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%	405.1 / NA	81	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (39/42);  total (39/42)

ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090296‑3090385                                              |                                             aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:5129966/1‑50 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                        <  1:4624390‑M1/50‑2 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:3401326‑M1/1‑48 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:3495838‑M1/1‑48 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:4016678‑M1/1‑48 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                      <  1:434773‑M1/50‑4 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:6321507‑M1/1‑47 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     <  1:5307580‑M1/50‑5 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     <  1:3063921‑M1/50‑5 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     <  1:2086561‑M1/50‑5 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   <  1:9331‑M1/50‑7 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   >  1:3697235‑M1/1‑44 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   >  1:1210598‑M1/1‑44 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:2603668‑M1/1‑43 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:4336149‑M1/50‑9 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:2323628‑M1/50‑9 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               >  1:1182569‑M1/1‑40 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:2185246‑M1/50‑11 (MQ=255)            tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              >  1:1238793‑M1/1‑39 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             <  1:6202583‑M1/49‑13 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:6014145‑M1/48‑12 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:5185833‑M1/48‑12 (MQ=255)               cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            >  1:5714424‑M1/1‑36 (MQ=255)               cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            <  1:6692669‑M1/49‑14 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑ACGTGcctacactagcggga                          >  1:273536‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggg                          >  1:1678439‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:6488200‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:190463‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggg                           <  1:7115543‑M1/49‑15 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:5155224‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:3232553‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:3948962‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:6556461‑M1/1‑34 (MQ=255)                  tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:4588737‑M1/1‑33 (MQ=255)                  tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:1628681‑M1/1‑33 (MQ=255)                  tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:2101498‑M1/1‑33 (MQ=255)                   aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       >  1:3583024‑M1/1‑32 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:6223327‑M1/50‑20 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       <  1:3353262‑M1/49‑19 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        <  1:2064595‑M1/48‑18 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:5553424‑M1/1‑30 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     <  1:4078080‑M1/50‑21 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:3114782‑M1/1‑30 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     <  1:1367203‑M1/50‑21 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:855640‑M1/1‑30 (MQ=255)                      ttGCTGTCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    >  1:2371932‑M1/1‑29 (MQ=255)                      ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    <  1:6541241‑M1/50‑22 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:6216416‑M1/1‑28 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:1947616‑M1/1‑28 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:4081392‑M1/1‑28 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  >  1:4203710‑M1/1‑27 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  >  1:1787945‑M1/1‑27 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   <  1:1243606‑M1/49‑23 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:3184414‑M1/49‑24 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta              <  1:2155793‑M1/50‑28 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:4534086‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:2939641‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                <  1:4946761‑M1/48‑26 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:3648873‑M1/1‑22 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:240231‑M1/1‑22 (MQ=255)                              tCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            >  1:4312245‑M1/1‑21 (MQ=255)                               cGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           >  1:5852231‑M1/1‑20 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:1197813‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:6653166‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:813100‑M1/50‑32 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:368314‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:1926114‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:3950448‑M1/48‑30 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:3700014‑M1/48‑30 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:5375701‑M1/1‑18 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:2428703‑M1/50‑33 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:5291731‑M1/49‑34 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac      >  1:1471342‑M1/1‑15 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       <  1:5978996‑M1/49‑35 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       <  1:1657477‑M1/49‑35 (MQ=255)                                     aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac      <  1:6579052‑M1/49‑36 (MQ=255)                                     aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac      <  1:2630526‑M1/49‑36 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcggggttctttttgttaacccctaccc    <  1:7083727‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:5430561‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:702219‑M1/50‑38 (MQ=255)                                        acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:6997075‑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 < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑