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%	158.2 / NA	33	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (9/24);  total (9/24)

CAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACT  >  NC_000913/3090298‑3090381                                            |                                         cAAAACAGCTTTCGCTACTTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                    <  1:1743047‑M1/49‑2 (MQ=255)    aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                 <  1:2113948‑M1/49‑5 (MQ=255)    aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                 <  1:1985117‑M1/49‑5 (MQ=255)    aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                 <  1:957286‑M1/49‑5 (MQ=255)      cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                               <  1:1039729‑M1/49‑7 (MQ=255)      cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                               <  1:699752‑M1/49‑7 (MQ=255)       aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                              >  1:2176‑M1/1‑42 (MQ=255)         cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                            <  1:992565‑M1/49‑10 (MQ=255)         cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                              >  1:1570082‑M1/1‑40 (MQ=255)           ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                          >  1:1735878‑M1/1‑38 (MQ=255)            tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                           <  1:493121‑M1/47‑11 (MQ=255)              gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                        >  1:668432‑M1/1‑35 (MQ=255)              gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                        >  1:597282‑M1/1‑35 (MQ=255)                  ccttgcTGGCTCTTTTTAACACGGAG‑AAGTGcctacactagcgggatt                    <  1:1361757‑M1/46‑18 (MQ=255)                  cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                   <  1:733179‑M1/49‑19 (MQ=255)                  cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                   <  1:950029‑M1/49‑19 (MQ=255)                  cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                   <  1:1076035‑M1/49‑19 (MQ=255)                  cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                    <  1:1296617‑M1/48‑18 (MQ=255)                  cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                     <  1:210612‑M1/47‑17 (MQ=255)                   gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                  >  1:647540‑M1/1‑30 (MQ=255)                   gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                  <  1:719889‑M1/49‑20 (MQ=255)                       cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt              <  1:1409014‑M1/49‑24 (MQ=255)                        tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg             >  1:563547‑M1/1‑25 (MQ=255)                          gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt           <  1:928520‑M1/49‑27 (MQ=255)                           cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta          <  1:141120‑M1/49‑28 (MQ=255)                           cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt           >  1:442718‑M1/1‑22 (MQ=255)                            tCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa         >  1:59552‑M1/1‑21 (MQ=255)                              gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac        <  1:1615100‑M1/48‑30 (MQ=255)                                 ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc     <  1:528218‑M1/48‑33 (MQ=255)                                 ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc     <  1:279183‑M1/48‑33 (MQ=255)                                 ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc     <  1:878560‑M1/48‑33 (MQ=255)                                  tAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct    <  1:478413‑M1/48‑34 (MQ=255)                                    acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac  <  1:1400220‑M1/48‑36 (MQ=255)                                            |                                         CAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACT  >  NC_000913/3090298‑3090381

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: ‑