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	22 [0]	[0] 22	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)	22 (1.300)	10/168	0.4	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAA  >  NZ_CP009273/2399378‑2399528                                                                                       |                                                                 cGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaag                                                               >  2:448000‑M1/1‑87 (MQ=255) cGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaag                                                               >  2:438218‑M1/1‑87 (MQ=255)      gTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                          >  1:10706‑M1/1‑82 (MQ=255)            gCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccat                                                    <  2:470485‑M1/90‑15 (MQ=255)                             gCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttatt                                   <  2:223984‑M1/90‑32 (MQ=255)                                  gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                              <  2:215671‑M1/90‑37 (MQ=255)                                     gTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcg                           <  2:150051‑M1/90‑40 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg             >  1:121800‑M1/1‑37 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg             >  1:399480‑M1/1‑37 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg             >  1:294300‑M1/1‑37 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcg                                                        <  1:370189‑M1/47‑11 (MQ=255)                                                   ggCTTTCACTGCCGCACGAACGGCCGGAAGCATCGAGaagccagtcg                                                        >  2:370189‑M1/1‑37 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  1:61587‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  2:121800‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  1:303258‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  2:340843‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  2:371597‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  2:399480‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  1:187866‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtagccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  1:438218‑M1/90‑60 (MQ=255)                                                         cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtagccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac       <  1:448000‑M1/90‑60 (MQ=255)                                                              ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct  <  1:234736‑M1/90‑65 (MQ=255)                                                                                       |                                                                 CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAA  >  NZ_CP009273/2399378‑2399528

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑