Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,684,749	0	A	C	43.6%	85.9 / 14.3	55	D164A (GAC→GCC)	tus	inhibitor of replication at Ter, DNA‑binding protein
Reads supporting (aligned to +/- strand):  ref base A (26/5);  new base C (0/24);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 7.81e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCACATCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGAGC  >  NC_000913/1684602‑1684898                                                                                                                                                    |                                                                                                                                                      aGCACATCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGAccc                                                                                                                                                    >  2:985566/1‑151 (MQ=255)  gCACATCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGAcccc                                                                                                                                                   <  1:960332/151‑1 (MQ=255)    acaTCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGc                                                                                                                                                 >  1:369144/1‑151 (MQ=255)        cAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACt                                                                                                                                             >  2:250780/1‑151 (MQ=255)         aaTAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACtt                                                                                                                                            >  1:692156/1‑151 (MQ=255)             aaCTCAAGCCCCCGTTCGAGCATATCGTCAGGTTTAAATCAGACCCCCCCCCCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCCCCTTTAATTCTTCCCCCACGCCCCCCTTTCTGCACGCCCCCGCCACTTTAc                                                                                                                                         <  1:384578/150‑1 (MQ=255)              aCTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGc                                                                                                                                       >  2:421578/1‑151 (MQ=255)                  aaGCCCCCGTTCGAGCATTCCGTCACGTTTAAACCAGACCCCCCCCCCGCGGCACTTTTTGAATGGGTGCTTCGTCATTTGCCGGGGCTGACCCCCCTTATTGCTTCCCGCACGCTCACCGTTCGGCCCGACCCCGCCACTTTACGCt                                                                                                                                      <  1:334047/148‑1 (MQ=255)                      ccACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTttggttg                                                                                                                               >  2:991009/1‑151 (MQ=255)                       cccGTTCGACCATATCGCCCCGGTTGAATCAGACCCCCCCCCCGCGCCACGTTTTGAATGGGTGCATCGTCTTTTGCCGGGCCTGATCCCCCTTATTGCTTCCCGCACGCTCCCCTTTCTGCCCGCCCCCGCCACTTTACGCTttggttgg                                                                                                                              <  1:79959/149‑1 (MQ=255)                           ttCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCt                                                                                                                           >  1:540022/1‑150 (MQ=255)                            gcGAGCTTACCGTCCGGGTTAAATCAAACCCCCCCCCCGCGGCACTTTTTGAGGGGGGGCATCGTCATTTGCGGGGGCTGACCCCCCTTAATGTTTCCCGCCCGCTCCCCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCta                                                                                                                          <  1:931799/149‑1 (MQ=255)                             cGAGCATAGCGCCACGGTGGAATCAAAACCCCCCCCCGGGGCACGTTTGAAAGGGGTGCATCGTCATTTGCCGGGGCTGATCCCCCTTAATGCTTACCGCACGCTCACCTTTCGCCACGACCCCGCCACTTTACGCTTTGGTTGGGCtaa                                                                                                                         <  2:65786/150‑1 (MQ=255)                             cGAGCATACCGCCACGGTTGAATCAGAACCCCCCCCCGCGGCGCTTTTTGAAGGGGTGCATCGTCTTTTGCCGGGGCTACTCCCCTTTAATGCTTCCCGCGCGCTCCCCTTTTTGCCCGCCCCCGCCACTTTACGCTTTGGTTGGGc                                                                                                                            <  1:988643/147‑1 (MQ=255)                               aGCATTTCGTCGCGGTTAAATCAGACCCCCCCCCCGCGGCTCTTTTTGAATGGGTGCATCGTCTTTTGCCGGGGCTGATCCCCCTAATTGTTTCCCGCACGCTCCCCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCtaa                                                                                                                         <  1:124804/148‑1 (MQ=255)                                gCATATCGTCACGGTTGAATCAGAACCCCCCCCCGCGGCACTTTTTGAATGGGTGCATCGTCATTGGCCGGGGCTGATCCCCCTTAATGCTTCCCGCCCGCTCCCCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCtaataa                                                                                                                      <  2:45892/150‑1 (MQ=255)                                    atCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACat                                                                                                                  >  2:121844/1‑150 (MQ=255)                                         cACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCAtt                                                                                                            >  2:792690/1‑151 (MQ=255)                                         cACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCAtt                                                                                                            >  1:575615/1‑151 (MQ=255)                                          aCGGTTAAACCAAACCCCCCCCCCGCGGCACTTTTTGAAGGGGTGCATCGTCTTTGGCGGGGGCTGACCCCCTTTAATGCTTCCCGCCCCCTCCCCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCAtt                                                                                                            <  2:593806/150‑1 (MQ=255)                                                     agacccccccccCGCGGCTCTTTTTGAATGGGTGCATCGTCTTTTGCGGGGGCTGATCCCCCTTAATGCTTACCGCCCGCTCCCCTTTCTCCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTAc                                                                                                  <  1:761549/143‑1 (MQ=255)                                                     aaacccccccccCGCGGCATGTTTTGAATGGTTGCATCGTTATTTGCGGGGTTTGTTCCCCTTTAATGCTTCCCCCACGCTCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTa                                                                                                   <  2:1014688/142‑1 (MQ=255)                                                         ccccccccCGCGGCATGTTTTGAAGGGGTGCATCGTCATTTGCGGGGGCTGATCCCCTTTAATGCTTCCCGCCCGCTCCCCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGtg                                                                                            <  2:384277/149‑1 (MQ=255)                                                                ccGCGGCCCGTTTTGAATGGGTGCATCGTCTTTTGCCGGGGCTGACCCCCCTTATTCCTTACCGCACGCCCACTTTTCTCCCCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGt                                                                                     <  1:1027/151‑1 (MQ=255)                                                                ccGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGt                                                                                     >  1:978274/1‑151 (MQ=255)                                                                 cgcgGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTc                                                                                    >  2:467532/1‑151 (MQ=255)                                                                          ttttGAGTGGTTGCATCGTCATTTGCCGGGGCTGCCCACCTTTAATGCTTCCCGCATTCTCACCTTTCTGCCCTCCTCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGcac                                                                             <  1:901339/149‑1 (MQ=255)                                                                           tttGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGc                                                                          >  2:279561/1‑151 (MQ=255)                                                                            ttGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCt                                                                         >  2:102714/1‑151 (MQ=255)                                                                             tGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTg                                                                        >  2:180725/1‑151 (MQ=255)                                                                               aaggggTGCATCGTCATTTGCCGGGGCTGATCCCCTTTAATGCTTCCCGCTCGCTCCCCGTTCTCCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTg                                                                        <  1:151200/146‑1 (MQ=255)                                                                               aaTGGGTGCATCGTCTTTTGCCGGGGCTGACCCCCTTTAATGCTTCCCGCCCGCTCCCCTTTCTGCCCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCt                                                                         <  1:854737/148‑1 (MQ=255)                                                                                       cATCGTCATTTGCCGGGGCTGATCCCCCTTAATGCTTCCCGCCCGCCCCCCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGcc                                                              <  2:138986/151‑1 (MQ=255)                                                                                        aTCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCt                                                             >  2:826447/1‑151 (MQ=255)                                                                                             cATTTGCCGGGGCTGATCCCCCTTAATGCTTCCCGCCCGCTCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGaaa                                                         <  2:315076/150‑1 (MQ=255)                                                                                                ttGCCGGGGCTGACCCCCCTTAATCCTCCCCCCACGCCCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATc                                                       <  2:592428/149‑1 (MQ=255)                                                                                                   cgggggCTGACCCCCCTTAATGCTTCCCGCCCCCTCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATcacc                                                    <  1:1007321/147‑1 (MQ=255)                                                                                                     ggggCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACg                                                 >  2:417403/1‑150 (MQ=255)                                                                                                            aTCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCg                                         >  1:76397/1‑151 (MQ=255)                                                                                                               ccccTTAATGCTTCCCCCCCGCTCCCTTTTCTGCCCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCg                                         <  1:898131/147‑1 (MQ=255)                                                                                                                cccTTAATGCTTCCCGCCCCCTCCCCTTTCTCCACCCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCa                                       <  2:518400/149‑1 (MQ=255)                                                                                                                 ccTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCg                                    >  2:678093/1‑151 (MQ=255)                                                                                                                           tACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGAcgcgcg                          >  1:432476/1‑151 (MQ=255)                                                                                                                            accgcactttttccGCTCTCCACGCCACCGCCACTTTACGCTTTGGTTGGTCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAGTCCCCACGCAGTGTCGCAc                                      <  1:807429/126‑1 (MQ=255)                                                                                                                             ccGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGAcgcgcg                          >  2:434941/1‑149 (MQ=255)                                                                                                                             ccGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGAcgcgcg                          >  1:239583/1‑149 (MQ=255)                                                                                                                                  cccTCCCCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTg                   <  2:923519/149‑1 (MQ=255)                                                                                                                                       cccGTTCTGCCCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCaa               <  2:136891/149‑1 (MQ=255)                                                                                                                                       cccGTCCCGCACACCCCCGCCACTTTACGCGTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCCCGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGc                 <  2:175193/147‑1 (MQ=255)                                                                                                                                        ccGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAg             <  1:1035351/151‑1 (MQ=255)                                                                                                                                          gTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGa            >  1:475300/1‑150 (MQ=255)                                                                                                                                             cTGCACGAACCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAAc        >  1:912501/1‑151 (MQ=255)                                                                                                                                                 aCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACt       <  1:421569/148‑1 (MQ=255)                                                                                                                                                  caaCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGa    <  2:160707/148‑1 (MQ=255)                                                                                                                                                   gACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGAGc  >  1:102125/1‑151 (MQ=255)                                                                                                                                                   gACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTCGCAAAGAAAACTGGAGc  >  1:777494/1‑151 (MQ=255)                                                                                                                                                    aCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGa    <  1:249392/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                      AGCACATCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGCTGATCACCCTTAATGCTTACCGCACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGAGC  >  NC_000913/1684602‑1684898

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑