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%	292.3 / NA	59	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (31/28);  total (31/28)

CCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGA  >  NC_000913/3090297‑3090383                                             |                                           ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                       <  1:2120686/49‑1 (MQ=255) ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                       >  1:1539309/1‑49 (MQ=255)    aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:191226‑M1/1‑46 (MQ=255)    aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:1557163‑M1/1‑46 (MQ=255)    aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:684656‑M1/1‑46 (MQ=255)    aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:2277728‑M1/1‑46 (MQ=255)    aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                     >  1:2440720‑M1/1‑46 (MQ=255)     aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                   <  1:2555376‑M1/49‑5 (MQ=255)     aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                   >  1:2301866‑M1/1‑45 (MQ=255)      aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                  <  1:1896751‑M1/49‑6 (MQ=255)       cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                 >  1:8594‑M1/1‑43 (MQ=255)        aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                >  1:2535283‑M1/1‑42 (MQ=255)        aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                >  1:984302‑M1/1‑42 (MQ=255)          cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                              <  1:2679502‑M1/49‑10 (MQ=255)          cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                              <  1:2019513‑M1/49‑10 (MQ=255)           tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                             >  1:1989169‑M1/1‑39 (MQ=255)            ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                            >  1:1500304‑M1/1‑38 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                            <  1:2187156‑M1/48‑12 (MQ=255)              cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                           <  1:261117‑M1/48‑13 (MQ=255)              cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                           <  1:225230‑M1/48‑13 (MQ=255)              cGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                           <  1:1593103‑M1/48‑13 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggg                         <  1:2127402‑M1/49‑15 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          <  1:1323765‑M1/48‑14 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:120225‑M1/1‑35 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:2424554‑M1/1‑35 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                          >  1:839449‑M1/1‑35 (MQ=255)                cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                        >  1:124232‑M1/1‑34 (MQ=255)                cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                        >  1:1516843‑M1/1‑34 (MQ=255)                cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                        >  1:2396651‑M1/1‑34 (MQ=255)                 tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                       >  1:1316922‑M1/1‑33 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                     <  1:603890‑M1/49‑19 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                      <  1:770427‑M1/48‑18 (MQ=255)                    gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                    <  1:438713‑M1/49‑20 (MQ=255)                     ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   >  1:2328265‑M1/1‑29 (MQ=255)                     ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   <  1:2467669‑M1/49‑21 (MQ=255)                     ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                   <  1:422613‑M1/49‑21 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                >  1:2133740‑M1/1‑26 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                <  1:842085‑M1/49‑24 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                <  1:1567208‑M1/49‑24 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                >  1:2465482‑M1/1‑26 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                <  1:2483385‑M1/49‑24 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                 <  1:958233‑M1/48‑23 (MQ=255)                           gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt              >  1:1257414‑M1/1‑23 (MQ=255)                           gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg               <  1:1007866‑M1/47‑25 (MQ=255)                            cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta            <  1:11610‑M1/49‑28 (MQ=255)                             tCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa           >  1:618472‑M1/1‑21 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         >  1:1368798‑M1/1‑19 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         >  1:611040‑M1/1‑19 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         >  1:2081128‑M1/1‑19 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc         <  1:1691709‑M1/49‑31 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac          <  1:2615829‑M1/48‑30 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa           <  1:1489709‑M1/47‑29 (MQ=255)                                 tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       >  1:1505407‑M1/1‑17 (MQ=255)                                 tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       >  1:1882840‑M1/1‑17 (MQ=255)                                  ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc       >  1:1545342‑M1/1‑16 (MQ=255)                                    aaCACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta     <  1:567858‑M1/48‑35 (MQ=255)                                     acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc   <  1:2451209‑M1/49‑37 (MQ=255)                                     acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctac    <  1:1502170‑M1/48‑36 (MQ=255)                                       acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc  >  1:514056‑M1/1‑11 (MQ=255)                                             |                                           CCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGA  >  NC_000913/3090297‑3090383

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑