Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	43.5%	48.0 / 35.7	46	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (6/20);  new base T (20/0);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 5.22e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413596‑1413885                                                                                                                                             |                                                                                                                                                        cTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTATATGaaaa                                                                                                                                               >  2:513914/1‑148 (MQ=255) cTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTACaataaaa                                                                                                                                               >  1:531280/1‑144 (MQ=255)  tttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTATCTGAACA‑cc                                                                                                                                            >  2:461251/1‑151 (MQ=255)  tttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGaaa                                                                                                                                                >  2:259767/1‑147 (MQ=255)    tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTATAATAACA‑cccc                                                                                                                                          >  2:358095/1‑149 (MQ=255)          ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTACATTAAGA‑CCTcccctat                                                                                                                                    >  1:107772/1‑146 (MQ=255)           tctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAAATTTTTTTATTAACA‑Ccccccct                                                                                                                                      >  1:524759/1‑145 (MQ=255)                     ccTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTTAATTAACACCCCCCATTTTTTTTTcattg                                                                                                                          >  2:576245/1‑147 (MQ=255)                        gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTTATTTAACA‑CCTCCCATAttttttttcatgg                                                                                                                        >  2:589423/1‑142 (MQ=255)                        gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTATATGAACA‑CCCCCCTTTTTATTTTTAGTgg                                                                                                                        >  2:435014/1‑149 (MQ=255)                        gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGtt                                                                                                                      <  1:251116/151‑1 (MQ=255)                             ttttttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAAATTTTTACATTAAAA‑ACCCCCTTATTTTTTCCCGTGGGTTGttt                                                                                                                 >  2:40877/1‑151 (MQ=255)                               ttttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTa                                                                                                                <  1:454606/150‑1 (MQ=255)                                    ccTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCAt                                                                                                          <  1:339479/151‑1 (MQ=255)                                       gagaGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCt                                                                                                        <  1:564021/150‑1 (MQ=255)                                               tttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TGATTTTATAACTGAAAA‑AACCAATTATTATTTTTAGTGGGTTGTTTTTTTTATCTTTCCAg                                                                                                  >  1:438349/1‑148 (MQ=255)                                                      cATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCtttt                                                                                        <  1:631434/151‑1 (MQ=255)                                                          cTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTAATTTTTAACA‑GAACA‑CCCCCCCTATTTTTTTCATGGGGTTGTTTTTTTCCTCTTTTGTGTGGTTCttttt                                                                                       >  2:470051/1‑148 (MQ=255)                                                           tGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TTATTTTTTTCATTAACA‑CCCCCCTTATTTTTTTCCTTGGGTTGTTTTTTTCATCTTTTTAGTGGTTCtttttt                                                                                      >  1:325647/1‑147 (MQ=255)                                                            gATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCa                                                                                     <  1:536694/148‑1 (MQ=255)                                                                 cGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTTAATTAAAA‑CCACCCTTTTTTTTTTTACTGGGTTTTTTTTTTCCTCTTTTTAGTGCttttttttttctttc                                                                                >  1:296091/1‑141 (MQ=255)                                                                         tAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTACATGAACA‑ACCCCCTTTTTATTTTCAGTGGGTTGTTTTTTTCATCTTTTTAGTGCTTCtttttttttttccccctaa                                                                         >  2:464761/1‑133 (MQ=255)                                                                         tAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTACAAGAAAA‑CCCCCCTTTTTATTTTCAGTGGGTTGTTTTTTTCCTCTTTTTAGGGGttttttttttctttccccctaa                                                                         >  2:674596/1‑133 (MQ=255)                                                                         tAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑CAATTTTTTACATGAACA‑CCTCCCTTATTATTTTCAGTGGGTCGTTTATTCCATCTTTCTAGTGCTTCTTTTTTACTTCCCCCATaa                                                                         >  2:484084/1‑147 (MQ=255)                                                                            aTTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTACAATAAAA‑CCCCCCTTATTTTTTTCCGTGGGTCGTTTTTTTCATCTTTCTTGTGCTTTTTTTTTACTTCCCCCATAAACGGtt                                                                   >  2:382079/1‑150 (MQ=255)                                                                            aTTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTc                                                                  <  2:635933/151‑1 (MQ=255)                                                                                tGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTTTAATAAAA‑ACCCCATTATTATTTTCAGTGGGTCGTTTTTTTTCTCTTTTGAGTGCTTCTTTTTTTTTTCCACCCTAAACCGTTCggg                                                               >  1:314274/1‑150 (MQ=255)                                                                                tGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAAATTTTTAAATAAAAA‑CCCCCCTTTTTTTTTTCAATGGGTCGTTTTTTTCCTCTTTTTTGGGGTTCTTTTTTTCTTCTACCCTaaaacg                                                                     >  2:278949/1‑140 (MQ=255)                                                                                  aaTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGAt                                                             <  1:379459/150‑1 (MQ=255)                                                                                   atatCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTc                                                           <  1:294047/151‑1 (MQ=255)                                                                                             cAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTa                                                 <  2:441962/151‑1 (MQ=255)                                                                                                  agtagGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACt                                             <  1:324922/150‑1 (MQ=255)                                                                                                                  tccttTTCAATAGTGGCGG‑TAATTTTTTAAATGAAAA‑ACCCCCTTTTTTTTTTCAGTGGGTTGTTTTTTTCCTCTTTTTAGGGGTTTTTTTTTTCTTCCACCCCAAACCGGTCGGGGTTTGCCTTCGCTTCACTtctctccagatctg                               >  2:324744/1‑140 (MQ=255)                                                                                                                  tccttTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCg                                      <  1:324667/141‑1 (MQ=255)                                                                                                                       ttCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaaa                        <  2:47562/150‑1 (MQ=255)                                                                                                                       ttCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaaa                        <  1:241318/150‑1 (MQ=255)                                                                                                                           aTAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCt                   <  1:576159/151‑1 (MQ=255)                                                                                                                              gTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTc                <  2:45692/151‑1 (MQ=255)                                                                                                                                 gCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCAcc             <  2:524841/151‑1 (MQ=255)                                                                                                                                  cGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCg            <  2:358892/151‑1 (MQ=255)                                                                                                                                  cGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCAATTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCg            >  2:171896/1‑151 (MQ=255)                                                                                                                                   gg‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGt           >  2:695921/1‑151 (MQ=255)                                                                                                                                       aaTTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGTCTTTCTCCGTTa         <  2:438441/150‑1 (MQ=255)                                                                                                                                         ttttATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg      >  2:56297/1‑151 (MQ=255)                                                                                                                                          tttATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg      <  2:428407/150‑1 (MQ=255)                                                                                                                                          tttATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg      >  2:664408/1‑150 (MQ=255)                                                                                                                                            tataCATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATg   >  1:621744/1‑151 (MQ=255)                                                                                                                                             ataCATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATgg  <  2:665780/151‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                        CTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTATACATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413596‑1413885

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: ‑