Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	3,090,347	Δ708 bp	coding (1‑708/708 nt)	endA →	DNA‑specific endonuclease I

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3090347	3091054	708	66 [0]	[0] 70	endA	DNA‑specific endonuclease I

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3090346	0 (0.000)	64 (0.890)	34/68	0.1	100%	intergenic (+94/‑1)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
	?	NC_000913	3091055 =	0 (0.000)					intergenic (+1/‑79)	endA/rsmE	DNA‑specific endonuclease I/16S rRNA m(3)U1498 methyltransferase

GCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTAC  >  NC_000913/3090311‑3090380                                    |                                   gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                    >  1:6056453/1‑35 (MQ=38) gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                    >  1:3693687/1‑35 (MQ=38)   tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                  <  1:3908414‑M1/35‑3 (MQ=255)   tACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                  <  1:2177859‑M1/35‑3 (MQ=255)    aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                 >  1:689587‑M1/1‑32 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                <  1:225991‑M1/35‑5 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                >  1:6080607‑M1/1‑31 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                <  1:6021868‑M1/35‑5 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                <  1:2507092‑M1/35‑5 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                <  1:2273427‑M1/35‑5 (MQ=255)     cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                >  1:1394794‑M1/1‑31 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                              >  1:510112‑M1/1‑29 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                              <  1:2358342‑M1/35‑7 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                              >  1:593796‑M1/1‑29 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                              <  1:4510385‑M1/35‑7 (MQ=255)       ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                              <  1:1624970‑M1/35‑7 (MQ=255)        tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                             <  1:5092017‑M1/35‑8 (MQ=255)        tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                             <  1:5861869‑M1/35‑8 (MQ=255)        tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                             <  1:7698674‑M1/35‑8 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                            >  1:6111772‑M1/1‑27 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                            >  1:3633951‑M1/1‑27 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                            >  1:266548‑M1/1‑27 (MQ=255)         gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                            >  1:1693118‑M1/1‑27 (MQ=255)          cTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                           >  1:4730412‑M1/1‑26 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                          <  1:7254144‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                          <  1:7331229‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                          <  1:4385485‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                          <  1:7649263‑M1/35‑11 (MQ=255)           tGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                          <  1:4756877‑M1/35‑11 (MQ=255)             gCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                        >  1:3240051‑M1/1‑23 (MQ=255)              cTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                       <  1:3323548‑M1/35‑14 (MQ=255)              cTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                       <  1:2234097‑M1/35‑14 (MQ=255)              cTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                       >  1:3911203‑M1/1‑22 (MQ=255)                cGTTTTAACACGGAG‑AAGTGcctacactagcggga                     >  1:7180784‑M1/1‑20 (MQ=255)                 gTTTTAACACGGAG‑AAGTGcctacactagcgggat                    >  1:6963385‑M1/1‑19 (MQ=255)                 gTTTTAACACGGAG‑AAGTGcctacactagcgggat                    <  1:4331204‑M1/35‑17 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt                   >  1:7852330‑M1/1‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt                   >  1:2966988‑M1/1‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt                   <  1:3782346‑M1/35‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt                   >  1:1561403‑M1/1‑18 (MQ=255)                  ttttAACACGGAG‑AAGTGcctacactagcgggatt                   <  1:222575‑M1/35‑18 (MQ=255)                   tttAACACGGAG‑AAGTGcctacactagcgggattc                  >  1:4103061‑M1/1‑17 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct                 <  1:5749858‑M1/35‑20 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct                 <  1:1627282‑M1/35‑20 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct                 >  1:2485784‑M1/1‑16 (MQ=255)                    ttAACACGGAG‑AAGTGcctacactagcgggattct                 >  1:3286049‑M1/1‑16 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt                >  1:654111‑M1/1‑15 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt                <  1:6096146‑M1/35‑21 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt                >  1:714305‑M1/1‑15 (MQ=255)                     tAACACGGAG‑AAGTGcctacactagcgggattctt                >  1:4693620‑M1/1‑15 (MQ=255)                      aaCACGGAG‑AAGTGcctacactagcgggattcttt               >  1:348195‑M1/1‑14 (MQ=255)                      aaCACGGAG‑AAGTGcctacactagcgggattcttt               <  1:3133425‑M1/35‑22 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt              >  1:778743‑M1/1‑13 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt              <  1:4513457‑M1/35‑23 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt              >  1:3111072‑M1/1‑13 (MQ=255)                       acacGGAG‑AAGTGcctacactagcgggattctttt              <  1:6168705‑M1/35‑23 (MQ=255)                        cacGGAG‑AAGTGcctacactagcgggattcttttt             >  1:7013817‑M1/1‑12 (MQ=255)                        cacGGAG‑AAGTGcctacactagcgggattcttttt             <  1:1996353‑M1/35‑24 (MQ=255)                         acGGAG‑AAGTGcctacactagcgggattctttttg            <  1:7384506‑M1/35‑25 (MQ=255)                                aaGTGcctacactagcgggattctttttgttaacc      >  1:5760189‑M1/1‑5 (MQ=255)                                aaGTGcctacactagcgggattctttttgttaacc      >  1:1467364‑M1/1‑5 (MQ=255)                                 aGTGcctacactagcgggattctttttgttaaccc     >  1:5982395‑M1/1‑4 (MQ=255)                                  gTGcctacactagcgggattctttttgttaacccc    <  1:3417444‑M1/35‑33 (MQ=255)                                    gcctacactagcgggattctttttgttaaccccta  <  1:348206‑M1/35‑35 (MQ=255)                                    gcctacactagcgggattctttttgttaaccccta  <  1:3518144‑M1/35‑35 (MQ=255)                                    gcctacactagcgggattctttttgttaaccccta  <  1:4891913‑M1/35‑35 (MQ=255)                                    |                                   GCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTAC  >  NC_000913/3090311‑3090380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑