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%	237.1 / NA	48	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (19/29);  total (19/29)

ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090296‑3090385                                              |                                             aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:3558153/1‑50 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:1882787/49‑1 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:155276‑M1/1‑47 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:216712‑M1/1‑47 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:425735‑M1/50‑6 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:597209‑M1/50‑6 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   <  1:3836958‑M1/50‑7 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   <  1:3128723‑M1/50‑7 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   <  1:957686‑M1/50‑7 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   >  1:21800‑M1/1‑44 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  <  1:3884880‑M1/50‑8 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:630692‑M1/50‑9 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:3731775‑M1/50‑9 (MQ=255)          gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                                <  1:2939099‑M1/50‑10 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:955608‑M1/50‑11 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               >  1:3731437‑M1/1‑40 (MQ=255)            tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              >  1:2392446‑M1/1‑39 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:521644‑M1/48‑12 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:1013320‑M1/48‑12 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:964072‑M1/1‑34 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      >  1:1989970‑M1/1‑31 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      >  1:1520805‑M1/1‑31 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:639502‑M1/50‑20 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        <  1:131480‑M1/48‑18 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:1520167‑M1/1‑30 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:2906160‑M1/1‑28 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 <  1:3816398‑M1/50‑25 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttta                 <  1:3533757‑M1/50‑25 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:156456‑M1/49‑24 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta              <  1:2898283‑M1/50‑28 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:3154285‑M1/49‑27 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:3203619‑M1/1‑22 (MQ=255)                              tCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            >  1:256611‑M1/1‑21 (MQ=255)                               cGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           >  1:570977‑M1/1‑20 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:967046‑M1/50‑32 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:942758‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:1803779‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:1595985‑M1/50‑32 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:2998940‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:1874803‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:2760530‑M1/48‑30 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       >  1:3219658‑M1/1‑16 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:400920‑M1/49‑34 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       <  1:2656496‑M1/49‑35 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:2435786‑M1/50‑38 (MQ=255)                                       cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc   <  1:3097051‑M1/50‑39 (MQ=255)                                       cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    >  1:2869835‑M1/1‑12 (MQ=255)                                        acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:2903666‑M1/1‑11 (MQ=255)                                              |                                             ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090296‑3090385

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: ‑