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%	351.0 / NA	71	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (27/44);  total (27/44)

CCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090297‑3090385                                             |                                             ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:2494442/49‑1 (MQ=255)    aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     <  1:2563160‑M1/50‑5 (MQ=255)     aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:4482302‑M1/50‑6 (MQ=255)      aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   <  1:106641‑M1/50‑7 (MQ=255)       cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  <  1:1609451‑M1/50‑8 (MQ=255)        aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:1281403‑M1/50‑9 (MQ=255)        aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:2216276‑M1/50‑9 (MQ=255)        aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:384110‑M1/50‑9 (MQ=255)        aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:3303881‑M1/1‑42 (MQ=255)         gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactg                                <  1:131936‑M1/50‑10 (MQ=255)          cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:5497648‑M1/50‑11 (MQ=255)           tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              >  1:4179097‑M1/1‑39 (MQ=255)            ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:5933337‑M1/1‑38 (MQ=255)            ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:3650928‑M1/1‑38 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            >  1:130760‑M1/1‑37 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             <  1:2772613‑M1/49‑13 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             <  1:3712708‑M1/49‑13 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:3710293‑M1/48‑12 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:3915409‑M1/48‑12 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:6041884‑M1/48‑12 (MQ=255)              cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            >  1:4359855‑M1/1‑36 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          <  1:4323941‑M1/50‑16 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          <  1:5579895‑M1/50‑16 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:2987005‑M1/1‑35 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggg                           <  1:1269355‑M1/49‑15 (MQ=255)                cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:2581710‑M1/1‑34 (MQ=255)                cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:1309411‑M1/1‑34 (MQ=255)                 tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:3918323‑M1/1‑33 (MQ=255)                 tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        >  1:3239794‑M1/1‑33 (MQ=255)                  aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       >  1:282988‑M1/1‑32 (MQ=255)                  aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       >  1:3903351‑M1/1‑32 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      >  1:5830150‑M1/1‑31 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:4011361‑M1/50‑20 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      >  1:566068‑M1/1‑31 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        <  1:701194‑M1/48‑18 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        <  1:4461351‑M1/48‑18 (MQ=255)                    gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:1478190‑M1/1‑30 (MQ=255)                     ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    >  1:3510322‑M1/1‑29 (MQ=255)                       gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   <  1:3177654‑M1/49‑23 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 <  1:5385173‑M1/50‑25 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 <  1:4077889‑M1/50‑25 (MQ=255)                         tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:345095‑M1/1‑25 (MQ=255)                         tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:3869947‑M1/1‑25 (MQ=255)                          ggCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:216170‑M1/1‑24 (MQ=255)                           gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta              <  1:3023500‑M1/50‑28 (MQ=255)                           gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                <  1:940536‑M1/48‑26 (MQ=255)                            cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:3600491‑M1/50‑29 (MQ=255)                            cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:663143‑M1/50‑29 (MQ=255)                            cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:2264502‑M1/1‑22 (MQ=255)                             tCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            >  1:631968‑M1/1‑21 (MQ=255)                              cGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           >  1:4209318‑M1/1‑20 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:2254233‑M1/48‑30 (MQ=255)                                ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:751288‑M1/1‑18 (MQ=255)                                ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:18337‑M1/50‑33 (MQ=255)                                ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:5419348‑M1/50‑33 (MQ=255)                                ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:936780‑M1/50‑33 (MQ=255)                                ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:2668182‑M1/1‑18 (MQ=255)                                ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         <  1:1711062‑M1/50‑33 (MQ=255)                                  ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:477383‑M1/49‑34 (MQ=255)                                  ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:5209441‑M1/49‑34 (MQ=255)                                  ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:5347946‑M1/49‑34 (MQ=255)                                  ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:1315407‑M1/49‑34 (MQ=255)                                   tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       <  1:1931497‑M1/49‑35 (MQ=255)                                     acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     <  1:1740083‑M1/49‑37 (MQ=255)                                     acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     <  1:2027570‑M1/49‑37 (MQ=255)                                      cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc   <  1:1459070‑M1/50‑39 (MQ=255)                                      cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc   <  1:554362‑M1/50‑39 (MQ=255)                                       acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  <  1:5302689‑M1/50‑40 (MQ=255)                                       acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:858891‑M1/1‑11 (MQ=255)                                       acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  <  1:1537586‑M1/50‑40 (MQ=255)                                       acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:183332‑M1/1‑11 (MQ=255)                                             |                                             CCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090297‑3090385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑