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%	351.3 / NA	70	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (26/44);  total (26/44)

ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090296‑3090385                                              |                                             aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:770975/1‑50 (MQ=255) aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:6111190/1‑50 (MQ=255) aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:5870007/1‑50 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:3515928/49‑1 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:2066981/49‑1 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                        <  1:4585690‑M1/50‑2 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                        <  1:3524513‑M1/50‑2 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                        <  1:3330842‑M1/50‑2 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                        >  1:3052715‑M1/1‑49 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:2531976‑M1/1‑47 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:2196783‑M1/1‑47 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     <  1:2861722‑M1/50‑5 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     >  1:2660713‑M1/1‑45 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   <  1:2234701‑M1/50‑7 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:935987‑M1/1‑42 (MQ=255)         aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:3529124‑M1/1‑42 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:3624043‑M1/50‑11 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:3398834‑M1/50‑11 (MQ=255)             ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:1432086‑M1/1‑38 (MQ=255)             ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:6370226‑M1/1‑38 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             <  1:2914830‑M1/49‑13 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:2194756‑M1/48‑12 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:4252225‑M1/48‑12 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:3178632‑M1/48‑12 (MQ=255)               cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            >  1:1765020‑M1/1‑36 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:1614392‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:5567536‑M1/1‑35 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:2466962‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:4829409‑M1/1‑34 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:3163485‑M1/1‑34 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:2773895‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:6651765‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:827071‑M1/50‑17 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:5447647‑M1/50‑20 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        <  1:4844675‑M1/48‑18 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     <  1:3318989‑M1/50‑21 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:4161369‑M1/1‑28 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:1028377‑M1/1‑28 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   <  1:4412311‑M1/49‑23 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacaagcgggattcttttt                  >  1:5808283‑M1/1‑27 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 >  1:163878‑M1/1‑26 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 <  1:5321220‑M1/50‑25 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:1191091‑M1/49‑24 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta              <  1:4082205‑M1/50‑28 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:1338996‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:4628736‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:1375210‑M1/49‑27 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                <  1:6503284‑M1/48‑26 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:6242623‑M1/50‑29 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:2672649‑M1/50‑32 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:6581275‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:265409‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:6287422‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:114214‑M1/48‑30 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:2995309‑M1/50‑33 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:196737‑M1/50‑33 (MQ=255)                                  tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:5261794‑M1/1‑17 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       >  1:6126776‑M1/1‑16 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       >  1:1723239‑M1/1‑16 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:3918850‑M1/49‑34 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       <  1:789669‑M1/49‑35 (MQ=255)                                    tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       <  1:5157004‑M1/49‑35 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:3423899‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     <  1:2313569‑M1/49‑37 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     <  1:3001450‑M1/49‑37 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     <  1:3191538‑M1/49‑37 (MQ=255)                                       cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc   <  1:6369193‑M1/50‑39 (MQ=255)                                       cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc   <  1:6269778‑M1/50‑39 (MQ=255)                                        acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:5942591‑M1/1‑11 (MQ=255)                                        acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:1281217‑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 < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑