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	47 [0]	[0] 47	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)	47 (0.990)	27/168	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

ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGC  >  NZ_CP009273/2399377‑2399548                                                                                        |                                                                                     acGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaa                                                                                    <  2:366531‑M1/90‑3 (MQ=255)  cGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaag                                                                                   >  1:54535‑M1/1‑87 (MQ=255)  cGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaag                                                                                   >  2:1376042‑M1/1‑87 (MQ=255)     aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCCCGAACGGCCGGAAGCGTCGAGacgcca                                                                                >  1:272464‑M1/1‑84 (MQ=255)     aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcca                                                                                >  2:165596‑M1/1‑84 (MQ=255)           gggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcc                                                                          >  1:551517‑M1/1‑78 (MQ=255)             gCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccat                                                                        <  2:1367979‑M1/90‑15 (MQ=255)              cTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                       <  1:12751‑M1/90‑16 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                     >  1:734174‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                     >  1:1009460‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                     >  1:1351741‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                       >  2:418090‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                       <  1:418090‑M1/88‑16 (MQ=255)                     tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                <  1:744044‑M1/90‑23 (MQ=255)                             ggCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttat                                                        >  1:1041472‑M1/1‑60 (MQ=255)                                   gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                  <  2:913325‑M1/90‑37 (MQ=255)                                   gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                  <  1:1306283‑M1/90‑37 (MQ=255)                                      gTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcg                                               <  2:734174‑M1/90‑40 (MQ=255)                                        cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                             <  2:612569‑M1/90‑42 (MQ=255)                                        cACGCCAAGACCGGCTTTCACTGCCGCACGAACAGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                             <  2:793464‑M1/90‑42 (MQ=255)                                                  ccGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatat                                   >  2:1008408‑M1/1‑39 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                                 >  2:809090‑M1/1‑37 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                                 >  2:1020840‑M1/1‑37 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                                 >  1:1259403‑M1/1‑37 (MQ=255)                                                     gCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgc                                <  2:54535‑M1/90‑55 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatcttctttattaagcgtcgccagcaccatatcgcgaaac                           <  2:1023138‑M1/90‑60 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                           >  1:1014627‑M1/1‑31 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                           <  1:1321343‑M1/90‑60 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                           <  2:551517‑M1/90‑60 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                           <  2:480617‑M1/90‑60 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                           <  1:314611‑M1/90‑60 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                           <  1:510517‑M1/90‑60 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggc                       >  1:661937‑M1/1‑27 (MQ=255)                                                               ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                      >  1:422530‑M1/1‑26 (MQ=255)                                                                   aCGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                  >  1:497569‑M1/1‑22 (MQ=255)                                                                   aCGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                  <  2:497569‑M1/58‑37 (MQ=255)                                                                       aCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcat              <  2:1286451‑M1/90‑73 (MQ=255)                                                                            cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc         <  2:1259403‑M1/90‑78 (MQ=255)                                                                            cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc         <  1:1223005‑M1/90‑78 (MQ=255)                                                                               aaGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaat      <  2:241702‑M1/90‑81 (MQ=255)                                                                               aaGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaat      <  2:456141‑M1/90‑81 (MQ=255)                                                                                aGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaata     <  2:178753‑M1/90‑82 (MQ=255)                                                                                 gCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatac    <  2:1041472‑M1/90‑83 (MQ=255)                                                                                  cGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaataca   >  1:616774‑M1/1‑7 (MQ=255)                                                                                   gTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaa  >  2:170841‑M1/1‑6 (MQ=255)                                                                                   gTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaa  >  1:1277143‑M1/1‑6 (MQ=255)                                                                                   gTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaa  >  2:834250‑M1/1‑6 (MQ=255)                                                                                        |                                                                                     ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGC  >  NZ_CP009273/2399377‑2399548

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: ‑