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 (0.920)	12/166	0.5	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

TCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCT  >  NZ_CP009273/2399391‑2399535                                                                                  |                                                                tccgggctcatcatctcacccggccttgccgtcacgccaagactggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                         <  2:400976‑M2/9‑1 (MQ=255)    gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                      >  2:27387‑M2/79‑90 (MQ=255)         catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                 >  2:477528‑M2/74‑90 (MQ=255)            catctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAata                                              <  1:114902‑M2/20‑1 (MQ=255)                       gccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttatt                                   <  1:539903‑M2/31‑1 (MQ=255)                            gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                              <  2:521509‑M2/36‑1 (MQ=255)                            gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                              <  2:264548‑M2/36‑1 (MQ=255)                                   cgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAg                       <  2:342266‑M2/43‑1 (MQ=255)                                             ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                              >  1:303476‑M2/38‑73 (MQ=255)                                             ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                              <  2:303476‑M2/36‑1 (MQ=255)                                                   cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc       <  1:27387‑M2/59‑1 (MQ=255)                                                   cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc       <  2:598690‑M2/59‑1 (MQ=255)                                                   cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc       <  2:362806‑M2/59‑1 (MQ=255)                                                   cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGCCGCCAGCACCATATCGCGAAAc       <  1:268506‑M2/59‑1 (MQ=255)                                                        ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCAt                                                    <  2:439766‑M2/14‑1 (MQ=255)                                                        ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCAt                                                    >  1:439766‑M2/27‑40 (MQ=255)                                                        ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt  <  2:273626‑M2/64‑1 (MQ=255)                                                        ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt  >  1:335373‑M2/27‑90 (MQ=255)                                                        ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt  >  1:310799‑M2/27‑90 (MQ=255)                                                                                  |                                                                TCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCT  >  NZ_CP009273/2399391‑2399535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑