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%	148.0 / NA	31	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (15/16);  total (15/16)

CAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAG  >  NC_000913/3090298‑3090384                                            |                                            cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                      <  1:735184‑M1/50‑3 (MQ=255)  aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                      >  1:1839778‑M1/1‑47 (MQ=255)     aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                  <  1:275199‑M1/50‑7 (MQ=255)       aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                 >  1:2117945‑M1/1‑42 (MQ=255)        gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                               <  1:428727‑M1/50‑10 (MQ=255)         cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                              <  1:862957‑M1/50‑11 (MQ=255)            tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                            <  1:2599960‑M1/49‑13 (MQ=255)                tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                       >  1:1757799‑M1/1‑33 (MQ=255)                tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                       >  1:798645‑M1/1‑33 (MQ=255)                  cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                     >  1:727379‑M1/1‑31 (MQ=255)                  cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                      <  1:1872481‑M1/49‑19 (MQ=255)                    ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                   >  1:1989546‑M1/1‑29 (MQ=255)                     tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                  >  1:452495‑M1/1‑28 (MQ=255)                     tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                  >  1:863624‑M1/1‑28 (MQ=255)                     tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                  >  1:911591‑M1/1‑28 (MQ=255)                      gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                  <  1:7067‑M1/49‑23 (MQ=255)                       cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                 <  1:1622436‑M1/49‑24 (MQ=255)                       cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                 <  1:249768‑M1/49‑24 (MQ=255)                          gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta             <  1:1404382‑M1/50‑28 (MQ=255)                          gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta             <  1:1018733‑M1/50‑28 (MQ=255)                          gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt              <  1:2381523‑M1/49‑27 (MQ=255)                             cGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc          >  1:249411‑M1/1‑20 (MQ=255)                              gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc         <  1:2728451‑M1/50‑32 (MQ=255)                              gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc         >  1:1008781‑M1/1‑19 (MQ=255)                               ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc        >  1:512695‑M1/1‑18 (MQ=255)                               ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc        >  1:1946649‑M1/1‑18 (MQ=255)                                  tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac     >  1:1299192‑M1/1‑15 (MQ=255)                                   aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac     <  1:924694‑M1/49‑36 (MQ=255)                                   aaCACGGAG‑AAGAGcctacactagcgggattctttttgttaacccctacc    >  1:2408855‑M1/1‑14 (MQ=255)                                     cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc  <  1:1660487‑M1/50‑39 (MQ=255)                                     cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc  <  1:1053275‑M1/50‑39 (MQ=255)                                            |                                            CAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAG  >  NC_000913/3090298‑3090384

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: ‑