Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,671,415	0	C	T	42.3%	66.0 / 27.1	53	K160K (AAG→AAA)	yhjB	putative DNA‑binding transcriptional response regulator
Reads supporting (aligned to +/- strand):  ref base C (25/5);  new base T (0/22);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 3.07e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCTGGCTGTAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTT  >  NC_000913/3671269‑3671553                                                                                                                                                   |                                                                                                                                           tgctgGCTGTAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTAt                                                                                                                                        >  2:323807/1‑151 (MQ=255)   ctggctgTAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTAttt                                                                                                                                      >  2:838129/1‑151 (MQ=255)   ctggctgTAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTAttt                                                                                                                                      >  2:445127/1‑151 (MQ=255)         gTAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTcg                                                                                                                                >  1:658740/1‑151 (MQ=255)           aaaaTTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTcgc                                                                                                                               <  2:749277/150‑1 (MQ=255)                tATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTcgcccgcc                                                                                                                          <  1:349402/150‑1 (MQ=255)                          aggaggAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGt                                                                                                               >  1:115111/1‑151 (MQ=255)                          aggaggAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGt                                                                                                               >  2:675066/1‑151 (MQ=255)                           ggaggaGATATTTAACATCTTTGCCGCGTGGGTGCGTTTTTTCCCTCCCAGAGGGCGATACAGGGATCCCGGATGCTTTTTTACCGTTCCGGTACTGATATTAAGCTCTCTGCCGATCTCTTTATTTTTTCCGCCCGCCGCTAACATg                                                                                                                 <  2:680922/148‑1 (MQ=255)                                agaTATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAAt                                                                                                         >  2:453262/1‑151 (MQ=255)                                  atatTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAAtct                                                                                                       >  2:126936/1‑151 (MQ=255)                                   tttttAACATCATGGCCGCCTGGGTGCTTTTTTTCACTCCCAGACGGCGATACAGGGATTCCAGATGCGTTTTTCCCTTTCCGTTACTGATATTCAGCCCTCTGCCGTTCTCTTTTTTTGATTCGCCCGCCGCTAACATGGTTAAAAtc                                                                                                        <  2:943558/147‑1 (MQ=255)                                   tatTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAAtctc                                                                                                      >  2:448668/1‑151 (MQ=255)                                           atcatTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTggc                                                                                              >  1:47614/1‑151 (MQ=255)                                             catTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTggcgg                                                                                            >  1:606932/1‑151 (MQ=255)                                              atTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTggcggg                                                                                           >  2:379214/1‑151 (MQ=255)                                               ttGCCGCCTGGGTGCTTTTTTCCCCTTCCAGACGGCAATACAGGGATTCAAGGTGCTTTTTTCCCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCTTTTTTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTg                                                                                                <  2:644868/145‑1 (MQ=255)                                                 gccgccTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGgcgc                                                                                        >  1:750722/1‑151 (MQ=255)                                                 gccgccTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGgcgc                                                                                        >  2:492030/1‑151 (MQ=255)                                                  ccgctggggTGCGTTTTTCCCCTCCCAGAGGGCAATACAGGGATTCCAGATGCGTTTTTCCCGTCCCGGTACTAATATTCACCGCTCTGCCGACCTCCTTATTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTggcgggcg                                                                                         <  2:290393/143‑1 (MQ=255)                                                  ccgcgTGGGTGCTTTTTTTCCCTCCCAGACGGCGATACAGGGATTCCAGATGCTTTTTTCCCGTCCCGGTACTGATATCCGGCGCTCTCCCGATCTCCTTTTTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCg                                                                                                   <  2:792220/139‑1 (MQ=255)                                                  ccgccgGGGTGCGTTTTTTCCCTCCCAGACGGCGATACAGGGATCCCAGATGCGTTTTTCCCTTCCGGGTACTGATATTCAGCCCTCTGCCGATCTCTTTTTTTTATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTggc                                                                                              <  1:827168/144‑1 (MQ=255)                                                    gccTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCtt                                                                                      >  2:293820/1‑150 (MQ=255)                                                      cTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAAc                                                                                   >  1:635056/1‑151 (MQ=255)                                                        gggtcctttttttCCCTCCCAGACGGCGATACAGGAATTCCAGATGCGTTTTTCCCGTCCCGGTACTGATATTCGGCGCTCTGCCGATCTCTTTTTTTGTTTCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCtt                                                                                      <  1:805703/138‑1 (MQ=255)                                                        gggTGCTTTTTTTCTCTCCCAGGCGGCGATAGAGGGATTCCAGATCCTTTTTTCCCGTCCCGTTACTAATATCCGGCGCTCTGCCGATCTCTTTTTTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACg                                                                                  <  2:796679/150‑1 (MQ=255)                                                        gggTGCTTTTTTCCCCTTCCAGACGGCGATACGGGGATTCAAGATGCGTTTTTCCCGTCCCGGTACTTATATTCAGCGCTCTGCCGTTCTCTTTATTTGTTTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACg                                                                                  <  2:805688/150‑1 (MQ=255)                                                         ggtggttttttcCACTCCCGGACGGGAATAGGGGGATCCAAGGTGCTTTTTTCCCGTCCCGTTACTGATTTCCGGCGCTCTGCCGTCCTCTTTATTTGTTCCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACg                                                                                  <  2:776513/142‑1 (MQ=255)                                                               tttttcCCCTCCCAGACGGCAATACGGGGTTCCCAGTTGCTTTTTTCCCTTTCCGGTACTAATATCCAGCGCTCTGCCGTTCTCTTTTTTTGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTgag                                                                           <  2:150387/149‑1 (MQ=255)                                                                ttttcCACCCCCAGGTGGCGATACAGGGCTTCCAGATCTTTTTTTACCCTTCCGGTATTGATACTCACCTCTCTGCCGTTCCCTTTTTTGGATTCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTgaga                                                                          <  2:556255/150‑1 (MQ=255)                                                                 ttttCCCTCCGAGAGGGCGATACGGGGTTTCCAATTGCTTTTTTCCCGTCCGGGTCCTGATATCCGGCGCTTCCCCGTTCTCTTTTTTTGATCGCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGAt                                                                         <  2:124190/150‑1 (MQ=255)                                                                 ttttCATTTACAGAAGGCGATACAGGGATTAAAGATGCGCCTTTACAATTCCGGTACTGATATTCAGCGCTCGGTTGATCTCGTTATTTGAATCGCCTGCCGCTCACATGGTTAAAATATCACTTTGGCGGGCGCTTAACGATTTg                                                                             >  2:731846/1‑146 (MQ=255)                                                                          ccAGACGGCGAAACGGGGATTCCAGATGCTCTTTTCCCGTCCCGGTCCTGATATTCAGCGCTCTGCCGATCTCCTTTTTTGTTTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAAt                                                                  <  2:500284/148‑1 (MQ=255)                                                                                ggCAATACAGGGATTCCAGATGCGTTTTTCCCGTCCCGGTACTGATATTCAGCGCTCTCCCGATCTCTTTTTTTGTTTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCttt                                                           <  2:64785/149‑1 (MQ=255)                                                                                  caaTACGGGGTTTCCAGATGCGTTTTTCCCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCTTTTTTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCg                                                       <  1:489794/149‑1 (MQ=255)                                                                                   gATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCgg                                                      >  2:569300/1‑151 (MQ=255)                                                                                     tACAGGGATTCCAGATGCGTTTTTACCTTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCTTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTcc                                                        <  1:564785/147‑1 (MQ=255)                                                                                     tACAGGGATCCCAGATGCGTTTTTCCCTTTCCGTTACTAATATTCAGCGCTCTGCCGTTCTCTTTATTTGTTTCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCg                                                       <  2:106666/148‑1 (MQ=255)                                                                                      acggggATTCCAGATGCTTTTTTCCCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCTTTATTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGcg                                                    <  1:270151/147‑1 (MQ=255)                                                                                         gggATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGcgtcg                                                 >  1:307592/1‑150 (MQ=255)                                                                                           gATTCCAGTGGCGTTTTTCCCGTTCCGTTACTGATATTCACCTCTCTGCCGATCTCTTTTTTGGTTCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTcc                                              <  2:233393/151‑1 (MQ=255)                                                                                                      cgcTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTcc                                    >  2:38188/1‑150 (MQ=255)                                                                                                          tttACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGc                                >  2:25016/1‑150 (MQ=255)                                                                                                            tACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGc                                >  2:441597/1‑148 (MQ=255)                                                                                                                gTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAAc                          >  1:426095/1‑150 (MQ=255)                                                                                                                   ccGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAAcatc                       >  2:522779/1‑150 (MQ=255)                                                                                                                     ggTACTATTTTTCGGCGCTTTCCCGTTCTCTTTTTTTTATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAAcatcat                     <  1:776786/150‑1 (MQ=255)                                                                                                                          tgatttccggcgcTCTCCCGATCTCTTTATTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATcccc                 <  1:931055/140‑1 (MQ=255)                                                                                                                               tccAGCCCTCTCCCGATCTCTTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATcgc            <  1:371695/147‑1 (MQ=255)                                                                                                                                 cAGCCCTCTGCCATTCTCTTTATTTGATCCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCAt               <  1:924129/144‑1 (MQ=255)                                                                                                                                     gcTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTAt    >  1:503664/1‑151 (MQ=255)                                                                                                                                       tctGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTAttt  >  1:878008/1‑151 (MQ=255)                                                                                                                                          ccctctctcTTTTTTTGATCCCCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATcg             <  2:130563/132‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                           TGCTGGCTGTAAAATTATCCTCTTCAGGAGGAGATATTTAACATCATTGCCGCCTGGGTGCGATTTTTCACTTCCAGACGGCGATACAGGGATTCCAGATGCGCTTTTACCGTTCCGGTACTGATATTCAGCGCTCTGCCGATCTCCTTATTTGATTCGCCCGCCGCTAACATGGTTAAAATCTCCCGCTGGCGGGCGCTTAACGATTTGAGATCTTTAATGTCCTTTTCCGGCGTCGTCCGCCAGTCTCCAGGCAGAAACATCATCCCCATCGCCGCACTATTT  >  NC_000913/3671269‑3671553

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: ‑