Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	233,118	0	T	C	47.2%	47.5 / 21.6	53	I280V (ATT→GTT)	mltD	putative membrane‑bound lytic murein transglycosylase D
Reads supporting (aligned to +/- strand):  ref base T (20/8);  new base C (0/25);  total (20/33)
Fisher's exact test for biased strand distribution p-value = 1.56e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACTGTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCAATGCCAGCATTTTAG  >  NC_000913/232970‑233261                                                                                                                                                       |                                                                                                                                                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)                                                                                                                                                    aaaCCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCAATGCCAGCATTTTAg  <  1:168860/147‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                GACTGTACAGCAGCAATTTCGCCTGAAGCCAGAGATTCACGCAGTTGATCTGCATGCTTCTTTGGCACCATCACGTACTGCGGGCCACTTGCGCCCAGCGTGGAGCCTTTT‑ACGCCAGCGTTGAATGTCTT‑CAGCTTGCTGACGGAAATCCCCGCCATATCTGCTACCTTCGCCATTTCAACCGGGCTGCTCAGGTGCACACGCGCCAGAGCACGGCTTTCATCGGTCGTTGGCAGACGTACGCCATAACGCTTGCTGTTTTTGAGAATATCACTCAATGCCAGCATTTTAG  >  NC_000913/232970‑233261

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: ‑