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	40 [0]	[0] 40	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)	40 (1.340)	23/168	0.2	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

AGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATC  >  NZ_CP009273/2399381‑2399544                                                                                    |                                                                                 aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcca                                                                            >  2:760972‑M1/1‑84 (MQ=255) aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcca                                                                            >  2:385730‑M1/1‑84 (MQ=255)    tCCGGGCTCATCATCCCAACCGGCCTTGCCGTCCCGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                         <  1:202840‑M1/90‑10 (MQ=255)     ccGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcg                                                                        <  1:257512‑M1/90‑11 (MQ=255)            catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                 >  1:171543‑M1/1‑73 (MQ=255)            catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                 >  2:73189‑M1/1‑73 (MQ=255)            catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                 >  1:406950‑M1/1‑73 (MQ=255)            catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                 >  1:575281‑M1/1‑73 (MQ=255)               catcTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaata                                                              <  2:232398‑M1/90‑21 (MQ=255)                    cAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                   >  1:159406‑M1/1‑65 (MQ=255)                    cAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                   <  2:159406‑M1/80‑16 (MQ=255)                      aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                       >  1:5834‑M1/1‑63 (MQ=255)                          gCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttatt                                                   <  2:844107‑M1/90‑32 (MQ=255)                              tGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagc                                               >  1:687619‑M1/1‑55 (MQ=255)                              tGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagc                                               >  1:854163‑M1/1‑55 (MQ=255)                               gCCGTCACGCCAAGACTGGCTTTCACTGTCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                              <  2:62663‑M1/90‑37 (MQ=255)                                ccGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgt                                             <  2:643543‑M1/90‑38 (MQ=255)                                    cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                         <  2:154320‑M1/90‑42 (MQ=255)                                                ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                         <  1:459739‑M1/78‑42 (MQ=255)                                                ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                         >  2:459739‑M1/1‑37 (MQ=255)                                                     tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                        <  2:180882‑M1/90‑59 (MQ=255)                                                      cACTGCCGCACGACCGGCCGGAAGGGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       <  2:229665‑M1/90‑60 (MQ=255)                                                      cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       <  1:816816‑M1/90‑60 (MQ=255)                                                      cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       <  1:362597‑M1/90‑60 (MQ=255)                                                      cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       <  2:764135‑M1/90‑60 (MQ=255)                                                      cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       <  2:594113‑M1/90‑60 (MQ=255)                                                      cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       <  1:385730‑M1/90‑60 (MQ=255)                                                            cGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggcta                 >  1:323957‑M1/1‑25 (MQ=255)                                                              cACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctagg               <  1:768223‑M1/90‑68 (MQ=255)                                                                      gCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatcca       <  1:680753‑M1/90‑76 (MQ=255)                                                                        cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc     <  1:402201‑M1/90‑78 (MQ=255)                                                                        cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc     <  2:382720‑M1/90‑78 (MQ=255)                                                                        cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc     <  2:323957‑M1/90‑78 (MQ=255)                                                                        cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc     <  1:675585‑M1/90‑78 (MQ=255)                                                                        cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc     <  1:98074‑M1/90‑78 (MQ=255)                                                                         ggAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       >  2:70397‑M1/1‑12 (MQ=255)                                                                         ggAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                       <  1:70397‑M1/71‑60 (MQ=255)                                                                           aaGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggccaggatcatccagcaat  <  2:824938‑M1/90‑81 (MQ=255)                                                                                tCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                        >  2:181034‑M1/1‑5 (MQ=255)                                                                                tCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                        <  1:181034‑M1/63‑59 (MQ=255)                                                                                    |                                                                                 AGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATC  >  NZ_CP009273/2399381‑2399544

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑