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%	118.0 / NA	25	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (15/10);  total (15/10)

AAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090299‑3090385                                           |                                             aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                      <  1:1317324‑M1/50‑4 (MQ=255)   aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:240856‑M1/50‑6 (MQ=255)      aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:1457386‑M1/50‑9 (MQ=255)            cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            >  1:802774‑M1/1‑36 (MQ=255)             gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:1778218‑M1/1‑35 (MQ=255)             gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:1799658‑M1/1‑35 (MQ=255)              cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:2124106‑M1/50‑17 (MQ=255)               tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:457157‑M1/1‑33 (MQ=255)               tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:1248880‑M1/1‑33 (MQ=255)               tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:344693‑M1/1‑33 (MQ=255)                aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       >  1:1339468‑M1/1‑32 (MQ=255)                 cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:2062400‑M1/50‑20 (MQ=255)                        ggCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:346155‑M1/1‑24 (MQ=255)                        ggCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:1405513‑M1/1‑24 (MQ=255)                          cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:1103962‑M1/50‑29 (MQ=255)                          cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:120382‑M1/1‑22 (MQ=255)                             gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:1660609‑M1/1‑19 (MQ=255)                             gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:10107‑M1/1‑19 (MQ=255)                              ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:318094‑M1/50‑33 (MQ=255)                                 tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac      >  1:1122285‑M1/1‑15 (MQ=255)                                   acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:1408156‑M1/50‑38 (MQ=255)                                   acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    >  1:861079‑M1/1‑13 (MQ=255)                                   acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     <  1:280129‑M1/49‑37 (MQ=255)                                     acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:322586‑M1/1‑11 (MQ=255)                                     acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  <  1:1355473‑M1/50‑40 (MQ=255)                                           |                                             AAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090299‑3090385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑