Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,233	0	G	A	40.5%	52.3 / 19.8	42	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (22/3);  new base A (0/17);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 4.48e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01

GTGTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCG  >  NC_000913/1222083‑1222374                                                                                                                                                         |                                                                                                                                              gtgtGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTg                                                                                                                                               <  2:801410/151‑1 (MQ=255)     gAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAat                                                                                                                                           <  1:931865/151‑1 (MQ=255)        aGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAatat                                                                                                                                         >  1:872359/1‑150 (MQ=255)            gAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGtt                                                                                                                                    >  2:327356/1‑151 (MQ=255)                   aTGGGGCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATcc                                                                                                                             <  1:871444/151‑1 (MQ=255)                        gCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCccgccg                                                                                                                        >  1:289659/1‑151 (MQ=255)                               aTTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCt                                                                                                                  >  2:965944/1‑150 (MQ=255)                                tttGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑GCACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTa                                                                                                                 >  1:498289/1‑150 (MQ=255)                                tttGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTa                                                                                                                 >  2:822434/1‑150 (MQ=255)                                      ggAAAATAAACTTGGGCGAAAAGGCCACCCAAAACCCGGCGGCCGGCTTGTGGGGAATGTGGGGGTGCGGGTGGGTAAAAATGGCTACAATC‑CCCCGGCAGTGAGGGGGGGCAAAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAAc                                                                                                           <  2:792711/151‑1 (MQ=255)                                       gAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACcg                                                                                                         >  2:879004/1‑151 (MQ=255)                                            tAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcg                                                                                                    >  1:897950/1‑151 (MQ=255)                                                cTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTAtt                                                                                                >  2:928666/1‑151 (MQ=255)                                                       gaaaaTGGAACCCTGAACCCAGCGGCAAGCGTCGGGGGAATGGGGGCGTGCAGCTGGGTGAAAATGGCAACAAGG‑CCCCCGAAGTGATGGGGGGCCTAAAATAAAAGTTTTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATc                                                                                            <  1:841190/147‑1 (MQ=255)                                                         aaaTGGCACCCTGAACCCAGCGGCCAGCGTCGGGGGAAGGTGGGCGTGCGGGGGGGTAAAAAGGGCTAAAATG‑ACCCCGAGGTGAGGGGGGGCCTAAAATAAAAGTTCTGCGCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCg                                                                                           <  2:607020/148‑1 (MQ=255)                                                            tGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGCATGTGGGCGTGCAGCTGGGCGATAATGGCTACAATG‑ACACCGCAGTGATGGTTGGCCTGAAATATAAGTTCTGATCCCGCCGATAGCTAAAAAACCGCGGCGTATTCATCGAcg                                                                                        >  2:928974/1‑148 (MQ=255)                                                                accttaaccccAGGGGCCGGCGTGTGGGGAGGGGGGGGGTGCAGCGGGGTGATAGGGTCTACAAGG‑ACCCCGCGGGGATGGTGGGCTTAAATTATAAGTTGTGAACCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACa                                                                                 <  2:327263/142‑1 (MQ=255)                                                                 cccTGAACCGAGCGGCCAGCGTTGGGGGATGGTGGGCGGGCAGTTGGTTAATAATGGCTACATTG‑ACCCCGGAGTGTGGGGGGGCTTAAAATATAATTTTGGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat                                                                                <  2:555086/150‑1 (MQ=255)                                                                    tGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg                                                                             >  1:175384/1‑151 (MQ=255)                                                                      aacccggCGGCCAGCGTCGGGGGAAGGGGGGGGGGCGGTTGGTTAATAATGGCTACAATG‑ACCCCGCAGTGATGGGGGGCCGAAAATAAAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaa                                                                           <  2:455301/145‑1 (MQ=255)                                                                      aacccAGCGGCCGGCGTGGGGGAAATGGGGGCGTGCGGCTGGGTAATAATGGCTACAATG‑ACCCCGCAGTGATGGTGGGCTTAAAATAAAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaa                                                                           <  2:380629/148‑1 (MQ=255)                                                                         ccAGCGCCCGGGTTCTGGGGATTGGGGGCGTGCGGGGGGGT‑AAAAAGGCTTCAATGTACCCCGAAGGGATGGGGGCCCTAAAATATAATTGCTCATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATg                                                                             <  1:167409/146‑1 (MQ=255)                                                                           aGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGGACATATGAAAtatt                                                                      >  1:803870/1‑151 (MQ=255)                                                                            gcgcCCGGCGTGGGGGGAATGGGGGGGGGCAGTTGGGTAATAAGGGCTAAAAAG‑CCCCCGGGGTGTGGGGGGGCATAAAATAAAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAatat                                                                       <  2:838956/149‑1 (MQ=255)                                                                                  atagtggggggAATGTGGGGGGCAAGTGGGGTAATAAGGGCTAAAATA‑CCCCCGAGTTAAGGGTGGAAATAAAATATATGTTCGGTCCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttttt                                                               <  2:733288/144‑1 (MQ=255)                                                                                  agcttgtGGGAAATGTGGGCGTGCAGGTGGGTGACAAGGTCTACAACG‑ACACCCCGGTAGTGGTGGTCAAAAAATAAATGTTTTGCTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttt                                                                 <  1:578151/143‑1 (MQ=255)                                                                                   gCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTg                                                              >  1:139800/1‑151 (MQ=255)                                                                                       cTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCg                                                           >  1:7642/1‑150 (MQ=255)                                                                                        tGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGAt                                                         >  1:56716/1‑151 (MQ=255)                                                                                         ggggatttggggCGTGAACCTGGGTAATAGTGGCTACAATG‑ACACCGAAGGGTTGGGGGCCCTAAAATAAAATTTTTGGTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttt                                                                 <  1:652376/133‑1 (MQ=255)                                                                                         ggggAATGGGGGGGTGCAGCTGGGGGATAATGGCTACAATG‑CCCCCGCGGTGATGGTGGGCCTAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATa                                                        <  1:869499/151‑1 (MQ=255)                                                                                         ggggAATGGGGGGGTGCAGCGGGGTAAAAATGGCTAAAATG‑ACCCCGCAGTGTTGGGGGGCCAAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGAt                                                         <  1:765426/150‑1 (MQ=255)                                                                                         ggggAATGGGGGCGTGCGGCTGGGTGAAAATGGCTACAATG‑CCCCCGAAGTGGTGGTGGGCCAAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATa                                                        <  1:344232/151‑1 (MQ=255)                                                                                                gggggCGTGCGGGTGGGTGAAAAGGGCTAAAATG‑ACCCCGCAGTGAGGGGGGGCAAAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACg                                                   <  1:770860/147‑1 (MQ=255)                                                                                                  gggggggcgggtGGGTGAAAATGGCTAAAAGG‑CCCCCGGAGTGAGGGTGGGCCTGAAAAAAAATTTCTATCCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATg                                               <  1:428332/140‑1 (MQ=255)                                                                                                                       tGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATc                          >  2:754307/1‑151 (MQ=255)                                                                                                                         gCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCa                         >  1:444967/1‑150 (MQ=255)                                                                                                                         gCTAAAATC‑ACCCCGAAGTGATGGTGGGCCTAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCaa                        <  2:578099/151‑1 (MQ=255)                                                                                                                            aCAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAAc                       >  1:4607/1‑149 (MQ=255)                                                                                                                                          aGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCt        >  1:37512/1‑151 (MQ=255)                                                                                                                                            tGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt      >  2:395211/1‑151 (MQ=255)                                                                                                                                             gATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt      >  1:352285/1‑150 (MQ=255)                                                                                                                                                ggtggGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgcg  >  2:753672/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                              GTGTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTT‑GGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATG‑ACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCG  >  NC_000913/1222083‑1222374

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: ‑