Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,808,863	G→A	pseudogene (548/1178 nt)	ygaY →	putative transporter YgaY, N‑terminal fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,808,863	0	G	A	100.0%	64.0 / NA	20	pseudogene (548/1178 nt)	ygaY	putative transporter YgaY, N‑terminal fragment
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/10);  total (10/10)

TCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTC  >  NC_000913/2808734‑2808989                                                                                                                                  |                                                                                                                               tCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACca                                                                                                                             >  1:286242/1‑133 (MQ=255) tCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACca                                                                                                                             >  1:338855/1‑133 (MQ=255) tCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCCGGCATTTTGGCGTCGTCTACca                                                                                                                             >  1:215699/1‑133 (MQ=255) tCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCCGGCATTATGGCGTAGTCTACca                                                                                                                             >  1:201193/1‑133 (MQ=255)           gggATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAAt                                                                                                                   >  2:106805/1‑133 (MQ=255)                     tGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCa                                                                                                         <  2:338855/133‑1 (MQ=255)                           ggACAGTTGCAGGATCGCTGGCGATTCTTGGCAGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCaa                                                                                                   <  2:201193/133‑1 (MQ=255)                                  tGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCca                                                                                            <  1:369611/133‑1 (MQ=255)                                         ttGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAgttgt                                                                                     >  1:491522/1‑133 (MQ=255)                                              ggCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGt                                                                                <  2:124832/133‑1 (MQ=255)                                                 gAATCTCGCCGGCTGGCGCACCGTCCTTTGGGTTGCTTGGGGGTTAATGGCACTGATGGCCCTGGCATCATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCCCAACTACCCACAGTTGTTGGGTTcc                                                                             >  2:369765/1‑133 (MQ=255)                                                        ggcggcTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCa                                                                      <  1:413120/133‑1 (MQ=255)                                                          cggcTGGCGCCCCGTGTTTTGGGTAGCTTCGGGGTTAATGGTACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGt                                                                    <  2:215699/133‑1 (MQ=255)                                                                             tGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATaaaa                                                 <  1:106805/133‑1 (MQ=255)                                                                                  tGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTATTCAGTACGTTGATAAGCGATAAAATTCTg                                            >  1:141957/1‑133 (MQ=255)                                                                                    cTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCg                                          >  1:469660/1‑133 (MQ=255)                                                                                                   cACTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCt                           >  1:42568/1‑133 (MQ=255)                                                                                                    aCTGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTg                          >  2:6820/1‑133 (MQ=255)                                                                                                      tGATGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTggg                        >  2:255734/1‑133 (MQ=255)                                                                                                         tGGCGCTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTg                     <  2:42568/133‑1 (MQ=255)                                                                                                           gcgcTGGCATTATGGCGTGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGcc                   <  2:23668/133‑1 (MQ=255)                                                                                                               tGGCATTATGTCGTGCTCTACCACCAATTAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGAc               <  2:141957/133‑1 (MQ=255)                                                                                                                            tGGTCTACCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTc  >  2:3171/1‑133 (MQ=255)                                                                                                                                  |                                                                                                                               TCTGCTGTTGGGGATCTTGCTGGCACGGACAGTTGCCGGATTGCTGGCGAATCTCGGCGGCTGGCGCACCGTCTTTTGGGTTGCTTCGGTGTTAATGGCACTGATGGCGCTGGCATTATGGCGTGGTCTGCCACAAATGAAATCAGAAACCCACCTCAACTACCCACAGTTGTTGGGTTCCGTTTTCAGTATGTTTATCAGCGATAAAATTCTGCGTACCCGCGCGTTGCTGGGCTGCCTGACCTTTGCCAATTTC  >  NC_000913/2808734‑2808989

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑