Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,655,636	C→A	12.3%	intergenic (‑91/+61)	epd ← / ← tktA	D‑erythrose 4‑phosphate dehydrogenase/transketolase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,655,636	0	C	A	12.3%	117.2 / 9.7	49	intergenic (‑91/+61)	epd/tktA	D‑erythrose 4‑phosphate dehydrogenase/transketolase A
Reads supporting (aligned to +/- strand):  ref base C (20/23);  new base A (4/2);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 4.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.40e-01

AGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGA  >  NC_002947/5655491‑5655783                                                                                                                                                   |                                                                                                                                                     aGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAAc                                                                                                                                                   >  5:74084/1‑149 (MQ=255)        gATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgtg                                                                                                                                            <  4:3344/149‑1 (MQ=255)         aTACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTgg                                                                                                                                           >  6:140039/1‑149 (MQ=255)          tACGGCCATAACCGTTGAGTGCAACTTTGTAGGTACGGTGGGTAATTTGGGGCTCTCGTAAGCTAACTATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑Ctgtg                                                                                                                                            <  1:265016/147‑1 (MQ=18)               ccATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCgg                                                                                                                                     <  5:72496/149‑1 (MQ=255)                 aTAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGc                                                                                                                                   <  5:140039/149‑1 (MQ=255)                     ccGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGc                                                                                                                                   <  7:136174/145‑1 (MQ=255)                     ccGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGc                                                                                                                                   >  8:136174/1‑145 (MQ=255)                          gAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCcgc                                                                                                                          >  7:181132/1‑148 (MQ=255)                           aGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCCGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCcgcg                                                                                                                         <  2:184941/148‑1 (MQ=255)                           aGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCcgcg                                                                                                                         <  1:209841/148‑1 (MQ=255)                                 aCTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAg                                                                                                                  <  7:7402/149‑1 (MQ=255)                                      gTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGa                                                                                                              >  2:219882/1‑148 (MQ=255)                                       tAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAC‑GGTTTACTGCAACCTGTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGcca                                                                                                            >  2:3498/1‑149 (MQ=39)                                         gggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTGCCACAC‑GGGTTGCTGCAACCTCTGTGGGATCCGGCTTG‑CCCGCGTATTAAGGGGGCAcc                                                                                                          >  5:24305/1‑149 (MQ=255)                                          ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGTCAccg                                                                                                         >  5:90446/1‑149 (MQ=255)                                          ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCATCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACAccg                                                                                                         >  5:107645/1‑149 (MQ=255)                                            aCGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGaa                                                                                                                   <  5:153496/137‑1 (MQ=255)                                            aCGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGaa                                                                                                                   >  6:153496/1‑137 (MQ=255)                                                  gggCATTCGGGGATCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGGGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCCGCGAATGAAGGCGACACCGCCCGCAg                                                                                                  <  1:3498/149‑1 (MQ=255)                                                    gCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACAccgcccg                                                                                                     >  2:79399/1‑143 (MQ=255)                                                    gCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATc                                                                                               <  1:79399/149‑1 (MQ=255)                                                       ttCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCtt                                                                                             >  4:209444/1‑148 (MQ=255)                                                             gCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCa                                                                                      <  6:291088/149‑1 (MQ=255)                                                              cacACGACACAGTTCAATTGTCGTCAGCCTGCGTAATTTGCGGTGGGGCATTCCCGGGCAAGCCCGCTCCCACAG‑GGTTTCATCCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAg                                                                                     <  1:166626/147‑1 (MQ=38)                                                                cACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCCACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGCCACCGCCCGCAGATATTTTAATCCGTc                                                                                   >  8:270294/1‑149 (MQ=38)                                                                 aCGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGt                                                                                    <  6:74084/147‑1 (MQ=255)                                                                     gaCAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCca                                                                              <  6:56913/149‑1 (MQ=255)                                                                        aGTTCAATTGTCTTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCcagca                                                                           <  6:107645/149‑1 (MQ=255)                                                                        aGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGTCACCGCCCGCAGATCTTTAAATCAGTCTTCcagca                                                                           <  6:90446/149‑1 (MQ=255)                                                                                              ggAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGTCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGAt                                                     <  5:155792/149‑1 (MQ=255)                                                                                                attttGCGGGGGGCCATTCGCGGCAACCCCCGCTCCCACTG‑GGTTTCATCCAACCTGTGTGGTAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATg                                                    <  5:48455/146‑1 (MQ=255)                                                                                                  tttGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTtc                                                 >  6:82947/1‑149 (MQ=255)                                                                                                             gCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGaa                                      <  1:219882/149‑1 (MQ=255)                                                                                                                   gcgGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATg                                                    <  7:170179/129‑1 (MQ=255)                                                                                                                   gcgGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATg                                                    >  8:170179/1‑129 (MQ=255)                                                                                                                      ggCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAActc                             <  5:82947/149‑1 (MQ=255)                                                                                                                       gCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAActct                            >  8:133778/1‑149 (MQ=255)                                                                                                                         aaGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTc                          >  3:139279/1‑149 (MQ=37)                                                                                                                                   ccACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAActct                            >  5:114264/1‑137 (MQ=37)                                                                                                                                   ccACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAActct                            <  6:114264/137‑1 (MQ=37)                                                                                                                                   ccACAGAGGTTGCATGAAACC‑ATGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGcc                >  7:56360/1‑149 (MQ=38)                                                                                                                                   ccACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGcc                <  8:181132/149‑1 (MQ=255)                                                                                                                                           gTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCg         <  6:24305/149‑1 (MQ=255)                                                                                                                                            tttCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCgg        >  3:305798/1‑149 (MQ=255)                                                                                                                                            tttCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTAATCGAACAATGCCGAAGCCgg        >  6:311752/1‑149 (MQ=255)                                                                                                                                               cATGAAACC‑CTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGcc    >  5:209453/1‑149 (MQ=255)                                                                                                                                                  gCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGa  >  6:48172/1‑149 (MQ=255)                                                                                                                                                  gCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGa  >  8:160970/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                     AGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTG‑CCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGA  >  NC_002947/5655491‑5655783

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: ‑