Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,655,636	C→A	20.7%	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	20.7%	61.5 / 11.4	29	intergenic (‑91/+61)	epd/tktA	D‑erythrose 4‑phosphate dehydrogenase/transketolase A
Reads supporting (aligned to +/- strand):  ref base C (11/12);  new base A (4/2);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 6.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.32e-01

CACAGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCG  >  NC_002947/5655488‑5655782                                                                                                                                                      |                                                                                                                                                    cacaGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGc                                                                                                                                                     <  6:232292/149‑1 (MQ=255)    aGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAAc                                                                                                                                                  <  2:66493/149‑1 (MQ=255)          cGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGAAGGTGGGGCATTCGGGTCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                            <  4:346833/149‑1 (MQ=255)           gATACGGCCATAACCGTTGAGTGCCACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCGGCTCCCACAG‑GGTTTCATGCAACCTCtgtg                                                                                                                                           <  1:38516/149‑1 (MQ=255)           gATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGTCTCACGAGACAGTTCAATTGTCGTCATCCTGCGGAATTTGCGGTGTGGCATTCTCGGGCAAGCCCGCTCCCACAT‑GGTTTCATGCAACCTCtgtg                                                                                                                                           <  2:399490/149‑1 (MQ=255)            aTACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTgg                                                                                                                                          <  6:78058/149‑1 (MQ=255)                  ccATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCgg                                                                                                                                    <  4:311401/149‑1 (MQ=37)                  ccATAACCGTTGAGTGCAACTTTGTAGGCACGGTGGGGCATTCGGGTCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTTGAATTCGCGGGCAAGCCCGCTCCCACAG‑GGAATCATGCAACCACTGAGGGAGCgg                                                                                                                                    >  5:113047/1‑149 (MQ=255)                   cATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGTGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCggg                                                                                                                                   <  7:233023/149‑1 (MQ=37)                    aTAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGc                                                                                                                                  <  4:13895/149‑1 (MQ=255)                       acagTTGAGTGCAACTTTGTAGTGAGGGTGGGGCATTCGGTGCGCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGGTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCtt                                                                                                                                <  6:113047/145‑1 (MQ=255)                       aCCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGGGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGTGAGCGGGCtt                                                                                                                                <  2:2236/148‑1 (MQ=255)                        ccGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGc                                                                                                                              <  5:292823/149‑1 (MQ=255)                           ttGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                            <  5:420239/132‑1 (MQ=255)                           ttGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                            >  6:420239/1‑132 (MQ=255)                                                                                                                                ccGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATGCCACACCGCAAATTCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGaa                      >  4:237633/1‑149 (MQ=17)                                                                                                                                ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCGGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGaa                      >  7:147684/1‑148 (MQ=255)                                                                                                                                ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTc                         <  5:304444/145‑1 (MQ=255)                                                                                                                                ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTc                         >  6:304444/1‑145 (MQ=255)                                                                                                                                    tCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATGCCACACCGCAAATTCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAAt                  >  3:213327/1‑149 (MQ=17)                                                                                                                                      ccACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGcc               >  2:370520/1‑149 (MQ=255)                                                                                                                                       cacagaggTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGcc               >  5:556/7‑148 (MQ=38)                                                                                                                                        acagaggTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATAAGACTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCg              >  5:355298/6‑148 (MQ=38)                                                                                                                                        acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCg              >  5:246563/1‑148 (MQ=255)                                                                                                                                        acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCAAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCg              >  7:276274/1‑148 (MQ=255)                                                                                                                                               tttCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGaa            <  7:49277/144‑1 (MQ=255)                                                                                                                                               tttCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGaa            >  8:49277/1‑144 (MQ=255)                                                                                                                                                   aTGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGcc   >  2:25528/1‑149 (MQ=255)                                                                                                                                                    tGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGcc   >  7:378191/1‑148 (MQ=255)                                                                                                                                                    tGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCg  >  8:318944/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                    CACAGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCG  >  NC_002947/5655488‑5655782

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: ‑