Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	44.4%	56.8 / 28.4	45	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (3/22);  new base T (20/0);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 6.32e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413589‑1413885                                                                                                                                                     |                                                                                                                                                           aGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACa                                                                                                                                                        <  1:102082/151‑1 (MQ=255)        cTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAaca                                                                                                                                                  <  2:663064/150‑1 (MQ=255)         tttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTACATGAacaac                                                                                                                                                >  1:891265/1‑149 (MQ=255)                   ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTATATGAACACCCCCcttttt                                                                                                                                       >  2:881073/1‑150 (MQ=255)                        aaCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TTA‑TTTTTTATATTAACACCCCCCTtttttttt                                                                                                                                   >  1:711814/1‑149 (MQ=255)                               gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGtt                                                                                                                         <  1:452861/151‑1 (MQ=255)                                 ttcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TTA‑TTTTATAAATTAACACCCCCCCTATTATTTTTAGC‑GGtttg                                                                                                                       >  1:753658/1‑149 (MQ=255)                                        ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTAtt                                                                                                                 <  2:242678/150‑1 (MQ=255)                                              gagaGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCtt                                                                                                          <  2:43885/151‑1 (MQ=255)                                                  gCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGa                                                                                                      <  2:261572/151‑1 (MQ=255)                                                    aTTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTTAATGAAAACCTCCATTATTTTTTTCAGT‑GGTTTGTTTTTTTTATCtttttag                                                                                                     >  2:554590/1‑146 (MQ=255)                                                           cGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTTCATGAAAAACCCCCTTTTTTTTTTCAGT‑GGGTTGTTTTTTTCCTCTTTTGA‑GTGcttttt                                                                                            >  1:521794/1‑151 (MQ=255)                                                                tCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTAAATGAACACCTCCCTTTTTTTTTTCCGT‑GGTTCGTTTTTTTCATCTTTTTC‑GTGCTTCtttttt                                                                                        >  1:106712/1‑149 (MQ=255)                                                                  tGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTAA‑TTTTTTA‑ATTAAAACCCCCATTTTTTTTTTCACT‑GGGTTGTTTTTTTCATTTTTTTA‑GTGCttttttttt                                                                                        >  2:326309/1‑147 (MQ=255)                                                                   gATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAc                                                                                      <  1:757163/149‑1 (MQ=255)                                                                   gATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑t                                                                                    <  1:12887/150‑1 (MQ=255)                                                                     tttCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTAAATGAACACCCCCCTTATTTTTTTTAGT‑GGGTCGTTTTTTTCATCTTTCGA‑GTGCTTCtttttttctt                                                                                    >  1:903152/1‑144 (MQ=255)                                                                      ttCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTTAAATAAAACCCCCCTTATTTTTTTCAGTGGGTTGGTTTTTTCCTTTTTTTG‑‑GTGGttttttttttctt                                                                                    >  2:1032556/1‑143 (MQ=255)                                                                           tAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCAt                                                                            <  1:941752/150‑1 (MQ=255)                                                                              tttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTAAATTAAAACCTCCCTTATTTTTTTCCGTGGGTTGGTTTTTTCC‑TCTTTTGG‑GGGCTTCTTTTTTTC‑TTTCCCCATaa                                                                          >  1:196108/1‑149 (MQ=255)                                                                               ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑cc                                                                       <  2:899299/150‑1 (MQ=255)                                                                                   aTTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTACATTAACACCTCCCCTTTTTTTTTCTAT‑CGGTCGTTTTTTTCCTCTTTTTAGGGGCTTTTTTTTTCT‑TTCCACCAAAC‑CCGGtt                                                                   >  1:983006/1‑151 (MQ=255)                                                                                       tGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCggg                                                               <  1:1025769/150‑1 (MQ=255)                                                                                        gAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGa                                                              <  2:888413/150‑1 (MQ=255)                                                                                            atCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑GAA‑TTTTTTAAATGAAAAACCCCCTTATTTTTTTCAGT‑GGGTCGTTTTTTTTCTCTTTTTA‑GTGGTTCTTTTTTTT‑TTTCCCCCTAA‑CCCGTTTGGGGtt                                                            >  2:162175/1‑148 (MQ=255)                                                                                             tCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAATTTTTTTAAATAAAAACC‑CCCTTTTTTTTTTCAGT‑GGTTCGTTTTTTTTATTTTTTGG‑GTGGTTCTTTTTTTCTTTCCCCCTAAA‑CCGGTTCGGGttt                                                            >  2:208499/1‑148 (MQ=255)                                                                                              cTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTAAATGAAAACCCCCCTTTTTTTTTTCCTC‑GGGTTGTGTTTTTCCTCTTTTTA‑GTTCTTCTTTTTTAC‑TTCCCCCCTaa                                                                          >  2:315828/1‑133 (MQ=255)                                                                                                tGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTACATTAACACCCCCCCTTTTTTTTCCTGT‑GGGTTGTTTTTTTCATCTTTTTA‑GTGGTTCTTTTTTTC‑TTTCCCCCTAACCCGGTTGGGGGTT‑GCATcc                                                     >  1:74787/1‑151 (MQ=255)                                                                                                  tCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTTCATGAAAAACCCCCCTTTTTTTTTCTGG‑GGGTCGGTTTTTTCTTCTTTCTT‑GGGCTTTTTTTTTTC‑TTTCACCACAA‑CCCGGTCGGGGTTTGCGTcc                                                     >  2:93805/1‑149 (MQ=255)                                                                                                   ccAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGtt                                                  <  2:931051/151‑1 (MQ=255)                                                                                                   ccAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGtt                                                  <  2:9285/151‑1 (MQ=255)                                                                                                    cAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTa                                                 <  1:524856/151‑1 (MQ=255)                                                                                                       ttAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTTAATTAAAAACCCCCCTTTTTTTTTCAGT‑GGGTTGTTTTTTTTCTCTTTTTA‑GTGCTTTTTTTTTTT‑TTTCCCCCTAA‑CCCGTTTGGGGTTTTCCTCCGtttc                                                >  2:724088/1‑147 (MQ=255)                                                                                                            agGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTACATGAAAACCCCCCTTTTTTTTTTCAGT‑GGGTCGTTTTTTTCCTCTTTTGG‑GTGGTTCTTTTTTTC‑TTCCCCCCCAA‑CCCGGTCGGGGTTTGCATCCCtt                                                  >  1:987048/1‑142 (MQ=255)                                                                                                              gAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTTTAAATGAACACCCCCCTTTTTTTTTTCAAT‑GGGTCGTTTTTTTCATCTTTTTT‑GTGCTTTTTTTTTTC‑TTCCACCCTAA‑CCGGTTCGGGGTTTGCCTCCGtt                                                  >  1:246495/1‑140 (MQ=255)                                                                                                              gAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTc                                       <  2:693992/151‑1 (MQ=255)                                                                                                                gTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCgg                                     <  1:12956/151‑1 (MQ=255)                                                                                                                 tGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑ATTTTTACATGAACACCCCCCTTTTTTTTTTCAGT‑GGGTTGTTTTTTTCATCTTTTGA‑GTGCTTCTTTTTTTC‑TTTCACCATAA‑ACCGGTCGGGGTTTGCATCCGTTACACtt                                            >  2:795291/1‑143 (MQ=255)                                                                                                                          ccttTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCt                            <  2:747033/150‑1 (MQ=255)                                                                                                                          ccttTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCt                            <  2:288253/150‑1 (MQ=255)                                                                                                                              ttCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaaa                        <  2:35838/150‑1 (MQ=255)                                                                                                                                 aaTAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGc                    <  1:546123/151‑1 (MQ=255)                                                                                                                                           g‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGtt          >  1:874615/1‑151 (MQ=255)                                                                                                                                               a‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACt       <  1:605886/151‑1 (MQ=255)                                                                                                                                               a‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACt       >  2:294693/1‑151 (MQ=255)                                                                                                                                                    tataCATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAt    <  2:304477/150‑1 (MQ=255)                                                                                                                                                    tataCATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATg   >  2:514551/1‑151 (MQ=255)                                                                                                                                                     ataCATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATgg  >  1:842558/1‑151 (MQ=255)                                                                                                                                                     ataCATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATg   <  2:897727/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                           AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGA‑GTGCTTCTTTTTCAC‑TTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413589‑1413885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑