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%	272.2 / NA	55	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (23/32);  total (23/32)

ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGA  >  NC_000913/3090296‑3090383                                              |                                           aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                       >  1:2168812/1‑50 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                       <  1:231506/49‑1 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                      <  1:3488126‑M1/50‑2 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                      <  1:3409249‑M1/50‑2 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:3137432‑M1/1‑48 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:1655272‑M1/1‑48 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                    <  1:88859‑M1/50‑4 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                    <  1:2849890‑M1/50‑4 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                   >  1:3532400‑M1/1‑46 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                  <  1:1716332‑M1/50‑6 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                 >  1:3164003‑M1/1‑44 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                <  1:3408611‑M1/50‑8 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                <  1:3951583‑M1/50‑8 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                >  1:2091500‑M1/1‑43 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                               <  1:3340382‑M1/50‑9 (MQ=255)          gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                              <  1:3366712‑M1/50‑10 (MQ=255)          gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                              <  1:871669‑M1/50‑10 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                             <  1:3921655‑M1/50‑11 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                             <  1:3819367‑M1/50‑11 (MQ=255)            tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                            >  1:2988311‑M1/1‑39 (MQ=255)             ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                           >  1:3847745‑M1/1‑38 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:2430685‑M1/1‑37 (MQ=255)               cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:2512613‑M1/1‑36 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                        >  1:1992429‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggg                         <  1:1003284‑M1/49‑15 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                       <  1:320987‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                       <  1:2385872‑M1/50‑17 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                    >  1:3768232‑M1/1‑31 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                      <  1:3791617‑M1/48‑18 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   >  1:3105435‑M1/1‑30 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   >  1:1592634‑M1/1‑30 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   <  1:1473182‑M1/50‑21 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                 <  1:3889984‑M1/49‑23 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                 <  1:512659‑M1/49‑23 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                <  1:3082810‑M1/49‑24 (MQ=255)                          tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt              >  1:760344‑M1/1‑25 (MQ=255)                           ggCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt              >  1:2232062‑M1/1‑24 (MQ=255)                           ggCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt              >  1:1220214‑M1/1‑24 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta            <  1:287034‑M1/50‑28 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt             <  1:992110‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt             <  1:2393937‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt             <  1:1796070‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt             <  1:1298844‑M1/49‑27 (MQ=255)                               cGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         >  1:3208340‑M1/1‑20 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         <  1:3610828‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         <  1:2836087‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac          <  1:1184494‑M1/48‑30 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       >  1:3564358‑M1/1‑18 (MQ=255)                                  tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       >  1:692449‑M1/1‑17 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta     <  1:2863102‑M1/49‑35 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta     <  1:2426820‑M1/49‑35 (MQ=255)                                     aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc   >  1:566675‑M1/1‑14 (MQ=255)                                     aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc   >  1:871219‑M1/1‑14 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc  <  1:4387507‑M1/50‑38 (MQ=255)                                       cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc  >  1:3355467‑M1/1‑12 (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: ‑