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%	306.3 / NA	59	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (29/30);  total (29/30)

GCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCT  >  NC_000913/3090311‑3090370                               |                              gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                          >  1:6056453/1‑35 (MQ=38) gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                          >  1:3693687/1‑35 (MQ=38)   tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                        <  1:3908414‑M1/35‑3 (MQ=255)   tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                        <  1:2177859‑M1/35‑3 (MQ=255)    aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                       >  1:689587‑M1/1‑32 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                      >  1:1394794‑M1/1‑31 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                      <  1:6021868‑M1/35‑5 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                      <  1:225991‑M1/35‑5 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                      <  1:2273427‑M1/35‑5 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                      >  1:6080607‑M1/1‑31 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                      <  1:2507092‑M1/35‑5 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                    >  1:510112‑M1/1‑29 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                    >  1:593796‑M1/1‑29 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                    <  1:4510385‑M1/35‑7 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                    <  1:1624970‑M1/35‑7 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                    <  1:2358342‑M1/35‑7 (MQ=255)        tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                   <  1:5092017‑M1/35‑8 (MQ=255)        tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                   <  1:5861869‑M1/35‑8 (MQ=255)        tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                   <  1:7698674‑M1/35‑8 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                  >  1:266548‑M1/1‑27 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                  >  1:6111772‑M1/1‑27 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                  >  1:3633951‑M1/1‑27 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                  >  1:1693118‑M1/1‑27 (MQ=255)          cTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                 >  1:4730412‑M1/1‑26 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                <  1:7331229‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                <  1:7649263‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                <  1:4756877‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                <  1:4385485‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                <  1:7254144‑M1/35‑11 (MQ=255)             gCTCGTTTTAACACGGAG‑AAGTGcctacactagcg              >  1:3240051‑M1/1‑23 (MQ=255)              cTCGTTTTAACACGGAG‑AAGTGcctacactagcgg             >  1:3911203‑M1/1‑22 (MQ=255)              cTCGTTTTAACACGGAG‑AAGTGcctacactagcgg             <  1:2234097‑M1/35‑14 (MQ=255)              cTCGTTTTAACACGGAG‑AAGTGcctacactagcgg             <  1:3323548‑M1/35‑14 (MQ=255)                cGTTTTAACACGGAG‑AAGTGcctacactagcggga           >  1:7180784‑M1/1‑20 (MQ=255)                 gTTTTAACACGGAG‑AAGTGcctacactagcgggat          <  1:4331204‑M1/35‑17 (MQ=255)                 gTTTTAACACGGAG‑AAGTGcctacactagcgggat          >  1:6963385‑M1/1‑19 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt         >  1:7852330‑M1/1‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt         >  1:1561403‑M1/1‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt         <  1:3782346‑M1/35‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt         <  1:222575‑M1/35‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt         >  1:2966988‑M1/1‑18 (MQ=255)                   tttAACACGGAG‑AAGTGcctacactagcgggattc        >  1:4103061‑M1/1‑17 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct       <  1:5749858‑M1/35‑20 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct       <  1:1627282‑M1/35‑20 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct       >  1:3286049‑M1/1‑16 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct       >  1:2485784‑M1/1‑16 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt      >  1:4693620‑M1/1‑15 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt      >  1:714305‑M1/1‑15 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt      >  1:654111‑M1/1‑15 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt      <  1:6096146‑M1/35‑21 (MQ=255)                      aaCACGGAG‑AAGTGcctacactagcgggattcttt     <  1:3133425‑M1/35‑22 (MQ=255)                      aaCACGGAG‑AAGTGcctacactagcgggattcttt     >  1:348195‑M1/1‑14 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt    >  1:3111072‑M1/1‑13 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt    <  1:6168705‑M1/35‑23 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt    >  1:778743‑M1/1‑13 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt    <  1:4513457‑M1/35‑23 (MQ=255)                        cacGGAG‑AAGTGcctacactagcgggattcttttt   >  1:7013817‑M1/1‑12 (MQ=255)                        cacGGAG‑AAGTGcctacactagcgggattcttttt   <  1:1996353‑M1/35‑24 (MQ=255)                         acGGAG‑AAGTGcctacactagcgggattctttttg  <  1:7384506‑M1/35‑25 (MQ=255)                               |                              GCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCT  >  NC_000913/3090311‑3090370

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑