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	21 [0]	[0] 21	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)	21 (1.390)	15/166	0.1	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCAT  >  NZ_CP009273/2399378‑2399543                                                                                       |                                                                                cGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaag                                                                              >  2:183207‑M1/1‑87 (MQ=255)   cAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcc                                                                            <  2:51484‑M1/90‑6 (MQ=255)                       cAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgc                                                        >  1:252215‑M1/1‑65 (MQ=255)                           cGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgcttta                                                    >  2:242103‑M1/1‑61 (MQ=255)                                       cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                        <  2:201184‑M1/90‑42 (MQ=255)                                       cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                        <  2:189902‑M1/90‑42 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                            >  1:108106‑M1/1‑37 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                        >  2:148990‑M1/1‑37 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                        <  1:148990‑M1/78‑42 (MQ=255)                                                        tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                       <  2:252215‑M1/90‑59 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                      <  2:229360‑M1/90‑60 (MQ=255)                                                           cTGCCGCACGAACGGCCGCAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgg                    >  1:105372‑M1/1‑29 (MQ=255)                                                             gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggc                  >  1:32046‑M1/1‑27 (MQ=255)                                                             gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggc                  >  2:427702‑M1/1‑27 (MQ=255)                                                                  aCGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatccgctttattaagcgtcgccagcaccatatcgcgaaacgggctagga             <  2:164056‑M1/90‑69 (MQ=255)                                                                           cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc    <  2:108106‑M1/90‑78 (MQ=255)                                                                           cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc    <  1:183207‑M1/90‑78 (MQ=255)                                                                           cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc    <  2:48546‑M1/90‑78 (MQ=255)                                                                             gAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaa  <  2:280890‑M1/90‑80 (MQ=255)                                                                                  gTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                 >  2:160820‑M1/1‑6 (MQ=255)                                                                                  gTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                 <  1:160820‑M1/70‑65 (MQ=255)                                                                                       |                                                                                CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCAT  >  NZ_CP009273/2399378‑2399543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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.