Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	233,114	0	G	A	49.1%	39.7 / 31.7	53	S281F (TCC→TTC)	mltD	putative membrane‑bound lytic murein transglycosylase D
Reads supporting (aligned to +/- strand):  ref base G (20/7);  new base A (0/26);  total (20/33)
Fisher's exact test for biased strand distribution p-value = 5.53e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCGTCGACTGTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCAATGCCAGCATT  >  NC_000913/232964‑233257                                                                                                                                                         |                                                                                                                                                aGCGTCGACTGTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACgg                                                                                                                                                 >  1:143765/1‑151 (MQ=255)  gCGTCGACTGTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGa                                                                                                                                                <  1:172926/151‑1 (MQ=255)       gACTGTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATcc                                                                                                                                           <  2:945112/151‑1 (MQ=255)           gTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGc                                                                                                                                       <  2:770596/151‑1 (MQ=255)            tACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGCTCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGACAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCACGcc                                                                                                                                      >  2:657415/1‑151 (MQ=255)                     aaTTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCt                                                                                                                             >  2:251782/1‑151 (MQ=255)                       tttCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTAc                                                                                                                           >  2:959577/1‑151 (MQ=255)                                  gCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCAttt                                                                                                                >  1:308466/1‑151 (MQ=255)                                   ccAGAGATCCACGCAGTTGATCTGCTTGTTTTTTGGCCACCATCCCGTCCGGCGGCCCCCTGCCCCCCGGGGGGGAGCTTTTT‑CCCCCAGCGTTGAATTTCTT‑CAGTTTGCGGACGAAAACCCCCGCCATATCTGCTACCTTCGCCAtt                                                                                                                 <  1:163069/149‑1 (MQ=255)                                       ataTTCCCGCAGTTGATCTGCATTTTTTTTTGGCCCCATCACGTCCGGCGGGCCACTGGCCCCCGGCGTGGAGCTTTTC‑CCGCCAGCGTTAATTGTCTT‑CGGTTTGCTGACGAAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAAc                                                                                                            <  2:349477/148‑1 (MQ=255)                                          tccccgagtttGATCTGCTTGTTTCTTGGGCCCCACCCCGTCCGGCGGCCCTCTCGCCCCCAGCGGGGACCTTTTT‑CCGCCAG‑TTTTAATTTCTTCCATTTTGCTGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTc                                                                                                               <  2:298508/135‑1 (MQ=255)                                          tccACGCAGTTGATTTGCTTGTTTTTTTGCCACCATCCCGTACTGCGGGCCCCTGGCGCCCAGGGGGGGCCTTTTT‑CCGCCAGCTTTGAATGTCTC‑CAGCTTCCTGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCgg                                                                                                         <  2:280566/148‑1 (MQ=255)                                            cACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGgct                                                                                                      >  2:98347/1‑151 (MQ=255)                                               gCAGTTGTTCTGCTTGCTTCTTTGCCCCCATCCCGGCCGGCGGGCCACTGGCCCCGGGCGTGGACCTTTTC‑CCCCCAGTTTTGATTGTCTT‑CAGTTTCCGGACGGAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGgctg                                                                                                     <  2:48219/149‑1 (MQ=255)                                                cAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTc                                                                                                  >  1:604876/1‑151 (MQ=255)                                                  gTTGATCTGCTTGTTTTTTTGCCCCCACCCCGTCCGGGGGGCCTCTTGCGCCCGGGGTGGGGCTTTTT‑CCGCCAGCTTTGATTGTCTC‑CAGTTTGCTGAGGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTc                                                                                                  <  1:189222/149‑1 (MQ=255)                                                  gTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTc                                                                                                  >  1:528904/1‑149 (MQ=255)                                                     gttctgcttttttcttGGGCCCCACCCCTTCCGGCGGCCCCCTTGCGCCAAGCGGGGTGCTTTTT‑CCCCCGGCGTTGATTGTCTT‑CGGTTGGCGGAGGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTg                                                                                             <  1:211711/140‑1 (MQ=255)                                                                ttttttGCCCCCATCCCGTTCGGCGGCCCCCTTCCCCCCAGCGGGGGGCTTTTT‑CCCCCAGCGTTGAATGTCTC‑CGGTTTGCTGACGAAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACAcgc                                                                                      <  1:494632/144‑1 (MQ=255)                                                                tttttgggCCCCATCCCGTGCGGCGGCCCCCTGGCGCCCGGCGTGG‑GCCTTTTCACGCCAGCGTTAATTGTCTT‑CAGTTTGCGGAGGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGc                                                                                            <  1:505226/135‑1 (MQ=255)                                                                    ttGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGc                                                                              >  1:300862/1‑151 (MQ=255)                                                                    ttGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGc                                                                              >  1:88788/1‑151 (MQ=255)                                                                        cACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACgg                                                                          >  1:549051/1‑151 (MQ=255)                                                                          ccATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCt                                                                        >  2:37269/1‑151 (MQ=255)                                                                                cgttcggCGGGCCTCTTGCGCCCAGCGTGGACCTTTTT‑CCGCGAGGGTTGAATGTCTT‑CAGCTTGCTGACGAAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCAt                                                                   <  1:263135/144‑1 (MQ=255)                                                                                cGTACGGCGGGCCTCTTGCCCCCAGCGTGGAGCTTTTT‑CCGCCGGCGTTGATTGTCTC‑CAGCTTGCTGACGAAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCAt                                                                   <  1:971161/150‑1 (MQ=255)                                                                                  tACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCgg                                                                >  2:5520/1‑151 (MQ=255)                                                                                   cgtGCGGGCCCCTTGCCCCCGGGGTGGACCTTTTT‑CCGCCAGCTTTAATTTTCTT‑CACCTTGCTGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCgg                                                                <  1:705536/148‑1 (MQ=255)                                                                                   aCTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGt                                                               >  1:95459/1‑151 (MQ=255)                                                                                      gCGGGCCCCTGGCCCCCGGGGGGGGCCTTTTT‑CCGCCAGTTTTGAATGCCTT‑CAGTTTGCTGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTc                                                              <  1:236445/149‑1 (MQ=255)                                                                                        gggCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTg                                                          >  1:783995/1‑151 (MQ=255)                                                                                        ggccctcTTGCGCCCGGGGTGGCGCTTTTT‑CCGCAGGGGTTGATTTTCTC‑CAGCTGGCTGACGGAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCg                                                             <  2:399494/142‑1 (MQ=255)                                                                                            ctctgccccccGGCGTGGACCTTTTT‑ACGCCGGGGTTAAATTTTTC‑CGTCTTGCGGACGAAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTgg                                                         <  1:712307/140‑1 (MQ=255)                                                                                                    cccgggggggcccttttt‑CCGCCAGCGTTAATTGTCTT‑CACTTTGCTGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACg                                               <  2:363039/136‑1 (MQ=255)                                                                                                    cccAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCTGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACg                                               <  2:455011/150‑1 (MQ=255)                                                                                                        gggTGGCGCTTTTC‑CCGCCAGGGTTGAGTTTCTT‑CAGCTTGCTGACGGAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCa                                            <  2:148056/147‑1 (MQ=255)                                                                                                        gCGTGGAGCTTTTT‑CCCCCAGCGTTAAATGTTTT‑CAGCTTGCGGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATa                                          <  2:787127/151‑1 (MQ=255)                                                                                                          gggggccttttt‑CCCCCGGCGTTGAATTTTTT‑CAGCTTGCGGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAAc                                        <  1:645174/143‑1 (MQ=255)                                                                                                                  tttt‑CCGCCGGTGTTGATTTTCTC‑CAGCTTGCGGACGAAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCt                                     <  2:143757/146‑1 (MQ=255)                                                                                                                  tttt‑CCGCCAGGTTGGATTGTTTC‑CGGCTTGCGGAGGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCtt                                    <  1:928103/147‑1 (MQ=255)                                                                                                                  tttt‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTg                                >  2:916929/1‑151 (MQ=255)                                                                                                                   tttcccGCCAGGTTTGATTTTTTC‑CAGTTTGCTGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCt                                 <  2:11621/145‑1 (MQ=255)                                                                                                                       aCGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGtttt                            >  1:419927/1‑151 (MQ=255)                                                                                                                        cGCCGGGGTTAATTGTCTT‑CTGTTTGCTGCCAAAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGtttt                            <  2:972319/150‑1 (MQ=255)                                                                                                                        cGCCAGCGTTGATTGTCTT‑CAGCTTGCTGACGAAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGttt                             <  1:619394/149‑1 (MQ=255)                                                                                                                          ccAGCGTTGAATTTCTT‑CAGTTTGCGGACGAAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTga                         <  2:506839/151‑1 (MQ=255)                                                                                                                            aGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTg                          >  2:812372/1‑148 (MQ=255)                                                                                                                              cGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAat                     >  2:729535/1‑151 (MQ=255)                                                                                                                                ttaattGTCTT‑CAGTTTGCTGACGAAACCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTgag                        <  2:875735/141‑1 (MQ=255)                                                                                                                                 tGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATc                  >  2:470796/1‑151 (MQ=255)                                                                                                                                         ctttagtgtGCTGACGAAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTTTTTTTgaga                       <  2:322023/131‑1 (MQ=255)                                                                                                                                          ttcggtttGCGGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCa             <  2:118703/142‑1 (MQ=255)                                                                                                                                                ttGCTGACGAAAACCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCAATGCCAg      <  1:513784/149‑1 (MQ=255)                                                                                                                                                  gCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCAATGCCAGCAtt  >  2:865568/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                AGCGTCGACTGTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCAATGCCAGCATT  >  NC_000913/232964‑233257

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑