Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,233	0	G	A	41.1%	56.5 / 30.5	57	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (26/7);  new base A (0/23);  total (26/31)
Fisher's exact test for biased strand distribution p-value = 7.85e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

GAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGC  >  NC_000913/1222094‑1222375                                                                                                                                            |                                                                                                                                               gAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGtt                                                                                                                                     <  1:198123/151‑1 (MQ=255) gAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGtt                                                                                                                                     >  2:504866/1‑151 (MQ=255)      aGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGa                                                                                                                                 >  2:748940/1‑150 (MQ=255)       gATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATc                                                                                                                               <  2:933870/151‑1 (MQ=255)                 gTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGtt                                                                                                                       >  1:491397/1‑149 (MQ=255)                 gTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGtt                                                                                                                       >  1:254004/1‑149 (MQ=255)                           ggAAATTAAACTTGGCGTAAATGGAAACCTGAATCCAGCCGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATTTAAGTTCTGATACCGCCGTTAGCTAAAAAAcc                                                                                                           >  2:1003951/1‑151 (MQ=255)                                 tAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGTAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcg                                                                                                     >  2:702135/1‑151 (MQ=255)                                 tAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcg                                                                                                     >  2:1067514/1‑151 (MQ=255)                                  aaaCTTGGCTTAAAGGGCACCCGAAATCCGGCGGCCAGCGTCTGGGGAATGGGGGCGTGCGGCTGGGTGATAATGTCTAAAAGGACCCCGAGGTGATGGGGGCCTTAAAATAAAATTTCGAACCCCGCCGTTAGCTAAAAAACCGcgtc                                                                                                      <  1:775771/149‑1 (MQ=255)                                   accTTGGCGAAAATGCAAACCTGAACCCAGGGCCCAGCGTCGGGGGAATGTGGGCGTGAAGCTGGGTGATAATGGCTAAAATGCCCCCGCAGTGATGGTGGGCCTAAAAAATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTa                                                                                                   <  1:1015365/149‑1 (MQ=255)                                   aaCTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcgt                                                                                                    >  2:649497/1‑150 (MQ=255)                                             taaTGGCAACCTAAACCCAGGGGCCGGTGTCGGGGAAAGGTGGGCGTGCAGTGGGGTGATAGTGACTAAAATGACCCGGCAGTGTGGGGGGGCCTAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAc                                                                                          <  1:968649/149‑1 (MQ=255)                                             aaaTGGCACCCTGAACCCAGCGGCCGGCGTGGGGGGAATGGGGGCGTGAAGTTGGGTTATAATGGCTAAAATGCCGCCGCAGTGATGGTGGCCCTAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAc                                                                                          <  1:603463/150‑1 (MQ=255)                                             aaaGGGCAACCTAAACCCGGCGGCCGGCGTCTGGGGAATGGGGGCGTGCGGCTGGGTGATATTGGCTACAACCCCCCCGCATTGTTGGGGGGCCTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcg                                                                                         <  2:108613/151‑1 (MQ=255)                                               aTGGCAACCTGAACCCGGCGGCCAGCGTGTGGGGAATGGGGGCGTGCAGCGGGGTGATAATGCCTAAAATGCCCCCGCAGTGATGGGGGCCCTAAAATAAAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgcg                                                                                       <  1:725875/151‑1 (MQ=255)                                                 ggCAACTTAAACCCAGCGGCCAGCGTCTGGGAAAGGTGGGCGTGAAGGTGGGTAATAAGGCATACAATGACCCTGAGGTGGTGGGGGGCCTGAAAAAAATTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgcg                                                                                       <  1:158364/149‑1 (MQ=255)                                                      ccTGAACGCGGCGGCCAGCGTCTGGGGAGGGGGGGGGGGGAGGGGGTTAATATGGGCTAAAATCCCACGGCAGTGGGGGGGGCCCGGAAAAAAAAGTCCGACTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCgg                                                                                      <  2:964017/145‑1 (MQ=255)                                                      ccTGAACCCAGGGCCCAGCGTGTGGGGATGGTGGGCTGGCAGCGGGGTGAAATTGGCTCAAAGGCCCCCGCAGTGATGGTGGGCCAGAAATTTAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat                                                                                 <  2:928203/150‑1 (MQ=255)                                                       cTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACatat                                                                               >  1:321690/1‑151 (MQ=255)                                                       cTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACatat                                                                               >  1:856577/1‑151 (MQ=255)                                                          aacccggCGGCCAGCGTCGGGGGAAGGGGGGCGTGCGGCTGGGTGAAAATGGCTAAAATGACCCCGAAGTGATGGGGGGCCTAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaa                                                                            <  1:299616/145‑1 (MQ=255)                                                           aTCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaa                                                                            >  2:762032/1‑150 (MQ=255)                                                           aTCCAGCAGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaa                                                                            >  1:684487/1‑150 (MQ=255)                                                                  ggCCGGCGTCGGGGGAAGGGGGGGGTGCAGGGGGTTAATAATGGCTACAAAAACCCCGCAGTGATGGTGGGCTTGAATTAAAGGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAAtattat                                                                     <  2:170492/150‑1 (MQ=255)                                                                    ccctcGTCTGGGGATCTTGTGGGTGAAGGTGGTGTATAAGGGCCACAATCACCCGTGAGTTGTGTTGGGCATTAATTATAAGTGCTGCTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttt                                                                  <  2:738733/147‑1 (MQ=255)                                                                     cAGCGTGTGGGGATGGGGGGCGTGCGGCTGGGTAATAATGGCTACAATGACCCCGCAGTGATGGTGGGCTTAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttt                                                                  <  2:16034/150‑1 (MQ=255)                                                                      cggtggtGGGGAATGTGGGCTTGTATTTGGTTGAAAATGGCTACAAGGACCCCGCATTTGTGGTGGGTGTAAAATTTATTTTTTGTTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAAGCGGTACATATGAAATATTAtttttt                                                                <  2:72244/145‑1 (MQ=255)                                                                      aGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGGTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttttt                                                                >  1:262617/1‑151 (MQ=255)                                                                      aGCGTCTGGGGAATGTGGGCGTGCAGCTGGGGGATAATTGCTACAATGACACCCCAGGGGTGGGGGGCCTGGAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCCCGTCGTATTTATCGACGCGGGACATATGAAATATTAtttttt                                                                >  1:1017966/1‑151 (MQ=255)                                                                       gCGTCTGGGGAATGGGGGTGTGCGGGGGGGTAATATTGGCTACAATGACCCCGCAGTGATGGTGGGCCTAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAAtatt                                                                       <  2:467726/143‑1 (MQ=255)                                                                         ggtgggggATGGTGGGCGTCGAGGGGGGTTATAATGGCTACAATGACCCTGAAGTGATGGTGGGCGTAAAATTTAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGc                                                              <  2:443065/146‑1 (MQ=255)                                                                         gTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGcc                                                             >  1:626908/1‑151 (MQ=255)                                                                             ggggATTGGGGGCGTGCGGTTGGTTAATATTGATAACAATAACCCATAATTGATGTTGGCCCTAAAATATATTTTTGAATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTg                                                               <  2:929301/145‑1 (MQ=255)                                                                             ggggAATGGGGGGGTGAAGCGGGGTGATAATGGCAAAAATGACCCCGGGGGGATGGGGGCCCTAAAATATAATTTTTGTCCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttt                                                                   <  1:986822/141‑1 (MQ=255)                                                                              gggATTGGGGGCGTGCAGCGGGGTGATAATGGCTACAAGGCCCCCGCTGTGATGGTGGGCTTAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAg                                                        <  1:856830/151‑1 (MQ=255)                                                                              gggAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGAt                                                          >  1:769963/1‑149 (MQ=255)                                                                               ggAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGc                                                       >  2:287357/1‑151 (MQ=255)                                                                                    gggggCGTGCAGCTGGGTGATAATGGCTACAATGACCCCGCAGTGATGGGGGGCCTAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCa                                                      <  1:227888/145‑1 (MQ=255)                                                                                          gTGCGGCGGGGTAATAAGGACTACAATGCCCCCGCAGTGAGGGTGGGCTTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtg                                             <  1:51703/150‑1 (MQ=255)                                                                                          gTGCAGCTGGGTAATAATGGCTAAAATGACCCCGAAGTGATGGTGGTCTTAAAATATAGGTTCTGTTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtgt                                            <  1:850957/151‑1 (MQ=255)                                                                                           tGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGtc                                           >  2:73916/1‑151 (MQ=255)                                                                                               gtgggttaaTAAGGCCTAAAATGCCCCCGAAGTGATGGTGGGCTTAAAATATAGGTTTTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGtcat                                         <  1:11943/141‑1 (MQ=255)                                                                                                  gggTGAAAATGGCTAAAATGCCCCCGCAGTGAGGGGGGGCCTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAAt                                     <  2:170554/150‑1 (MQ=255)                                                                                                   ggtaaaattGGCTAAAATGCCCCCGAAGGGGTGGTGGACTGAAAATATAGTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgt                                              <  2:580119/132‑1 (MQ=255)                                                                                                             gCTAAAATGACCCCGCGGTGATGGTGGGCCTGAAATATAAGTCCTCATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCaa                         <  2:262593/151‑1 (MQ=255)                                                                                                                   atgcccccGCAGTGATGGTGGGCCTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCAt                   <  1:227752/145‑1 (MQ=255)                                                                                                                       ccccgaggTGAGGGTGGGCCTAAAATATAATTTTGGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTg                <  2:854894/143‑1 (MQ=255)                                                                                                                        acCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCg              >  2:1069763/1‑151 (MQ=255)                                                                                                                             aGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCt         >  1:590674/1‑151 (MQ=255)                                                                                                                              gTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCtt        >  1:994446/1‑151 (MQ=255)                                                                                                                               tGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt       >  2:87891/1‑151 (MQ=255)                                                                                                                               tGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt       >  2:487819/1‑151 (MQ=255)                                                                                                                                gATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt       >  2:598733/1‑150 (MQ=255)                                                                                                                                   ggtggGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgcg   >  1:841740/1‑151 (MQ=255)                                                                                                                                   ggtggGCCTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAg     <  2:207138/149‑1 (MQ=255)                                                                                                                                    gtggGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgcgc  >  1:220950/1‑151 (MQ=255)                                                                                                                                            |                                                                                                                                               GAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGC  >  NC_000913/1222094‑1222375

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑