Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,655,641	Δ1 bp	21.4%	intergenic (‑96/+56)	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	5,655,641	0	T	.	21.4%	65.3 / 16.9	28	intergenic (‑96/+56)	epd/tktA	D‑erythrose 4‑phosphate dehydrogenase/transketolase A
Reads supporting (aligned to +/- strand):  ref base T (10/11);  new base . (4/2);  total (15/13)
Fisher's exact test for biased strand distribution p-value = 6.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.72e-01

CGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGACTCACC  >  NC_002947/5655497‑5655789                                                                                                                                                  |                                                                                                                                                      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                                                                                                                                                   >  6:420239/1‑132 (MQ=255)                  ttGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                                   <  5:420239/132‑1 (MQ=255)                                                                                                                       ccGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATGCCACACCGCAAATTCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGaa                             >  4:237633/1‑149 (MQ=17)                                                                                                                       ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCGGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGaa                             >  7:147684/1‑148 (MQ=255)                                                                                                                       ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTc                                >  6:304444/1‑145 (MQ=255)                                                                                                                       ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTc                                <  5:304444/145‑1 (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)                                                                                                                                                  tctGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGACTCAcc  >  4:338466/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                      CGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATG‑AAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGCCGGCGCCGACTCACC  >  NC_002947/5655497‑5655789

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: ‑