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%	407.6 / NA	82	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (41/41);  total (41/41)

ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090296‑3090385                                              |                                             aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:8306515/1‑50 (MQ=255) aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:3798364/1‑50 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:6092308/49‑1 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:279733/49‑1 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                      <  1:8052151‑M1/50‑4 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:7698139‑M1/1‑47 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     >  1:4746293‑M1/1‑46 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:7987398‑M1/50‑6 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:2339936‑M1/50‑6 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     >  1:6740749‑M1/1‑45 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   >  1:5209006‑M1/1‑44 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   <  1:7971996‑M1/50‑7 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  <  1:1323607‑M1/50‑8 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:7455321‑M1/1‑43 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:5009897‑M1/1‑43 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:864107‑M1/1‑43 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGactacact                                 <  1:5417568‑M1/50‑9 (MQ=255)          gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                                <  1:5376756‑M1/50‑10 (MQ=255)          gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                                <  1:2071617‑M1/50‑10 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               >  1:3479872‑M1/1‑40 (MQ=255)            tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              >  1:6751581‑M1/1‑39 (MQ=255)            tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              >  1:7266371‑M1/1‑39 (MQ=255)             ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:2356603‑M1/1‑38 (MQ=255)             ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:4243730‑M1/1‑38 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             <  1:5489956‑M1/49‑13 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:7840404‑M1/48‑12 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:6567609‑M1/48‑12 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:4308077‑M1/48‑12 (MQ=255)               cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            >  1:3789049‑M1/1‑36 (MQ=255)               cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            <  1:3478099‑M1/49‑14 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:3658536‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:3984538‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggg                           <  1:1535765‑M1/49‑15 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:4688765‑M1/1‑34 (MQ=255)                  tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:2208084‑M1/1‑33 (MQ=255)                   aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       >  1:4386390‑M1/1‑32 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:24619‑M1/50‑20 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      >  1:5701501‑M1/1‑31 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       <  1:1750766‑M1/49‑19 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        <  1:680221‑M1/48‑18 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     <  1:324145‑M1/50‑21 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     <  1:2594673‑M1/50‑21 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:5431753‑M1/1‑30 (MQ=255)                      ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    >  1:5764933‑M1/1‑29 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:7600277‑M1/1‑28 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:338493‑M1/1‑28 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:3263881‑M1/1‑28 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   <  1:4601294‑M1/49‑23 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 >  1:5221413‑M1/1‑26 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 >  1:3175504‑M1/1‑26 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 >  1:3654711‑M1/1‑26 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:4870385‑M1/49‑24 (MQ=255)                          tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:5591996‑M1/1‑25 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta              <  1:5652963‑M1/50‑28 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta              <  1:5805792‑M1/50‑28 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:5494311‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               >  1:6742304‑M1/1‑23 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:7920827‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:7455525‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                <  1:2207640‑M1/48‑26 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:1773237‑M1/50‑29 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:6505487‑M1/50‑29 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:4607096‑M1/1‑22 (MQ=255)                              tCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            >  1:910108‑M1/1‑21 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttatccc          <  1:3769537‑M1/50‑32 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:4073267‑M1/50‑32 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:605953‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:7793077‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:1881827‑M1/48‑30 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:3842016‑M1/50‑33 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:3702195‑M1/1‑18 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:3766374‑M1/49‑34 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:7007008‑M1/49‑34 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:602469‑M1/49‑34 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac      >  1:544401‑M1/1‑15 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac      >  1:3951391‑M1/1‑15 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac      >  1:2132190‑M1/1‑15 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       <  1:772558‑M1/49‑35 (MQ=255)                                     aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     >  1:7656928‑M1/1‑14 (MQ=255)                                     aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     >  1:6786532‑M1/1‑14 (MQ=255)                                       cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    >  1:5525500‑M1/1‑12 (MQ=255)                                        acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:7602922‑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: ‑