Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9110GA42.1% 40.4 / 18.3 38intergenic (‑122/+199)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
Reads supporting (aligned to +/- strand):  ref base G (20/2);  new base A (0/16);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 6.88e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGC  >  NC_000913/2001768‑2002054
                                                                                                                                               |                                                                                                                                               
cAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGaaaaaa                                                                                                                                           >  2:448070/1‑150 (MQ=255)
cAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGaaaaaa                                                                                                                                           <  2:137943/150‑1 (MQ=255)
         agagTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCgg                                                                                                                                 >  1:255244/1‑151 (MQ=255)
            gTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTgg                                                                                                                              >  1:48201/1‑151 (MQ=255)
                     cGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGc                                                                                                                     >  1:65958/1‑151 (MQ=255)
                               cccTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGAAAATCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCt                                                                                                             <  1:209952/149‑1 (MQ=255)
                                   gCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaa                                                                                                        >  1:152745/1‑150 (MQ=255)
                                        atatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGTTGAAATGGGGGGTTTTTTGGGGGTAAAAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgc                                                                                                   <  1:283424/150‑1 (MQ=255)
                                                  tCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTg                                                                                        >  2:178283/1‑151 (MQ=255)
                                                   cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGc                                                                                       >  1:226909/1‑151 (MQ=255)
                                                    ggCATGATTATCCTTTTCTGCGGGTTTTTTAACCGGACGATTAGGGGGTAAAATGGGGGGTTATTTGGGGGTTACAGGAAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGtt                                                                                         <  2:96385/148‑1 (MQ=255)
                                                       aTGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCgg                                                                                    >  2:10803/1‑150 (MQ=255)
                                                           ttttCCTTTTCTGCGGGTTTTTTAATCGGACGATTAGTGGGAGAAAGGGGGGTTTTTTTGGGGGTTACAGGTAAATCCCGGGCAAAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGa                                                                                   <  2:359434/144‑1 (MQ=255)
                                                                  tttgggCAGGGTTTTTAAACGAAGGTTAAGTGGTTGAAATGGGGGGTTTTTTGGGGTTAACGGGAAATTACCAGGCAAAAAAAACCTCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcggc                                                                             <  1:466894/141‑1 (MQ=255)
                                                                     cTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGc                                                                     >  1:490804/1‑151 (MQ=255)
                                                                        cAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCtt                                                                  >  1:4123/1‑151 (MQ=255)
                                                                                ttAAGCGGACGATAAGTGGGTGAAAGGAGGGTTTATTTGGGGGTAACAGTAAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCgg                                                            <  1:38348/149‑1 (MQ=38)
                                                                                  aaTCGGACGTTGATGGGGGGAAGTGAGGGGTTGTTTGGGGGGGACAGTAAAATACCAGGCAAAAAAAATCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTa                                                        <  1:485830/151‑1 (MQ=25)
                                                                                      ggACGATTAGTGGGTGAAATGAGGGGTTTTTTGGGGGTTACAGATAATTCCCGGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaa                                                    <  1:536285/151‑1 (MQ=38)
                                                                                          gATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAtg                                                >  1:66407/1‑151 (MQ=255)
                                                                                             tAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGc                                             >  1:327659/1‑151 (MQ=255)
                                                                                               gggggTAAAATGAGGGTTTATTTGGGGTTTAAAGTTAAATCCAAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCa                                            <  1:200580/148‑1 (MQ=37)
                                                                                                tGGGGGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGc                                             >  1:293045/1‑148 (MQ=255)
                                                                                                  ggTGAAAGGGGGGGTTTTTGGGGGGTTACAGTTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAAtt                                        <  1:408170/151‑1 (MQ=37)
                                                                                                   gTGAAGTGAGGGGTTAATTGGAGGTTACAGGTAAATTCCAGGCGGCAAAAAACCCCGCCGGTGGGGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGTGGCGTAAAAGCCTTATCCGGGCCAAGAAAATGTGCAAAt                                         >  1:467653/1‑149 (MQ=255)
                                                                                                          gAGGGTTTATTGGGGGTTTCAAGGTAAATTCCAGGAAAAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATaaa                                 <  2:294816/150‑1 (MQ=37)
                                                                                                            gggtTTATTGGGGGGTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTg                              <  2:461780/151‑1 (MQ=255)
                                                                                                                 tATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAtt                         >  2:452431/1‑151 (MQ=255)
                                                                                                                  aTTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                        >  1:573898/1‑151 (MQ=255)
                                                                                                                       ggggTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACtt                   >  2:528528/1‑151 (MQ=255)
                                                                                                                           ttACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGt                 >  2:128224/1‑149 (MQ=255)
                                                                                                                             aCAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc             >  2:375752/1‑151 (MQ=255)
                                                                                                                             aCAGGTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc             <  1:43091/151‑1 (MQ=255)
                                                                                                                                   aaaTCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGa         <  2:410411/149‑1 (MQ=255)
                                                                                                                                   aaaTCCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAt        <  2:62202/150‑1 (MQ=255)
                                                                                                                                    atttCCGGGAAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATaa      <  2:312145/149‑1 (MQ=255)
                                                                                                                                        ccAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgc  >  2:328955/1‑151 (MQ=255)
                                                                                                                                        ccAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcg   <  2:504096/150‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                               
CAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGC  >  NC_000913/2001768‑2002054

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑