Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NZ_CP009273	2,399,465	Δ7 bp	coding (650‑656/939 nt)	lrhA ←	transcriptional regulator LrhA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	2399465	2399471	7	19 [0]	[0] 19	lrhA	transcriptional regulator LrhA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 2399464	0 (0.000)	19 (0.790)	12/168	0.6	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAA  >  NZ_CP009273/2399378‑2399550                                                                                       |                                                                                       cGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaag                                                                                     >  2:539071‑M1/1‑87 (MQ=255)            gCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccat                                                                          <  1:7158‑M1/90‑15 (MQ=255)                    tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  2:58280‑M1/90‑23 (MQ=255)                    tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  2:566513‑M1/90‑23 (MQ=255)                       cAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgc                                                               >  1:169296‑M1/1‑65 (MQ=255)                         aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                             >  1:324133‑M1/1‑63 (MQ=255)                                  gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                    <  2:492043‑M1/90‑37 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                                   >  2:492522‑M1/1‑37 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:97218‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:656091‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:398851‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:299336‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTAGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:398840‑M1/90‑60 (MQ=255)                                                              ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                        <  1:413729‑M1/90‑65 (MQ=255)                                                                           cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           <  2:324133‑M1/90‑78 (MQ=255)                                                                           cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           <  2:662715‑M1/90‑78 (MQ=255)                                                                                  gTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaa    >  2:631971‑M1/1‑6 (MQ=255)                                                                                  gTCGAGaagccagtcgccatggaataactgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaa    >  1:156714‑M1/1‑6 (MQ=255)                                                                                    cGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaaga  <  1:492522‑M1/90‑87 (MQ=255)                                                                                       |                                                                                       CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAA  >  NZ_CP009273/2399378‑2399550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.