Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,233	0	G	A	42.2%	40.6 / 25.9	45	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (19/7);  new base A (0/19);  total (19/26)
Fisher's exact test for biased strand distribution p-value = 2.93e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACC  >  NC_000913/1222090‑1222380                                                                                                                                                 |                                                                                                                                                     aGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGAGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGGGATAATGGCTACAATGACACCGCAGCGATGGTGGGCCT‑G‑AAata                                                                                                                                                >  1:226541/1‑149 (MQ=255)  gTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAAtata                                                                                                                                              >  2:39447/1‑150 (MQ=255)    cGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGt                                                                                                                                           <  1:407370/151‑1 (MQ=255)         aaGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGAGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGa                                                                                                                                      <  2:226628/151‑1 (MQ=255)                   gAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGtt                                                                                                                            >  1:782875/1‑151 (MQ=255)                        aTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGCGATAATGGCTACAATGACACCGCAGTGACGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGc                                                                                                                         >  2:43204/1‑149 (MQ=255)                               ggAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAAcc                                                                                                                >  2:77491/1‑151 (MQ=255)                                 aaaTAAAACTGGGCGAAAAGGGAACCCTGAACCCGGGGGCCAGCGTCGGGGGAAGGTGGGCGTGCAGTTGGGTAATAAGGGCTAAAATGACCCCGCGGTGATGGTGGGACT‑G‑AAATAAACGTTCTTTCCCCGCCGTTAGCTAAAAAACcgc                                                                                                              <  1:1004481/151‑1 (MQ=255)                                 aaaTAAAACTGGGCAAAAAGGGCACCCTGAACCCAGCGGCCAGCGTGGGGGGAGTGTGGGCGTGCAGCGGGGTGATAATGGCTAAAATGACCCCGAGGTAATGGGGGGCCT‑A‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACcgc                                                                                                              <  1:61313/151‑1 (MQ=255)                                       aaCTGGGCGTAAAGGGCACCCTAAACCCAGCGGCCGGCGTGGGGGGAATGGGGGGGTGCAGCGGGGTAATAATGCCTACAATGACCCCGAAGTGAGGGGGGGCCT‑A‑AAATATAGTTTCTAATCCCGCCGTTAGCTAAAAAACCGcgtcg                                                                                                          <  1:468613/149‑1 (MQ=255)                                         cTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTAtt                                                                                                      >  2:706406/1‑151 (MQ=255)                                            ggggaaaaTGCCACCCTGAATCCAGCGCCAGGCGTCGGGGGAAGGTGGGGGTGCAGCTGGGTAATAATGCCAACAACGCCCCCGCGGTAATGGGGGGCCT‑A‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCa                                                                                                    <  1:647043/145‑1 (MQ=255)                                            ggCGTAAATGGCAACCTGAACCCAGCGGCCGGCGTTTGGGAAATGTGGGGGTGCAGGGGGGTAATAATGGCTACAATGACCCCGCAGTGATGGTGGGCCT‑A‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTc                                                                                                     <  2:711351/149‑1 (MQ=255)                                            ggCGAAAATGGCAACCTAAATCCGGGGGCCGGCGTGTGGGGAAGGGGGGGGTGCAGGTGGTTGATAATGGCTAAAATGACCCCGAGGTGAGGGGGGGCCT‑A‑AAATAAAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCa                                                                                                    <  1:457083/150‑1 (MQ=255)                                             gCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCT‑AAAAACCGCGGCGTATTTATCg                                                                                                 >  2:112068/1‑151 (MQ=255)                                                    tGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCgg                                                                                           >  1:965429/1‑151 (MQ=255)                                                        accttGAACCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCGGGGTGAAAATGGCTAAAATGACCCCGCAGTGAGGGTGGGCCT‑A‑AAATAAAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACa                                                                                       <  2:936417/147‑1 (MQ=255)                                                          ccTAAACCCAGCGGCCGGCTTCGGGGGAATGGGGGCGGGCAGCGGGGTTATAAGGGCAAAAATGCCCCCGCAGTGATGGTGGGCCT‑A‑AAATAAAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat                                                                                      <  2:950824/150‑1 (MQ=255)                                                              aaTCCAGCGGCCAGCGTCGGGGGAATGGGGGCGTGCAGCGGGGTAAAAAGGGCTACAATGACACCGCAGTGATGGGGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACatat                                                                                    <  2:342757/148‑1 (MQ=255)                                                               aTCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AGATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGaa                                                                                 >  1:208362/1‑150 (MQ=255)                                                                 ccAGCGGCCAGCGTCCGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAat                                                                               >  2:782026/1‑150 (MQ=255)                                                                   aGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAAtatt                                                                            >  1:909417/1‑151 (MQ=255)                                                                      ggCCAGGGTCGGGGGATTGGGGGGGTGCAGGTGGGTAATAATGGCTAAAATGCCCCCGAGGTGATGGGGGGCCT‑A‑AAATATAAGTTCTAATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAAtattat                                                                          <  2:266395/150‑1 (MQ=255)                                                                       gCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttt                                                                        >  2:967242/1‑151 (MQ=255)                                                                        ccggCGTCGGGGGAATGGGGGGGTGAAGTTGGGTGAAAATGGCTACAATGCCCCCGAAGTGATGGGGGGCAT‑A‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttt                                                                        <  1:1012395/147‑1 (MQ=255)                                                                        ccAGCGTCGGGGGAATGGGGGCGTGCGGGTGGGTGATAATGGCTACAATGCCCCCGCAGTGATGGGGGGCCA‑A‑AAATAAAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAata                                                                              <  2:118172/144‑1 (MQ=255)                                                                          ggcgtagggggAATGGGGTCGTGCAGGTGGTTGTTAATGACTACATGGCCCCCAGGGTG‑GGGTGGGGCTAA‑AAATTTAGGTTCATTTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttttt                                                                      <  1:279756/143‑1 (MQ=255)                                                                          aGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttttt                                                                     >  2:495302/1‑151 (MQ=255)                                                                                tGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGAt                                                               >  2:1042089/1‑151 (MQ=255)                                                                                tGGGGAATGTGGGCGAGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGAt                                                               >  1:660447/1‑151 (MQ=255)                                                                                 ggggAATGGGGGGGGGCAGCGGGGTAAAAATGGCTACAAGGCCCCGGTAGTGAT‑GTGGGGCT‑GAAAATATAGTTTCTAATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCg                                                                 <  1:776706/148‑1 (MQ=255)                                                                                  gggAAGGTGGGCGGGCAGTTGGGTGATAATGCCTACAAGAACACCGCAGTGATGGGGGGCTT‑A‑AAATATAAGTTCTGTTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAg                                                             <  1:66396/151‑1 (MQ=255)                                                                                          ggggGTGCGGCGGGTTAATAAGGGCTAAAATGACACCGAGGTGAGGGGGGGCCT‑A‑AAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGc                                                        <  1:38765/148‑1 (MQ=255)                                                                                          gggCGTGCGGCGGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCAT‑G‑AAATATAAGTTCTTATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACg                                                         <  1:773218/147‑1 (MQ=255)                                                                                              gTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtgt                                                 >  2:90294/1‑151 (MQ=255)                                                                                                gcggtggggTAATAATTTCTAAAATGACCCCGAAGTGGTGGTGGGCTT‑A‑AAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtgt                                                 <  1:149981/143‑1 (MQ=255)                                                                                                  aGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGtcatc                                             >  2:767595/1‑151 (MQ=255)                                                                                                      ggttaatatggacTAAAATGACCCCGGGTTGGTGGGGGGCTA‑A‑AAATAAAAGTTCTGTTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAAtt                                         <  1:80717/139‑1 (MQ=255)                                                                                                             aaTGGCTACAATGCCCCCGCGGGGGTGGTGGGCCT‑A‑AAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGt                                    <  1:279630/149‑1 (MQ=255)                                                                                                                ggCTACAATGACCCCGAGGTGATGGTGGGCCA‑A‑AAATAAAATTTTTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAAt                                          <  2:581631/140‑1 (MQ=255)                                                                                                                           ccccGCAGTGAGGGGGGGCCT‑A‑AAATATATTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGc                    <  2:961237/149‑1 (MQ=255)                                                                                                                             ccGCAGTGATGGGGGGCCT‑A‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTg                     <  2:960342/148‑1 (MQ=255)                                                                                                                                          gggCTT‑G‑AAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCaa     <  1:493725/151‑1 (MQ=255)                                                                                                                                            gCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAAc   >  2:482064/1‑151 (MQ=255)                                                                                                                                             ccT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAAcc  >  2:589333/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                     AGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCT‑G‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACC  >  NC_000913/1222090‑1222380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑