Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,090,341	Δ1 bp	intergenic (+89/‑6)	yggI → / → endA	conserved protein YggI/DNA‑specific endonuclease I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,090,341	0	T	.	100.0%	107.5 / NA	23	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (13/10);  total (13/10)

ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGA  >  NC_000913/3090296‑3090383                                              |                                           aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                       >  1:1985454/1‑50 (MQ=255) aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                       >  1:82553/1‑50 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:1385854‑M1/1‑48 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                   <  1:2650877‑M1/50‑5 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                   >  1:1519790‑M1/1‑45 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                >  1:1937881‑M1/1‑43 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                               <  1:220887‑M1/50‑9 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                             <  1:58697‑M1/50‑11 (MQ=255)               cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:877734‑M1/1‑36 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                       <  1:198590‑M1/50‑17 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                    >  1:1416272‑M1/1‑31 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   >  1:1426068‑M1/1‑30 (MQ=255)                      ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                  <  1:2061011‑M1/50‑22 (MQ=255)                      ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                  >  1:2521843‑M1/1‑29 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                 <  1:907123‑M1/49‑23 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt             >  1:2099428‑M1/1‑23 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt             <  1:1691872‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt              <  1:1859657‑M1/48‑26 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc        >  1:517117‑M1/1‑19 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccct       >  1:760155‑M1/1‑18 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       <  1:239187‑M1/50‑33 (MQ=255)                                  tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       >  1:2149456‑M1/1‑17 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc  <  1:2187623‑M1/50‑38 (MQ=255)                                              |                                           ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGA  >  NC_000913/3090296‑3090383

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑