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	25 [0]	[0] 25	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)	25 (0.980)	17/168	0.3	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

GGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACA  >  NZ_CP009273/2399388‑2399554                                                                                     |                                                                                   aggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCa                                                                               >  2:424241‑M2/85‑90 (MQ=255)   gtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                             >  1:243354‑M2/83‑90 (MQ=255)    tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                            <  2:100090‑M2/9‑1 (MQ=255)        ggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCa                                                                        <  2:569503‑M2/13‑1 (MQ=255)        ggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCa                                                                        >  2:389031‑M2/78‑90 (MQ=255)                 tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  1:732370‑M2/22‑1 (MQ=255)                 tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  2:201529‑M2/22‑1 (MQ=255)                          gccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttatt                                                      >  2:658224‑M2/60‑90 (MQ=255)                           ccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttatta                                                     >  1:315348‑M2/59‑90 (MQ=255)                               gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                 <  2:315348‑M2/36‑1 (MQ=255)                                    cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                            <  1:462450‑M2/9‑1 (MQ=255)                                    cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                            >  2:462450‑M2/50‑58 (MQ=255)                                       gccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGc                                         <  2:511274‑M2/44‑1 (MQ=255)                                                ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCATTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                >  2:703757‑M2/38‑90 (MQ=255)                                                ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                >  1:8492‑M2/38‑90 (MQ=255)                                                     tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                           <  1:538848‑M2/58‑1 (MQ=255)                                                     tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                           <  1:706122‑M2/58‑1 (MQ=255)                                                      cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  1:302740‑M2/59‑1 (MQ=255)                                                      cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  2:462297‑M2/59‑1 (MQ=255)                                                      cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  2:400661‑M2/59‑1 (MQ=255)                                                      cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  1:559720‑M2/59‑1 (MQ=255)                                                                      gccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCa          <  2:288690‑M2/75‑1 (MQ=255)                                                                        cggaagcgtcgagAAGCCAGTCGCCATGGAATTTCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc        <  1:692859‑M2/77‑1 (MQ=255)                                                                        cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc        <  2:699205‑M2/77‑1 (MQ=255)                                                                              cgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACa  >  2:296027‑M2/8‑90 (MQ=255)                                                                                     |                                                                                   GGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACA  >  NZ_CP009273/2399388‑2399554

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑