Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	524,349	G→C	13.1%	intergenic (+216/‑600)	tyrS → / → PP_16SC	tyrosine‑‑tRNA ligase/16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	524,349	0	G	C	13.1%	143.8 / 10.5	53	intergenic (+216/‑600)	tyrS/PP_16SC	tyrosine‑‑tRNA ligase/16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base G (25/21);  new base C (3/4);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 6.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GTGGTTGCTGTTGTAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATCCCCTTATAATGCGCCCCACTTCCA  >  NC_002947/524204‑524494                                                                                                                                                   |                                                                                                                                                   gtggtTGCTGTTGTAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCgcgg                                                                                                                                                 >  1:139167/1‑149 (MQ=255)        gtggtgtAGGGGGACGGGGCCGTTTTGACCGGGGGTTGGCGGTGAGATGTGGCCGCCACAACCCTTGCATCGCCTGTGAGATCCGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGggcggc                                                                                                                                            <  1:110434/144‑1 (MQ=37)         tgttgtAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAGACCGAGCGCCGCCCGCGCGGCGCt                                                                                                                                         >  2:286607/1‑149 (MQ=255)         tgttgtAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCt                                                                                                                                         >  8:38638/1‑149 (MQ=255)         tgttgtAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCCCGCGCGGCGCt                                                                                                                                         >  3:252851/1‑149 (MQ=255)           ttgtCGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCg                                                                                                                                       <  7:105573/149‑1 (MQ=255)           ttgtAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAGACCGAGCGCCGCCCGCGCGGCGCTCg                                                                                                                                       <  1:286607/149‑1 (MQ=255)           ttgtAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTc                                                                                                                                        <  2:8266/148‑1 (MQ=255)           ttgtAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCCCGCGCGGCGCTCg                                                                                                                                       <  4:252851/149‑1 (MQ=255)            ggtAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCCCGCGCGGCGCTCg                                                                                                                                       <  5:109965/147‑1 (MQ=255)              tAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGtc                                                                                                                                    >  7:312287/1‑149 (MQ=255)               agggggagggggCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGtct                                                                                                                                   >  4:103618/1‑149 (MQ=255)                gggggagggggCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGtct                                                                                                                                   <  3:103618/148‑1 (MQ=255)                 ggggagggggCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCa                                                                                                                                 >  2:219886/1‑149 (MQ=255)                 ggggagggggCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCa                                                                                                                                 <  2:298280/149‑1 (MQ=255)                    gagggggCTGTTTTGAGCGGGGGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAg                                                                                                                              <  7:155960/149‑1 (MQ=255)                         ggCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCt                                                                                                                         <  1:219886/149‑1 (MQ=255)                              ttttGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGGCTCATAGGCGCTGAAAc                                                                                                                    >  5:156971/1‑149 (MQ=255)                                      gggTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGtctc                                                                                                                                  >  2:231777/1‑127 (MQ=255)                                      gggTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑gg                                                                                                           >  5:292516/1‑149 (MQ=255)                                                        gtgtCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑g                                                                                                            <  6:218785/130‑1 (MQ=255)                                                        gtgtCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑g                                                                                                            >  5:218785/1‑130 (MQ=255)                                                                 acaACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTgg                                                                                                >  6:241915/1‑133 (MQ=255)                                                                 acaACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTgg                                                                                                <  5:241915/133‑1 (MQ=255)                                                                 acaACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTc                                                                                >  2:316592/1‑149 (MQ=255)                                                                   aaCCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCtt                                                                              >  1:178361/1‑149 (MQ=255)                                                                   aaCCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCtt                                                                              >  8:252288/1‑149 (MQ=255)                                                                      ccTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTc                                                                           >  8:182256/1‑149 (MQ=255)                                                                          gCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTcccc                                                                        <  8:46263/148‑1 (MQ=255)                                                                            aGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCCCATAGGCGCTCAAACAGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCtt                                                                      >  7:61102/1‑148 (MQ=255)                                                                               gcCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCt                                                                                          >  4:208280/1‑125 (MQ=255)                                                                               gcCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCt                                                                                          <  3:208280/125‑1 (MQ=255)                                                                                 cggtgATAT‑CGAGCGCCGCCGGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATAttt                                                                <  8:312287/147‑1 (MQ=255)                                                                                  tgtgAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATAttt                                                                >  4:224607/1‑148 (MQ=255)                                                                                    tgAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTccc                                                                         >  8:164242/1‑137 (MQ=255)                                                                                    tgAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTccc                                                                         <  7:164242/137‑1 (MQ=255)                                                                                              gcgcCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGaa                                                    <  2:139167/149‑1 (MQ=255)                                                                                               cgccgcCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGaa                                                    <  1:316592/148‑1 (MQ=255)                                                                                                    cccgcGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTaaa                                              <  5:111496/149‑1 (MQ=255)                                                                                                                  gagaCATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCctc                                 <  7:182256/148‑1 (MQ=255)                                                                                                                  gacagtttCAGCGCCTATGAGACCGAGCGCCGCCCGCGCGGCGCTCGGTTTCATAGGCGGTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTc                                                         >  6:59635/7‑124 (MQ=11)                                                                                                                  gacagtttCAGCGCCTATGAGACCGAGCGCCGCCCGCGCGGCGCTCGGTTTCATAGGCGGTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTc                                                         <  5:59635/118‑1 (MQ=11)                                                                                                                   agaCATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCctct                                <  6:292516/148‑1 (MQ=255)                                                                                                                        ttCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATc                          >  2:15131/1‑149 (MQ=255)                                                                                                                            ccGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATc                          <  7:62979/145‑1 (MQ=255)                                                                                                                            ccGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATc                          >  8:62979/1‑145 (MQ=255)                                                                                                                                cTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATCCCCTtat                   >  8:23027/1‑148 (MQ=255)                                                                                                                                    gAAACCGAGGGCCGCGCGGGCGGCGCTCGGTCCCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATCCCCTTATAATg               <  8:61102/148‑1 (MQ=255)                                                                                                                                     aaaCCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGTAAGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCGCGAATGCCCTTTTATTgc              >  1:96978/1‑149 (MQ=14)                                                                                                                                     aaaCCGAGCGCCGCGCGGGCGGCGATCGGTCTCATAGGCGCTGAAACTGTCGTGGGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTATCGAATCCCCTTATAATga              >  1:283339/1‑148 (MQ=255)                                                                                                                                      aaCAGAGCGCCGCGCTGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATCCCCTTATAATgcgc            <  4:257574/149‑1 (MQ=255)                                                                                                                                         cGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGCAGCCCTCTCGAATCCCCTTATAATTCGcccc         >  6:210786/1‑149 (MQ=255)                                                                                                                                          gAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATCCCCTTATAATGCGCCCCa        >  4:123955/1‑149 (MQ=255)                                                                                                                                          gAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGAAGCCCTCTCGAATCCCCTTATAATGCGCCCCa        >  8:16290/1‑149 (MQ=255)                                                                                                                                                cgcgcgGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATCCCCTTATAATGCGCCCCACTTCCa  <  7:252288/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                   GTGGTTGCTGTTGTAGGGGGAGGGGGCTGTTTTGAGAGGGTGTTGGCGGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGAT‑CGAGCGCCGCCCGCGTCCGGCTTGAGACATTCACCGCCTATGAAACCGAGCGCCGCGCGGGCGGCGCTCGGTCTCATAGGCGCTGAAACTGTCGT‑GGCGAACACTTGGCAGCCTCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACGCCCTCTCGAATCCCCTTATAATGCGCCCCACTTCCA  >  NC_002947/524204‑524494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑