTTAATGTTTTTTATTTTTAAAATTTTTTGTTTTAAGAAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACa                                                                                                            <  1:499535/147‑1 (MQ=255)
                                            gAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACaa                                                                                                           >  1:474097/1‑149 (MQ=255)
                                             aaaGTATGGGTTTGTTAATAATTTGTGCTGTTTTATTCTTTTAAAAAATCTAAATAGGTTTGTTAAGGTATTTTTTTTTTACAATTTTTTGTTTTTGGGAATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACaa                                                                                                           <  2:801610/148‑1 (MQ=255)
                                              aaGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACtt                                                                                                        >  1:691191/1‑150 (MQ=255)
                                              aaGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACtt                                                                                                        >  1:335476/1‑150 (MQ=255)
                                                   ttGGGTTGCTGATAATTTGAGCTTTTCTTTTTTTTTTAAATATCTATATAGGTCTTTTAATGGATTTTATTTTTACATTTTTTTGTTTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑Caa                                                                                                  <  2:670234/150‑1 (MQ=255)
                                                    tGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTTAAACTTAG‑Caa                                                                                                  >  2:614511/1‑149 (MQ=255)
                                                            taaTAATTTGAGCTGTTCTATTTTTTTAAAATATCTATATAGGTTTATTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGTCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCAt                                                                                          <  2:624244/147‑1 (MQ=255)
                                                            tGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCAtt                                                                                         >  1:689111/1‑150 (MQ=255)
                                                                        cTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAAAGC‑TTGatat                                                                            >  1:133752/1‑150 (MQ=255)
                                                                         ttttttATTTTTTTTAAATATCTATATAGCTTTGTTAATGGATTTTATTTTTAAAATTTTTTGTGTTAAGGAATAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATc                                                                           <  1:496427/145‑1 (MQ=255)
                                                                         tGTTTTTTTTTTTTTAATTATCTATATAGGTTTTTTAATGTTTTTTTTTTTTACATTTTTTTGTGTTAAGACATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTg                                                                                <  1:584122/145‑1 (MQ=255)
                                                                           ttCTTTTTTTTTTAAATATCTATATAGGTCTGTTAATGGTTTTTTTTTTTACATTTTTTTGTTTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGc                                                                         <  2:334599/150‑1 (MQ=255)
                                                                                ttttttttAAATATTTATATAGTTTTTTAAATGGTTTTTATTTTTACAATTTTTTTTTTTTAGCAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTa                                                                    <  1:402289/147‑1 (MQ=255)
                                                                                       tAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTcgcg                                                            >  2:126556/1‑151 (MQ=255)
                                                                                        aaaTATTTATATGGGTTTTTAAAAGCATTTTATTTTAAAAATTTTTTGTGTTTAGAAATAAAAAAACCCACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCACCCATTAACGC‑TTGATATCGCTTTTAAAGTcg                                                              <  1:390813/148‑1 (MQ=255)
                                                                                            atCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGttttt                                                       >  1:372315/1‑151 (MQ=255)
                                                                                                 tataGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAAAGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCata                                                   >  2:363772/1‑150 (MQ=255)
                                                                                                  ataGTTCTTTTAATGATTTTTATTTTTACATTTTTTTTTTTTAAGGAAAAAAAAAACCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCa                                                     <  1:784936/147‑1 (MQ=255)
                                                                                                   taGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCTATATGAACGGCGGGTTTTAATATTTACAACATAGATAAACAACAATT‑ACCC‑TTGGTATCGCCTTTTAAATCTCTTTTTTCCTATcc                                                >  1:709801/1‑151 (MQ=255)
                                                                                                   taGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATcc                                                >  2:71531/1‑151 (MQ=255)
                                                                                                           taaaTGTATTTTATTTTTATAATTTTTTGTTTTTAGGCATAAAAAAAACAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGtata                                          <  2:489393/147‑1 (MQ=255)
                                                                                                           taaaTGGATTTTTTTTTTACAATTTTTTGTTTTTAGGCATAAAAAAATCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGtata                                          <  2:118179/147‑1 (MQ=255)
                                                                                                                   ttttattttTACATTTTTTTGTGTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTg                                    <  1:431119/147‑1 (MQ=255)
                                                                                                                     ttattttTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTTATATCCTGTATACAGCTGACGCgg                              >  2:494277/1‑151 (MQ=255)
                                                                                                                           ttaaatttttttGTTTTTAGGCATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACggg                         <  1:674385/144‑1 (MQ=255)
                                                                                                                             aCATTTTTTTGTTTTTAGAAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCa                       <  1:582614/150‑1 (MQ=255)
                                                                                                                               aaTTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGGTTAAATATTTACAAATTAG‑CAATCAACCATTAACGC‑TTGATATCGCCTTTAAAGGCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATc                    >  1:518086/1‑151 (MQ=255)
                                                                                                                                 ttttttGTGTTTAGGAATAAAAAAACCACCCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCaa                      <  2:549958/147‑1 (MQ=255)
                                                                                                                                  tttttGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTTAGATATTTAAAAATTAA‑CAAAGCACCATTAAAGCTTTGGATTCGCTTTT‑AAGTGGGGTTTTTTATAACCTGTATATAGCTGACGCGGAAGGGCAAACtt                  >  1:297343/1‑150 (MQ=255)
                                                                                                                                  tttttGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCtt                  >  2:398263/1‑150 (MQ=255)
                                                                                                                                          tttAGGAATAAAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGt          <  2:255146/150‑1 (MQ=255)
                                                                                                                                                cATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTTCAACTTAG‑CAATCAACCATTAAAGC‑TTGATATCGCTTTTTAAGTCGCGTTTTTTATATTCTGTATACAGCTGACGCGGACGGGCAATCTTCATAACCTCACtgt    >  1:273260/1‑150 (MQ=255)
                                                                                                                                                    taAAAATCAACCCGCCATATGAACGGCGGGTTTAAATATTTTCAAAATTA‑CAATTAACCAATAAAGC‑TTGATATTGCTTTTTAAGTCGCGTTTTTCATATTCTGTATAAAACTGACGCGGACGGGCAATCTTCATAACGTCACTGTGc  >  1:714930/1‑148 (MQ=255)
                                                                                                                                                    |                                                                                                                                                     
ATTTTCATAGGGTTATAAATGCGACTACCATGAAGTTTTTAATTGAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATAGGTCTGTTAATGGATTTTATTTTTACAATTTTTTGTGTTTAGGCATATAAAAATCAACCCGCCATATGAACGGCGGGTTAAAATATTTACAACTTAG‑CAATCAACCATTAACGC‑TTGATATCGCTTTTAAAGTCGCGTTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGC  >  NC_000913/752977‑753272

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑