Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,671,415	0	C	T	43.8%	56.7 / 26.6	48	K160K (AAG→AAA)	yhjB	putative DNA‑binding transcriptional response regulator
Reads supporting (aligned to +/- strand):  ref base C (25/2);  new base T (0/21);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.13e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTTACCGCCAACG  >  NC_000913/3671278‑3671563                                                                                                                                              |                                                                                                                                                     tAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTcgc                                                                                                                                         >  2:135008/1‑151 (MQ=255)   aaaTTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTcgccc                                                                                                                                       >  2:484022/1‑151 (MQ=255)       tATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCccgccg                                                                                                                                   >  1:947485/1‑151 (MQ=255)         tCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCt                                                                                                                                 >  1:719304/1‑151 (MQ=255)                      gagaTATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTaaa                                                                                                                     >  1:96839/1‑150 (MQ=255)                         atatTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAAtct                                                                                                                 >  1:257688/1‑151 (MQ=255)                             ttAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCg                                                                                                             >  1:642804/1‑151 (MQ=255)                              tAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGc                                                                                                            >  1:214608/1‑151 (MQ=255)                                         ccgccTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCt                                                                                                 >  1:521987/1‑151 (MQ=255)                                               gggTGCGTTTTTTCACTCCCGGAGGGGGATACAGGGATCCCAGATGCGTTTTTCCCGTC‑CC‑GT‑T‑ACTGATATTCAGCGCTCTGCCGATCTCTTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGa                                                                                           <  2:482684/151‑1 (MQ=255)                                                 gTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGAtt                                                                                         >  1:114116/1‑151 (MQ=255)                                                         tttCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCt                                                                                 >  1:554259/1‑151 (MQ=255)                                                             cctcccAGCCGGCGATAGGGGGATCCAAGTTGCCTTTTTCCCGTT‑CC‑GG‑T‑ACTTATATCCGGCTGTCGCCCGTTTTCTTTTTGTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTaa                                                                             <  2:2772/147‑1 (MQ=255)                                                                 ccagcgggCGATACGGGGATTCCAGATGCTTTTTTCCCGTT‑CC‑GG‑T‑ACTAATATTCAGCGCTCTGCCGCTCTCTTTATTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTc                                                                         <  2:527517/145‑1 (MQ=255)                                                                 ccAGACGGCGAAACGGGGATTCCAGTTGCTTTTTTCCCGTC‑CC‑GT‑T‑ACTAATTTTCAGCCCTCTCCCGATCTCTTTTTTTTTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTa                                                                              <  2:714487/146‑1 (MQ=255)                                                                    gACGGGGATAGAGGGATTCCAGATGCTTTTTTACCGTT‑CC‑GG‑T‑TTTGATATTCACCCCTTTGCCTCTCTCTTTTTTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCt                                                                       <  1:101707/150‑1 (MQ=255)                                                                       ggttaTACAGGTATTGGAGTTGCGTTTTTCCCGTC‑CC‑GG‑A‑ACTGTTCTCCAGCTCTCTGCCGATCTCCTTTTTTATTGCGGCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTc                                                                   <  2:390987/147‑1 (MQ=255)                                                                       ggCAATAGAGGGATTCCAGATGCGTTTTTCCCGTT‑CG‑GT‑T‑ACTTATATTCAGCGCTCTGCCGATCTCTTTTTTTGTTTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCtt                                                                      <  2:327544/148‑1 (MQ=255)                                                                         cGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCg                                                                 >  1:704779/1‑151 (MQ=255)                                                                           aTACAGGTATCCCAGTTGCGCTTTTACC‑TT‑CC‑GGTT‑ACTAATATTCCGCGCTCGCCCGATCTCTTTTTTTATTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCgg                                                                <  2:573192/150‑1 (MQ=255)                                                                           aTACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCgg                                                                >  2:84141/1‑150 (MQ=255)                                                                             aCAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGcgt                                                             >  2:556062/1‑151 (MQ=255)                                                                                gggATTCCAGATGCGTTTTTCCCGTT‑CC‑GG‑T‑ACTGATTTTCAGCGCTCTGCCGATCTCTTTTTTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGcgt                                                             <  1:957061/148‑1 (MQ=255)                                                                                gggATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGcgtcgt                                                          >  2:478601/1‑151 (MQ=255)                                                                                gggATTCCAGATGCCCTTTTCCCTTC‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGcgtc                                                            <  2:475891/149‑1 (MQ=255)                                                                                gggATTCC‑GATTCCTTTTTTCCGTT‑CC‑GG‑TGTCGGATAGTCAGCGCTCTGCCGTCTTCTTTTTTTTATTCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGcg                                                              <  1:639433/147‑1 (MQ=255)                                                                                 ggATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCgtcgtc                                                         >  1:794987/1‑151 (MQ=255)                                                                                      ccAGTTGCGTTTTTCCCGTC‑CG‑GG‑T‑ACTGATATCCAGCGCTCTGCCGATCTCTTTATTTGTTTCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGcc                                                     <  2:513952/150‑1 (MQ=255)                                                                                         agttgcgttttTCCGTTCCC‑GG‑T‑ACGTATTTCCTGCCCTCGGCCTTTCTCTTTTTTTTTTTCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAg                                                   <  1:311975/143‑1 (MQ=255)                                                                                              gcTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTcc                                              >  2:40527/1‑149 (MQ=255)                                                                                                ttttCCCGTT‑CG‑GG‑T‑ACTGATTTTCGGCGCTCTGCCGATTTCTTTATTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGtc                                                 <  1:207825/144‑1 (MQ=255)                                                                                                ttttCCCGTC‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGTTCTCTTTTTTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCa                                             <  2:981206/148‑1 (MQ=255)                                                                                                 ttttCCCTT‑CCGGG‑T‑ACTAATATCCAGCGCTCTCCCTTTCTCTTTTTTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAgg                                           <  2:188235/150‑1 (MQ=255)                                                                                                 tttCCCCTT‑CC‑GGTT‑ACTAATTTTCAGCCCTCTGCCGTTCTCTTTTTTTTATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTcc                                              <  2:185450/147‑1 (MQ=255)                                                                                                           cc‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCTTTTTTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGaaa                                     <  2:467817/146‑1 (MQ=255)                                                                                                           cc‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAAcatc                                 >  1:301854/1‑150 (MQ=255)                                                                                                               gtt‑ACTGATTTTCGGCGCTCTGCCGTTTTCTTTTTTTGTTCCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGaaa                                     <  1:310803/142‑1 (MQ=255)                                                                                                                     tGATTTTCAGCCCTCTGCCGATCTCTTTTTTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATcccc                           <  2:993019/149‑1 (MQ=255)                                                                                                                     tGATATCCACCGCTCTCCCGTTCTCTTTTTTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATccc                            <  1:843112/148‑1 (MQ=255)                                                                                                                      gATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATc                        >  2:1042859/1‑151 (MQ=255)                                                                                                                            cAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATcgccgc                   >  2:904971/1‑150 (MQ=255)                                                                                                                                 ctctGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTAtt             >  1:824770/1‑151 (MQ=255)                                                                                                                                   ctcccaaTCTCTTTATTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACt                <  2:627141/140‑1 (MQ=255)                                                                                                                                    tGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTTAc          >  1:528376/1‑151 (MQ=255)                                                                                                                                      cctttctcTTTTTTTGTTTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTTACCg        <  2:683829/147‑1 (MQ=255)                                                                                                                                        gATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTTACCGcc      >  2:273373/1‑151 (MQ=255)                                                                                                                                            tcCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTTACCGCCAACg  >  1:713387/1‑151 (MQ=255)                                                                                                                                            tcCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTTACCGCCAACg  >  2:95232/1‑151 (MQ=255)                                                                                                                                              |                                                                                                                                                     TAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTT‑CC‑GG‑T‑ACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTTACCGCCAACG  >  NC_000913/3671278‑3671563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑