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	32 [0]	[0] 32	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)	32 (0.690)	20/168	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

CCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  NZ_CP009273/2399385‑2399556                                                                                        |                                                                                     cgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAg                                                                                    >  1:174077‑M2/88‑90 (MQ=255)    aggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagGAGCCa                                                                                 >  1:1190538‑M2/85‑90 (MQ=255)    aggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCa                                                                                 >  2:1103656‑M2/85‑90 (MQ=255)          gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                           <  1:415735‑M2/12‑1 (MQ=255)               catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                      >  2:872314‑M2/74‑90 (MQ=255)                    tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                 <  2:1034640‑M2/22‑1 (MQ=255)                        aaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCt                                                             <  2:689398‑M2/26‑1 (MQ=255)                        aaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCt                                                             <  1:872314‑M2/26‑1 (MQ=255)                            ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttat                                                         >  2:1066472‑M2/61‑90 (MQ=255)                                  gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                   <  2:893642‑M2/36‑1 (MQ=255)                                  gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                   <  2:736854‑M2/36‑1 (MQ=255)                                  gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                   <  1:993138‑M2/36‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                   <  1:1324623‑M2/36‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                   >  2:1324623‑M2/50‑85 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                              <  1:437386‑M2/41‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                              >  2:423636‑M2/50‑90 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                              >  2:278734‑M2/50‑90 (MQ=255)                                            caagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCAc                                         <  1:335313‑M2/46‑1 (MQ=255)                                               gaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCat                                      <  2:997546‑M2/49‑1 (MQ=255)                                                   ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                  >  1:237375‑M2/38‑90 (MQ=255)                                                   ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                  >  2:927043‑M2/38‑90 (MQ=255)                                                        tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                             <  2:317088‑M2/58‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  2:10737‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  1:363107‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  1:278734‑M2/59‑1 (MQ=255)                                                                        ggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATcc             >  1:850016‑M2/17‑90 (MQ=255)                                                                         gccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCa            <  1:312632‑M2/75‑1 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc          <  2:1001660‑M2/77‑1 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc          <  1:973838‑M2/77‑1 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc          <  2:338688‑M2/77‑1 (MQ=255)                                                                                gcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATAc     <  1:1207981‑M2/82‑1 (MQ=255)                                                                                   tcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAag  <  2:551503‑M2/85‑1 (MQ=255)                                                                                        |                                                                                     CCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  NZ_CP009273/2399385‑2399556

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: ‑