Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,601,176	0	T	C	46.3%	46.1 / 37.4	54	E304G (GAA→GGA)	ftsX	putative ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base T (28/1);  new base C (0/25);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.54e-14
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACGTTA  >  NC_000913/3601029‑3601322                                                                                                                                                      |                                                                                                                                                   tattCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCg                                                                                                                                                 >  2:151173/1‑151 (MQ=255)          gTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAAccgccg                                                                                                                                        >  2:673872/1‑151 (MQ=255)                                       aaGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGAc                                                                                                           >  1:242237/1‑151 (MQ=255)                                        aGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGCG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCt                                                                                                              >  2:184083/1‑147 (MQ=255)                                          ccccgccccccccaaGCAAACCACCGACCATCCCAGCAACAATAGCAGGCATTCATCAAATAAAAACCCTTTAATAACAATCTCCTTCCCAAAAC‑CCTGTC‑CCCCTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTc                                                                                                               <  2:265903/130‑1 (MQ=255)                                          ccccGCTGCCCCCCACCCAATCACCGAGCATCCCAGCAGAAATAGCAGGCTTTCATCAAATAATAAGCCATTGATATAAACCTTCGTCCCAAAAC‑CCTGTC‑CCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACa                                                                                                          <  1:647414/146‑1 (MQ=255)                                          ccccGCTCCCCCCCACCCAATCATCGACCATCCCAGCAGAAATAGCAGGCATCCATCAAATAATAAGCATTTGATATCAACCTCCGTCCCAAAAC‑CCTGTG‑CCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACaa                                                                                                         <  1:620526/147‑1 (MQ=255)                                           cACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACaaa                                                                                                        >  1:346152/1‑150 (MQ=255)                                             cGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAAtt                                                                                                     >  1:530979/1‑151 (MQ=255)                                              gCTGCCCCCCAGCCAATCAGCGAGCATCCAAGCAAAAATAGCGGGCTTTATTCAAATGATAAGCCATTAATA‑CAAACCTCCGTCCGAAAACCCTGTC‑CCCCTCCCACAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAAt                                                                                                      <  1:859601/149‑1 (MQ=255)                                                  ccccccACCAAATCACCGAAAATCCCAGCAGAAAAAGAGGGCATCCATCAATTGAAAACCCTTTAATACCAACCTTCTTCCCAAAAC‑CCTGGC‑CCCCTCCCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTaa                                                                                                   <  1:232333/145‑1 (MQ=255)                                                  ccACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATg                                                                                                 >  1:499092/1‑150 (MQ=255)                                                   cACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGac                                                                                               >  2:867206/1‑151 (MQ=255)                                                       cAGCAAACCACCGAGCATCCCAGCAGCAATAGCAGGCATTCATCAAATGATAAGCTTTTAATATCAACCTTCGTCCCGAAAC‑CCTGTC‑CCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGacaac                                                                                            <  1:452731/150‑1 (MQ=255)                                                          ccAATCACCGAGCAAACCAGAAGCAATAGCGGGCATACATCGAAGAAAAACCCTTTAATA‑CAAAACTCCTTCCAAAAACCCTGTC‑CCCCTCCCAAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAAt                                                                                         <  2:553624/150‑1 (MQ=255)                                                            aaTCAGCGACCATCCCAAAAACAATGGCGGGCATACATCGAATAATAAGCCATTAATACCAATCTTCGTCCAAAAAC‑CCTGTC‑CCCCTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGacaaca                                                                                           <  2:673096/146‑1 (MQ=255)                                                               catcGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGcc                                                                                    >  1:328768/1‑150 (MQ=255)                                                                accGAGCATACCAGCAGCAATAGCAGGCATTCATCAAATGAAAAGCAATTGATACAAATCTTCGTCCCAAAAC‑CCTGTC‑CCCCTCCCACAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATgcgc                                                                                     <  2:104025/146‑1 (MQ=255)                                                                 tcGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATgcg                                                                                      >  2:973588/1‑146 (MQ=255)                                                                  cGAGAATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGa                                                                                 >  2:100802/1‑150 (MQ=255)                                                                      cATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATc                                                                            >  2:458394/1‑151 (MQ=255)                                                                       atcccAACAGAAATAGCAGCAATACATCAAATGATAAGCAATTAAAATCAACCTTCCTCCCAAAAC‑CCTGTC‑CCCCTCCACCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAg                                                                                  <  2:775251/141‑1 (MQ=255)                                                                       ataccaaaaaaaaTAGCAGCCTTTCATCGAATGAAAAGCCATTGATACCAACCTTC‑TTCCCAAAA‑CCCTTGCCCCCTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGaaaa                                                                              <  1:643170/137‑1 (MQ=255)                                                                          ccAGCAGAAATAGCAGGCTTTCACCGAATAATAAGCATTTAATAACAACCTTCGTCCCAAAAC‑CCTGTC‑CCCCTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAAt                                                                             <  1:764603/146‑1 (MQ=255)                                                                               agcaATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTg                                                                   >  1:544090/1‑151 (MQ=255)                                                                                  aaTAGCAGTCATTCATCAAATGAAAACCTATTAATATAAACCTTCGTCCCAAAAC‑CCTGTC‑CCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCcagc                                                                       <  1:548743/144‑1 (MQ=255)                                                                                  aaTAGCAGACTCTCATCAAATGAAAACCCATTAATA‑CAAACCTCCTTCCCAAAA‑CCCGGGCCCCCTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGt                                                                    <  2:419573/147‑1 (MQ=255)                                                                                      gCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAAAGACAACAATGCGCCAGAAAATCCCAGCAGTGCGccacc                                                            >  1:715240/1‑151 (MQ=255)                                                                                         ggCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCAt                                                          >  1:214463/1‑150 (MQ=255)                                                                                          ccttccATCAAATAATACCCCTTTAATAACAACCTCCTTCCCAAAAC‑CCTGTC‑CCCCTCCCGCACCCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATa                                                         <  2:102108/145‑1 (MQ=255)                                                                                                aTCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAAc                                                  >  1:391827/1‑151 (MQ=255)                                                                                                aTCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAAc                                                  >  1:347176/1‑151 (MQ=255)                                                                                                aTCGAATAATAACCCTTTGAAACAAAACTTC‑TTCCAAAAACCCTGCC‑CCCCTCCCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGa                                                    <  2:728896/149‑1 (MQ=255)                                                                                                aTCGAATAAAACGCTTTTAATAACAACCTTCGTTCCGCAAC‑CCTGTG‑CCACTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAAc                                                  <  1:563401/151‑1 (MQ=255)                                                                                                   gAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACggg                                               >  1:121688/1‑151 (MQ=255)                                                                                                    aataatAACCCATTGTTATCAACCTTCGTCCCAAAAC‑CCTGTC‑CCCCTCCCACAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAgg                                                     <  2:242221/144‑1 (MQ=255)                                                                                                    aagaaaaaccatttaatacCAAACTTCTTCCCAAAAC‑CCTGTC‑CCCCTCCCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGgc                                              <  2:363189/136‑1 (MQ=255)                                                                                                          aacccATTGATACCAACCTTCTTCCCAAAAC‑CCTGGC‑CCCCTCCCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGgcg                                             <  2:527215/143‑1 (MQ=255)                                                                                                                ttGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATc                                  >  1:691304/1‑151 (MQ=255)                                                                                                                ttGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATc                                  >  1:530423/1‑151 (MQ=255)                                                                                                                    tatCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATc                              >  1:165426/1‑151 (MQ=255)                                                                                                                     atCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCt                             >  2:466767/1‑151 (MQ=255)                                                                                                                        aaaCTCCGTCCCAAAAC‑CCTGCC‑CCCCCCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCt                             <  2:295563/148‑1 (MQ=255)                                                                                                                          aCTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGc                        >  1:619431/1‑151 (MQ=255)                                                                                                                              cGTCCCGAAAC‑CCTGTG‑CCACTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCAc                      <  1:660146/149‑1 (MQ=255)                                                                                                                                  caaaaac‑CCTGGC‑CCACTCCCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCa                <  1:294238/148‑1 (MQ=255)                                                                                                                                    gAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGt              >  2:121404/1‑151 (MQ=255)                                                                                                                                     aaac‑CCTGTC‑CCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCa                <  1:77094/148‑1 (MQ=255)                                                                                                                                     aaac‑CCTGTC‑CCCCTCCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAg               <  1:909033/149‑1 (MQ=255)                                                                                                                                     aaac‑CCTGCC‑CCCCTCCCACAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGtt             <  2:877487/151‑1 (MQ=255)                                                                                                                                        a‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCt          >  2:978062/1‑151 (MQ=255)                                                                                                                                             gtg‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTAc      >  2:13271/1‑151 (MQ=255)                                                                                                                                                  cACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACGtt   >  1:258377/1‑150 (MQ=255)                                                                                                                                                   aCTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACGTTa  >  2:234343/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                   TATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCCGAAAA‑CCTGTG‑CCACTTCCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACGTTA  >  NC_000913/3601029‑3601322

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑