Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	43.1%	57.8 / 32.5	51	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (3/26);  new base T (22/0);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.47e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

TACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413594‑1413885                                                                                                                                              |                                                                                                                                                         tACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑aa                                                                                                                                                 <  2:235337/150‑1 (MQ=255)   cTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGCGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGGAATTTTTTTCATgtaa                                                                                                                                                 >  2:174531/1‑146 (MQ=255)     ttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATT‑aaaaac                                                                                                                                             >  2:165404/1‑146 (MQ=255)     ttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑Aacac                                                                                                                                              <  2:319988/149‑1 (MQ=255)      tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATa‑aaaa                                                                                                                                               >  2:564851/1‑145 (MQ=255)      tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATATATT‑AACAcc                                                                                                                                             >  2:626363/1‑149 (MQ=255)       cTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTGAATTTTTACATG‑AACAACTcc                                                                                                                                          >  2:474098/1‑151 (MQ=255)        tGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTTAATGAAACACCTc                                                                                                                                           >  1:745932/1‑150 (MQ=255)         gCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTc                                                                                                                                           <  1:144278/148‑1 (MQ=255)            ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCatt                                                                                                                                       <  2:698120/149‑1 (MQ=255)            ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCatt                                                                                                                                       <  1:471812/149‑1 (MQ=255)             tctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATG‑AAAAACCCCcttatt                                                                                                                                    >  2:376160/1‑151 (MQ=255)              ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATG‑AACAACTCCattatt                                                                                                                                    >  2:355601/1‑150 (MQ=255)              ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCatta                                                                                                                                      <  1:679283/148‑1 (MQ=255)                ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCattatta                                                                                                                                   <  2:291489/149‑1 (MQ=255)                    aCGCCTTCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCa                                                                                                                             <  1:657733/151‑1 (MQ=255)                     cGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTTATTG‑AAACCCTCCCTTAtttttt                                                                                                                                >  1:444603/1‑147 (MQ=255)                     cGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAg                                                                                                                            <  2:467530/151‑1 (MQ=255)                        cTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATG‑GAAACCTCCCTttttttttttcggg                                                                                                                          >  1:249673/1‑144 (MQ=255)                          gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGtt                                                                                                                      <  2:546688/151‑1 (MQ=255)                            ttcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATAAT‑TACACCTCCCTTTTTAtttt                                                                                                                               >  1:60979/1‑140 (MQ=255)                             tcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATG‑AAAACCTCCCTTATTTTTTTCAG‑Tgggttgt                                                                                                                   >  2:36040/1‑146 (MQ=255)                                tttttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGt                                                                                                                   <  2:306265/148‑1 (MQ=255)                                  tttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTAt                                                                                                               <  2:727891/150‑1 (MQ=255)                                   ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATT‑AAAAACTCCATTTTTTTTTTCAG‑TGGGTCGttttttt                                                                                                             >  1:393938/1‑150 (MQ=255)                                   ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATAAG‑AACACCCCCCTTTTTTTTTTCAG‑TGGtttttttttt                                                                                                              >  2:543422/1‑142 (MQ=255)                                      ccTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCCTCCTTTTCAATAGTGGCGGTAATTTTTTTCATG‑AAAACCCCCCCTTTTTTTTTCCG‑TGGGTTGtttttt                                                                                                              >  1:300032/1‑147 (MQ=255)                                       cTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATT‑AACACCCCCCTTTTTATTTTCAG‑TGGGTCTtttttt                                                                                                              >  2:411712/1‑146 (MQ=255)                                          agagCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCtt                                                                                                       <  1:305533/150‑1 (MQ=255)                                                  ttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTAAACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGc                                                                                               <  2:84916/150‑1 (MQ=255)                                                        cATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCtttt                                                                                        <  1:356913/151‑1 (MQ=255)                                                         aTTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATT‑AGAACCACCATTTTTTTTTTCAG‑TGGGTTGTTTTTTTCATTCTTCGTGCGGTTCttttt                                                                                       >  1:235427/1‑151 (MQ=255)                                                               aTTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAATT‑AAAAACTCCCTTTTTTTTTTCCG‑TGGTTTGTTTTTTTCTTCTTTCTTGTGCttttttttttctt                                                                                  >  1:848129/1‑145 (MQ=255)                                                                 ttCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATT‑AACACCTCCCTTATTTTTTTTAC‑TGGTTCGTTTTTTTCATCTTTTTTGTGCttttttttttttt                                                                                  >  1:745089/1‑143 (MQ=255)                                                                         tttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTACATG‑AACACCCCCCCTTTTTTTTTTAGCGGGTTCTTTTTTTCC‑TCTTTTCAGGGTTTCTTTTTTTCTTccacc                                                                             >  2:379806/1‑145 (MQ=255)                                                                              aTTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTc                                                                  <  2:336876/151‑1 (MQ=255)                                                                                    aaTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATG‑AAAAACCCCCATCTTATTTTCTC‑TGGGTCGTTTTTTTCATCTTTTTGGGGCTTCTTTTTTTCTTTAACCCTAACCggatttggg                                                              >  1:389421/1‑142 (MQ=255)                                                                                     atatCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AGCACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCTGGAtt                                                            <  1:805463/150‑1 (MQ=255)                                                                                                   tagtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATT‑AACACCCCCCTTTTTTTTTTCTG‑TGGGGTTTTTTTTTCATCTTTTTTGTGCTTTTTTTTTTCTTTCCCCACAAACCGTTCTGGGTTTGCCTc                                                      >  1:667423/1‑142 (MQ=255)                                                                                                    agtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACtt                                            <  1:130554/151‑1 (MQ=255)                                                                                                     gtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTc                                           <  2:829952/151‑1 (MQ=255)                                                                                                           gTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCgg                                     <  2:749380/151‑1 (MQ=255)                                                                                                                aCCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAata                                <  2:546905/151‑1 (MQ=255)                                                                                                                      cttTTCAATAGTGGCGGTAAATTTTTTTATA‑AACACCTACCTTATTATTTTCAG‑CGGGTTGTTTTTTTCTTCTTTTTAGTGGTTTTTTTTTTCTTTCCCCCTAACCCGTTTGGGGTTTGCATCCGTTTCACTTCGCTc                                       >  1:852998/1‑138 (MQ=255)                                                                                                                        tttCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaa                         <  1:264190/150‑1 (MQ=255)                                                                                                                           cAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATg                      <  2:556965/150‑1 (MQ=255)                                                                                                                               aGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCttt                 <  1:34236/151‑1 (MQ=255)                                                                                                                                 tGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTc                >  1:500853/1‑150 (MQ=255)                                                                                                                                        aagtttATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTa         <  2:281829/147‑1 (MQ=255)                                                                                                                                         aTTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACt       <  1:165367/151‑1 (MQ=255)                                                                                                                                            ttATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGCAATCTCCTGAAATGGCTTTCACCGTTACTGAt    >  1:208946/1‑151 (MQ=255)                                                                                                                                             tataCATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATg   >  1:558044/1‑151 (MQ=255)                                                                                                                                              ataCATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATgg  >  2:876493/1‑151 (MQ=255)                                                                                                                                              ataCATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATg   <  2:459066/150‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                         TACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATG‑AACACCTCCATTATTATTTCCAG‑TGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413594‑1413885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑