Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,040,075	0	C	G	45.8%	49.2 / 18.3	49	L200V (CTG→GTG)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
Reads supporting (aligned to +/- strand):  ref base C (10/16);  new base G (22/0);  total (32/17)
Fisher's exact test for biased strand distribution p-value = 4.36e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATGGTGGTGCCGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGCTTTAAAGGG  >  NC_000913/2039930‑2040224                                                                                                                                                  |                                                                                                                                                        gATGGTGGAGCCGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGCGGGGTgg                                                                                                                                                      >  1:1076787/1‑148 (MQ=255)  aTGGTGGTGCCGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTg                                                                                                                                                       >  1:436351/1‑147 (MQ=255)   tggtggTGCCGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGaaa                                                                                                                                                    >  2:650972/1‑149 (MQ=255)    ggtggtGCCGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGGAata                                                                                                                                                  >  2:984519/1‑150 (MQ=255)          gCCGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGGGGGGTGGAAAATCCTTAt                                                                                                                                           >  2:1092329/1‑151 (MQ=255)          gCCGTGGATTGGGTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTAt                                                                                                                                           <  1:743747/151‑1 (MQ=255)            cGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGGAATATCCtt                                                                                                                                             >  2:770087/1‑147 (MQ=255)            cGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATCCTTAttt                                                                                                                                         >  2:558749/1‑149 (MQ=255)                  ttGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAACATCCTTCTGttgtacg                                                                                                                                   >  1:19844/1‑145 (MQ=255)                        ttCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGc                                                                                                                            <  1:416689/150‑1 (MQ=255)                        ttCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGc                                                                                                                            <  2:149073/150‑1 (MQ=255)                              tGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGGGGGGGGAAAAAACCTTCTGTC‑GACAGGATTggtcctg                                                                                                                       >  1:537132/1‑144 (MQ=255)                               gCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATCCTTATTTC‑GA‑AGGATTTCGt                                                                                                                          >  2:94239/1‑145 (MQ=255)                                   aaaTTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGAGGGGTGGAATATCCTTTTGTC‑GG‑AGGGTTGCgcgtccacg                                                                                                                   >  2:1044369/1‑140 (MQ=255)                                         cTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAAACCTTTTTTC‑GA‑AGGATTGCGTCTCGACGAAGCaa                                                                                                             >  2:317969/1‑148 (MQ=255)                                                ttGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGGAATATCCTTATGTC‑GA‑AGGGTTGCGTCTCGACGAAGCAATGGATCCGCt                                                                                                   >  2:1089552/1‑151 (MQ=255)                                                  gCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTca                                                                                                 <  2:812023/151‑1 (MQ=255)                                                      aaCCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGGAAAATCCTTTTGTC‑GA‑AGGAGTGCGTTTCCACGGAGACAAGCATCCCCTCccac                                                                                              >  2:211283/1‑150 (MQ=255)                                                       aCCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACtg                                                                                            <  2:673957/151‑1 (MQ=255)                                                          tACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAATAACCTTATTTCTGA‑GGGATT‑CGTCTTGACGAAAGAATGCGACCGCTCACCCtgat                                                                                          >  2:169531/1‑150 (MQ=255)                                                           aCCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGGAATATCCCTTTTTC‑GA‑AGGGTTTCGTCTCGACGAAGCAAAGCATCCCCTCACCCtgat                                                                                          >  2:270922/1‑149 (MQ=255)                                                           aCCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAATATCCTTTTGTC‑GA‑AGGATTGCGTCTCGGCGAAGCAATGCATCCGCTCCCACtgat                                                                                          >  2:929287/1‑149 (MQ=255)                                                            ccAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGAc                                                                                       <  2:221521/151‑1 (MQ=255)                                                             cAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAATATCCTTATGTC‑GA‑AGGATTTCGGTTCCCCGAAGCAAAGCATCCCCCCACACCGATGAcc                                                                                      >  2:150482/1‑151 (MQ=255)                                                                   tGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGGGGAAAATCCTTATGTC‑GA‑AGGATTTCGTCTCGACGGAGCAAAGCATCCGCTCACACTGATGACCGCAgg                                                                                 >  2:756077/1‑150 (MQ=255)                                                                      gAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAAATCCTATTTC‑GA‑AGGGTTTCGTCCCGACGGAGCAAAGCATCCCCCCACCCCGATGACCGTAGGGGtt                                                                             >  2:336065/1‑151 (MQ=255)                                                                           aTGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGGGTTTAttg                                                                        >  2:762191/1‑149 (MQ=255)                                                                           aTGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATgg                                                                        <  2:727313/151‑1 (MQ=255)                                                                           aTGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATg                                                                         <  1:650632/150‑1 (MQ=255)                                                                           aTGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGCGGGCTGGAATATCCTTTTGTC‑GC‑AGGAGTTGGTCTCGGCGAAGAAAAACATCCCCTCCCACTGGTGTACGGAGGTGttttt                                                                          >  1:546644/1‑147 (MQ=255)                                                                            tGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACt                                                                                             <  2:421548/129‑1 (MQ=255)                                                                                gCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATACTTATTTC‑GA‑AAGATTTCGTCTCGACGAAGAAAAGCATCCGCCCACACTGATGACCGTAGGGGTTTATgg                                                                        >  2:457082/1‑146 (MQ=255)                                                                                gCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAAAATCCTTATGTC‑GA‑AGGATTTCGTCTCGACGAAGCAAAGCATCCGCTCCCACTGATGACCGTGGGGGttttt                                                                          >  2:452881/1‑142 (MQ=255)                                                                                        aaCAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATCCTTATGTT‑TA‑AGGGTTTCGTCCCGACGAAGCAATGCATCCGCCCACACCGATGACCGCAGGGGGTTTTGGCAAggggct                                                               >  2:266996/1‑143 (MQ=255)                                                                                        aaCAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCg                                                           <  2:279206/151‑1 (MQ=255)                                                                                               tATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGGTGAAAAATCCTTATGTC‑GA‑AGGGTTTCGGCTCGACGAAGCAAAGCATCCGCTCACACTGATGACCGTAGGGGGTTTTGGCAAAGGGTTACCGCCACaa                                                     >  2:887798/1‑150 (MQ=255)                                                                                                  gCACGGGAACAGTGGCCAGGCCAGCGGGACCTCTTTGACGGCGGTGGGCTTAAATATCCTGATGTC‑GA‑TGGTTTGCTTGTCGACGAAGCAATGCATCCGCCCACACTGATGACCGTCGGTGTTTATGGCAAGGCGTAACCGCCACAAAAt                                                  <  1:512774/150‑1 (MQ=255)                                                                                                       ggAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAAAATCCTTATTTC‑GA‑AGGATTTCGTCTCGACGAAGCAATGCATCCCCTCACACTGATGACCGGAGGGGTTTATGGCAAGGCGTTACCCCCACaaaaaagcg                                              >  2:770327/1‑144 (MQ=255)                                                                                                                 ccaggccagCAGGCCCGTTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTAGGGCAAGGCTTTACCGCCACAAAATGGCGCGCCGGTGCGAc                                  <  2:487493/151‑1 (MQ=255)                                                                                                                            ggACCTTTTTATCGGGGGTGGGCTGAAATTTCCTTATGTC‑GA‑GGGATTGCGTCTCGACGAAGAAATGCACCCGCTCACCCGGATGACCGTGGGTGTTTATGGCAAGGCTTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCg                       <  2:546948/151‑1 (MQ=255)                                                                                                                            ggACCGTTTTATGGGCGGTGGGCTGAAATATCCTTATGCC‑GA‑AGGATGGCGTCTCGAGGAAGCAATGCATCCGCTCACACTGAGGCCCGTAGGTGTTTATGGCAGGGGGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATtgtg                          <  2:1004604/148‑1 (MQ=255)                                                                                                                               ccGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTTTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTg                     <  2:693461/150‑1 (MQ=255)                                                                                                                                   tttACCGGCGGTGGGCAAAAATATCCTTATGTC‑GA‑AGGGTTGCTTCTCGAGGAAGAAAGCCACCCGCCCACACTGATGACCGTGGGTTTTTAGGGAAGGGGTTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGaaa                 <  1:935936/150‑1 (MQ=255)                                                                                                                                       tCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATgg            >  2:463591/1‑151 (MQ=255)                                                                                                                                        cggcggTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGc           >  2:2165/1‑151 (MQ=255)                                                                                                                                        cgccggTGGGCTGGAATATCCTTATGCC‑GA‑AGGATTGCGGCTCGACGAAGGAATGCATCCGCTCACACTGATGACCGTAGCTGCTTATGGCAAAGCGTTACCGCCAAAAAATGGCGCGCCGGTGCGACCGATTGTGCCGTGGGAATATgg            >  1:48763/4‑150 (MQ=255)                                                                                                                                          gcggTGGGTGAAAATATCTTTAGGTG‑GA‑GGTATGGCTTCTCGAGGAGGAAATGCATCCGCCACCACTGATGCCCGGGGGTGTTTAGGGCGAGGCGTAACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGCtt         <  1:94211/151‑1 (MQ=255)                                                                                                                                            ggTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGCttt        >  1:635930/1‑150 (MQ=255)                                                                                                                                            ggTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGCttt        >  2:540401/1‑150 (MQ=255)                                                                                                                                                  cTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGCTTTAAAggg  >  2:809340/1‑150 (MQ=255)                                                                                                                                                  cTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGCTTTAAAggg  >  2:754575/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                        GATGGTGGTGCCGTGGATTGGTTTTCCGCTGCACAAATTGCTGGCGCTTGCCGAACCTACCAGCAATGCGAAGTATGTCGCTTTCGAAACAATTTATGCACCGGAACAGATGCCAGGCCAGCAGGACCGCTTTATCGGCGGTGGGCTGAAATATCCTTATGTC‑GA‑AGGATTGCGTCTCGACGAAGCAATGCATCCGCTCACACTGATGACCGTAGGTGTTTATGGCAAGGCGTTACCGCCACAAAATGGCGCGCCGGTGCGACTGATTGTGCCGTGGAAATATGGCTTTAAAGGG  >  NC_000913/2039930‑2040224

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑