Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,441	0	A	C	42.3%	95.1 / 13.4	52	G384G (GGT→GGG)	yqeF	short chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (28/2);  new base C (0/22);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 1.02e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTG  >  NC_000913/2984291‑2984582                                                                                                                                                       |                                                                                                                                               cGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCcaca                                                                                                                                                <  1:475602/151‑1 (MQ=255)   aaTATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACAcc                                                                                                                                              >  2:633466/1‑151 (MQ=255)      atGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTg                                                                                                                                           >  2:828361/1‑151 (MQ=255)                   ggAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGAt                                                                                                                              >  2:810546/1‑150 (MQ=255)                       aaaTGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACaa                                                                                                                          >  2:311017/1‑150 (MQ=255)                            aGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTTAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGtt                                                                                                                    >  2:793921/1‑151 (MQ=255)                                aGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGcc                                                                                                                 >  2:462135/1‑150 (MQ=255)                                  cacAGAAAATGTATGTCGACTTGCCAGCCATCATTATACAAAAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTTTTCGTCACGTTAAATGGTCAACCCCCCCCCCGGG‑CCCCCGCCGATACAAAGCGTTGCCa                                                                                                                <  1:504697/147‑1 (MQ=255)                                     aaaaatTGTATGTCGTCTTGCCAGCCATCATTATTCAAAAAATAAAGGACGGCAGATTTTTATCGGTAAGGAGAAAATGCAGAGTTTTTCGTCACGTTAAATGGACAATGCCACACCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCt                                                                                                           <  2:30450/149‑1 (MQ=255)                                     aaaaaaTGTATGTCGACTTCCCAGCCATCATTATTAAACAGATAAATGCCGGAAGTTATTTAGCGGTAAGGAGAAAATGCAGACTTTTTCGTCCCGTTAAATGGTC‑ATGCCCCCCCCCGGCCCCCCGCCGATACAAAGCGTTGCCAGTCCt                                                                                                           <  1:619632/149‑1 (MQ=255)                                     aGAAAATGTATGTCGCTTTCCCACCCATCATTATTAAACAAATTAATGACGGCAGATATTTATCGGTAAGGAGAAAATGCAGAGTTTTTCTTCCCTTTAAATGGTAAATCCCACCCCCGGG‑CCCCCGCCGATACAAAGCGTTGCCAGt                                                                                                              <  2:835717/148‑1 (MQ=255)                                     aGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCt                                                                                                           >  1:324524/1‑151 (MQ=255)                                           tgtatgtCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAACGCGCTGCCAGTCCTTTGCgg                                                                                                     >  1:450235/1‑151 (MQ=255)                                           tgtatgtCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCgg                                                                                                     >  2:366582/1‑151 (MQ=255)                                               tgtCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCAt                                                                                                 >  2:742629/1‑151 (MQ=255)                                                   gACTTGCCAGCCATAATTATTCAAAAGATAAATGAGGGAAGATTTTTATCGGAAAGGAGAAAATGCAGAGCTTTTCGTCACTTTAAATGGTAAATGCCCCCCCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACg                                                                                             <  2:289145/151‑1 (MQ=255)                                                      ttcccacccaTCATTATACAAAAAATTAATGCCGGCAGTTTTTAATCGGAAGGGAGAAAATGAAGGGTTTTTCGTCACTTTAAATGGTAAATGCCACCCCCGGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGtt                                                                                           <  2:492243/147‑1 (MQ=255)                                                      ttGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGttt                                                                                          >  1:342176/1‑151 (MQ=255)                                                      ttGCCACCCATCTTTATTAAACAGATTAAGGAGGGAAGATATTTATGGGAAAGGAGAAAAGGAAAAGTTTTTCGTCACTTTAAATGGTCAACCCCCCCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTa                                                                                               <  1:1082842/146‑1 (MQ=255)                                                           agccaTCATTATCAAACAGATTAAGGACGGAAGATATTTATCGGTAAGGAGAAAATGCAGAGTTTTTCGTCACGTTAAATGGTCAATCCCACCCCCGGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGttt                                                                                          <  2:421236/146‑1 (MQ=255)                                                             ccaTCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAtt                                                                                   >  2:17377/1‑151 (MQ=255)                                                             ccaTAATTATTAAACAGATTAATGACGGCAGATATTTATGGGAAAGGAGAAAATGCAGAGCTTTTCGTCCCGTTAAATGGTAAATCCCACCCCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCa                                                                                     <  2:299611/149‑1 (MQ=255)                                                                  attattCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATg                                                                              >  2:277829/1‑151 (MQ=255)                                                                   ttataCAACAGAATAAGGACGAGAGTTATTGATCGGAAAGGAAAAAATGCAGAGTTTTTCTTCATGTTCAGGGATCAAGCCCACCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTc                                                                                 <  1:223184/147‑1 (MQ=255)                                                                     attCAAAAAATAAAGGGCGGCAAATTTTTATGGGAAGGGAGAAAAGGCAGAGTTTTTCGCCCCTTTCAAGGTCCAATCCCCCCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCAt                                                                               <  1:738969/147‑1 (MQ=255)                                                                         aaCAAATAAATGACGGCAGATTTTTATGGGTAAGGAGGAAATGCAGAGTTTTTCTCCCCTTTAAGTGGTCAATCCCCCCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGaa                                                                            <  1:370724/146‑1 (MQ=255)                                                                            aGATTAAGGAGGGCATATTTTTATGGGAAGGGAGAAAATGCAGATTTTTTCTTCACGTTCAATGGTCAATCCCCCCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGaa                                                                    <  1:1024959/151‑1 (MQ=255)                                                                              aTTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAAc                                                                  >  2:1072713/1‑151 (MQ=255)                                                                                 aaTGACGGCAAATTTTTACCGGTAAGGAGAAAAGGCAGAGCTATTCGTCACTTTCAATGGTAAATCCCACCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAAcc                                                                 <  2:483494/149‑1 (MQ=255)                                                                                    gACGGAAGATATTTATCGTTAAGGAGGAAATGCAGAGTTTTTCGTCACTTTAAATGGTCATTCCCACCCCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGa                                                             <  2:1027110/150‑1 (MQ=255)                                                                                           gATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCa                                                      >  2:438786/1‑150 (MQ=255)                                                                                             tatTTATCGGAAAGGAGAAAATGCAGAGCTATTCGTCACGTTAAATGGTCAATCCCCCCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCgg                                                        <  1:1106889/146‑1 (MQ=255)                                                                                                ttaggggaaaGGAGAAATTGCAGACCTTTTCGTCGTTTGCAAGGGTAAACGCCCCCCCCTCC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAAcc                                                   <  2:856265/140‑1 (MQ=255)                                                                                                 tacaggTAAGGACGAATTGCAGAGATGTTCCTCATGTAAAAGGGTCAAGCCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGa                                                <  1:541414/146‑1 (MQ=255)                                                                                                 tATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCgg                                                 >  1:156087/1‑149 (MQ=255)                                                                                                  aTCGGTAAGGAGGAAATGCAGATCTTTTCGTCACGTTCAAGGTTCAATCCCCCCCCCTGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAg                                              <  1:207359/151‑1 (MQ=255)                                                                                                     ggTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAgcgc                                           >  2:689269/1‑151 (MQ=255)                                                                                                             ggaAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCggg                                   >  1:744228/1‑151 (MQ=255)                                                                                                               aaaTGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTg                                 >  2:1011047/1‑151 (MQ=255)                                                                                                                aaTGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTg                                 >  1:66069/1‑150 (MQ=255)                                                                                                                    cAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCg                             >  1:908202/1‑150 (MQ=255)                                                                                                                    cAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCg                             >  2:652822/1‑150 (MQ=255)                                                                                                                     agagTTTTTCGTCCCTTTAATGGGTCAATGCCCCCCCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGAcc                              <  2:852140/148‑1 (MQ=255)                                                                                                                                tCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCgcgc                >  1:980856/1‑151 (MQ=255)                                                                                                                                 ccctttaaaTGGCAAATCCCCCCCCCGGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCgcgc                <  2:91579/143‑1 (MQ=255)                                                                                                                                  aCGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAAGCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCGATCGGGTGACCGAGTGCGATc                    >  2:456986/1‑145 (MQ=255)                                                                                                                                   cGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGccac             >  2:701217/1‑151 (MQ=255)                                                                                                                                      tCAATGGTCAATGCCACACCCTGT‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGCTGACCGAGTGCGATCGCGccacc            >  1:372189/1‑149 (MQ=255)                                                                                                                                        aaTGGACAATGCCACCCCCGGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcat          <  2:1022939/149‑1 (MQ=255)                                                                                                                                          tGGTCAATGCCACCCCCGGC‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGccacca           <  1:1089238/146‑1 (MQ=255)                                                                                                                                             tCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacatt   >  2:533525/1‑151 (MQ=255)                                                                                                                                               aaTGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacattg  >  1:199850/1‑150 (MQ=255)                                                                                                                                               aaTCCCACCCCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgaca     <  1:181945/147‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                               CGAATATGTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATGCCACACCCTGG‑CCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTG  >  NC_000913/2984291‑2984582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑