Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	884,346	0	C	G	52.6%	41.6 / 71.4	38	A225G (GCG→GGG)	mdfA	multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (1/17);  new base G (20/0);  total (21/17)
Fisher's exact test for biased strand distribution p-value = 6.25e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.40e-06

TGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGT  >  NC_000913/884199‑884495                                                                                                                                                    |                                                                                                                                                         tgtttgCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGggcgc                                                                                                                                                        <  1:248763/150‑1 (MQ=255)              ggCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGgctggggctggg                                                                                                                                              >  1:928617/1‑147 (MQ=255)                 aGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGt                                                                                                                                        <  1:227268/150‑1 (MQ=255)                    gATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGGGCGGGGGGTCGTTAGt                                                                                                                                    >  1:323498/1‑151 (MQ=255)                     aTCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGGGGGGCTgggggttgtttgtt                                                                                                                                   >  2:913975/1‑140 (MQ=255)                       ctcCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCGGGGGCCgggggttgtttgttt                                                                                                                                  >  1:307874/1‑138 (MQ=255)                             tttCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGAGCggggggtcctttggttgt                                                                                                                                >  2:540752/1‑132 (MQ=255)                               tCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCGGGTGCTGGGGTTTGtttg                                                                                                                                     >  1:308225/1‑137 (MQ=255)                                  gTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGCGCCGGGGTTCGTTAGTCTGCCGtttgtgg                                                                                                                       >  1:550106/1‑145 (MQ=255)                                   tCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGc                                                                                                                      <  1:843555/150‑1 (MQ=255)                                       cAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGGGCTGGGGTTTGTTTGTATGCCCTTGCTGGCGTggg                                                                                                                 >  1:436095/1‑150 (MQ=255)                                         aCGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑c                                                                                                              <  1:667645/151‑1 (MQ=255)                                             gCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGccc                                                                                                          <  1:228123/151‑1 (MQ=255)                                               cATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAg                                                                                                        <  1:928405/151‑1 (MQ=255)                                                aTGCCTGAAGCCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGccc                                                                                                          <  2:300836/148‑1 (MQ=255)                                                          ccGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTat                                                                                            <  2:735788/151‑1 (MQ=255)                                                                  cgTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGGGCTGGGGTTCGTTTGTCTGCCGCTGCTGGCGTGGGT‑CGCCCCCTCG‑CCGCtttttat                                                                                         >  2:164820/1‑141 (MQ=255)                                                                   gTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGGGGCGGGGTTTGTTTGTCTTCCCTTGTTGGGGGGGGT‑CGccccccccccgcgttt                                                                                             >  1:955321/1‑129 (MQ=255)                                                                       aGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCGGGCGCGGGGGTTTGTTAGTTTGCCGGTGCTGGGGGGGGT‑CGCCCCGGCG‑CCGGTTTTTATCATTACCgg                                                                                >  1:555989/1‑150 (MQ=255)                                                                       aGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCgg                                                                                <  1:960133/150‑1 (MQ=255)                                                                       aGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGc                                                                               <  2:160250/151‑1 (MQ=255)                                                                              aaaCTCTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGCGGGGCTGGGGTTTGGTAGTCTGCCGTTGGTGGGGGGGGG‑CGGCCCGGCG‑CCGGTTTTTATCATTAACCgcgcgcggg                                                                        >  2:280940/1‑148 (MQ=255)                                                                                        tGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGGGCTGGGGTTTGTTTGTTTGCCGTTGGTGGCGGGGGG‑TGCCCCGGCG‑CCGATTTTTATCCTTTACGGCggg                                                                            >  1:609560/1‑135 (MQ=255)                                                                                              aaCTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCCGGGGCCGGGGTTTGTTTGTTTGCCGTTGCTGGCGGGGGTCCCCCCGGCCC‑CCGATT‑TTATCATTAACCGCGGGCCGGTGAGGAG‑GCATGaa                                                         >  1:226662/1‑149 (MQ=255)                                                                                                   ggTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGCGCTGGGGTTTGTTTGTTTGCCGTTGTTGGCGTGGGT‑CGCCCCGCCG‑CCGATTATTATCATTACCCGGGGGCCGTTGTGCAG‑GTATGAata                                                       >  1:412183/1‑146 (MQ=255)                                                                                                    gTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCtt                                                 <  2:858026/151‑1 (MQ=255)                                                                                                       gTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGGGGCGGGGGTCGTTAAACTGGCGTTGTTGGGGGGGGG‑GGCCCCGCCG‑CCGGATTTCCTTATTTCCCGCGGGCAGGTTGGCCG‑GCATGAATATTGCTtgt                                               >  2:255095/1‑149 (MQ=255)                                                                                                               aaGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGc                                      <  2:206410/151‑1 (MQ=255)                                                                                                                 gCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCt                                    <  1:346042/151‑1 (MQ=255)                                                                                                                  cTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCGGGGGCTGGGGGTTGTTAGTCTGCCGCTGCTGGGGGGGGG‑CGCCCCCGCGCCCGCTTTTC‑TTATTACCCGCGGGCAGGTTAGGAG‑CCAATAATATAGCTttctgcgcggggc                                     >  2:3349/1‑142 (MQ=255)                                                                                                                    ggTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTAt                                  <  1:579701/150‑1 (MQ=255)                                                                                                                     gTGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGGTGGGGGGGGGGGTCGTTAGTCTGCCGGTGCTGGGGGGGGT‑CGGCCCGCCG‑CCGGCTATTATCCTTATCGGCGCGCAGGTGAGGAG‑CGATTAATATTGGTTGCTGCAAGTGGCTAttt                                >  2:366686/1‑151 (MQ=255)                                                                                                                     gTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTAttt                                <  2:270547/151‑1 (MQ=255)                                                                                                                      tGCTGAAGAACGGCCGCTTTGTGGCGGGGGGGCTGGCGCCGGGGTTCGTTAGTCTTCCGCTGCTGGCGTGGGG‑CGCCCACGCG‑CCGCTTTTTATCATTTCCCGCGGGGCGGTGAGCAG‑CGGTGAAAATTGCTTTTTGCCAGGGGCTAtttt                               >  1:593497/1‑151 (MQ=255)                                                                                                                          gaagaaCGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCg                             <  2:711820/149‑1 (MQ=255)                                                                                                                            agaaCGGCCGCTTTGTGGCGGGGGGGCTGGGGCGGGGGATCGTTAGTTTGGCGTTTCTGGGGGGGGG‑GGCTCAAGCG‑CCCGATGTTAAAATTACCGGCGGGCAGGTGTGGAGACAATG‑ATATTGTTTGGTGCAAGTGGCTTTTTTTggggg                         >  1:406954/1‑150 (MQ=255)                                                                                                                                     gCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGc                <  1:97964/151‑1 (MQ=255)                                                                                                                                        ttGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCg               <  2:928604/149‑1 (MQ=255)                                                                                                                                                 gggCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCt    >  1:143330/1‑151 (MQ=255)                                                                                                                                                  ggcgctggcgctGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTg   >  2:324318/1‑151 (MQ=255)                                                                                                                                                  ggcgctggcgctGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTg   <  1:615363/151‑1 (MQ=255)                                                                                                                                                   gcgctggcgctgGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTAGTTTCGGGGCGTTAATTGCGGGTAACTTGCTGt  <  2:1005015/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                         TGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGAGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCGTTAGTCTGCCGTTGCTGGCGTGGAT‑CGCCCAGTCG‑CCGATTATCATCATTACCGGCGAGCAGTTGAGCAG‑CTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGT  >  NC_000913/884199‑884495

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑