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%	108.1 / NA	23	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (12/11);  total (12/11)

ACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGA  >  NC_000913/3090302‑3090383                                        |                                           aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                  <  1:726366‑M1/49‑6 (MQ=255)    gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                               <  1:1836166‑M1/49‑9 (MQ=255)        tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                            <  1:867579‑M1/48‑12 (MQ=255)         cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:663058‑M1/1‑36 (MQ=255)          gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:1529984‑M1/1‑35 (MQ=255)          gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          <  1:1915402‑M1/48‑14 (MQ=255)           cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                        <  1:1174175‑M1/49‑16 (MQ=255)              cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                     >  1:598484‑M1/1‑31 (MQ=255)              cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                       <  1:939430‑M1/47‑17 (MQ=255)               gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                    >  1:1377741‑M1/1‑30 (MQ=255)                ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   <  1:1089063‑M1/49‑21 (MQ=255)                 tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                  >  1:1862378‑M1/1‑28 (MQ=255)                   cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                >  1:689051‑M1/1‑26 (MQ=255)                   cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                 <  1:487537‑M1/48‑23 (MQ=255)                       cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt             >  1:1681236‑M1/1‑22 (MQ=255)                         cGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac          >  1:1943675‑M1/1‑20 (MQ=255)                          gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         >  1:1820298‑M1/1‑19 (MQ=255)                          gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         >  1:443852‑M1/1‑19 (MQ=255)                             ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       <  1:265066‑M1/48‑33 (MQ=255)                               aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta     <  1:1499357‑M1/48‑35 (MQ=255)                               aaCACGGAG‑AAGTGcctacactagcgggattctctttgttaaccccta     <  1:1367644‑M1/48‑35 (MQ=255)                                 cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc  >  1:1078018‑M1/1‑12 (MQ=255)                                  acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc  >  1:1448064‑M1/1‑11 (MQ=255)                                        |                                           ACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGA  >  NC_000913/3090302‑3090383

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: ‑