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	45 [0]	[0] 45	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)	44 (1.400)	27/166	0.1	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

ACACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAA  >  NZ_CP009273/2399375‑2399550                                                                                          |                                                                                       acacGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAg                                                                                        <  2:417333/90‑1 (MQ=255)         gTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                                >  2:742360‑M1/1‑82 (MQ=255)         gTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                                >  2:692088‑M1/1‑82 (MQ=255)             gggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcc                                                                            <  2:306413‑M1/90‑13 (MQ=255)             gggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcc                                                                            >  1:691507‑M1/1‑78 (MQ=255)                cTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                         <  2:461305‑M1/90‑16 (MQ=255)                cTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                         >  1:504913‑M1/1‑75 (MQ=255)                  catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCTGAAGCGTCGAGaagccagtcgccatgga                                                                       >  1:267725‑M1/1‑73 (MQ=255)                  catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                       >  2:2776‑M1/1‑73 (MQ=255)                  catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                       >  1:631759‑M1/1‑73 (MQ=255)                     catcTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaata                                                                    <  1:692088‑M1/90‑21 (MQ=255)                       tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  2:13849‑M1/90‑23 (MQ=255)                       tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  >  1:827223‑M1/1‑68 (MQ=255)                          cAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgc                                                               >  2:381899‑M1/1‑65 (MQ=255)                           aaCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGTGaagccagtcgccatggaatatctgct                                                              <  2:439360‑M1/90‑27 (MQ=255)                                    tGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagc                                                     >  1:440347‑M1/1‑55 (MQ=255)                                     gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCTGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                    <  2:267725‑M1/90‑37 (MQ=255)                                     gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                    <  2:440347‑M1/90‑37 (MQ=255)                                                  gACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagccgccagcaccatat                                       >  2:60557‑M1/1‑41 (MQ=255)                                                      ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                                   >  2:572350‑M1/1‑37 (MQ=255)                                                           tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                              <  2:504913‑M1/90‑59 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:742360‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:827223‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:382828‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:284856‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:285248‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:316367‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:726266‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:209214‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:168355‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:626814‑M1/90‑60 (MQ=255)                                                                gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggc                         >  2:891859‑M1/1‑27 (MQ=255)                                                                 ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  2:123604‑M1/48‑23 (MQ=255)                                                                 ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  >  1:123604‑M1/1‑26 (MQ=255)                                                                    cACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctagg                     <  1:699866‑M1/90‑68 (MQ=255)                                                                        aaCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:411560‑M1/78‑60 (MQ=255)                                                                        aaCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             >  1:411560‑M1/1‑19 (MQ=255)                                                                         aCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcat                <  2:887904‑M1/90‑73 (MQ=255)                                                                              cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           <  1:775556‑M1/90‑78 (MQ=255)                                                                              cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           <  2:631759‑M1/90‑78 (MQ=255)                                                                                 aaGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           <  2:338597‑M1/87‑78 (MQ=255)                                                                                 aaGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           >  1:338597‑M1/1‑10 (MQ=255)                                                                                   gCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatac      <  1:14712‑M1/90‑83 (MQ=255)                                                                                      tCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaag   <  2:191250‑M1/90‑86 (MQ=255)                                                                                       cGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaaga  <  2:109552‑M1/90‑87 (MQ=255)                                                                                          |                                                                                       ACACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAA  >  NZ_CP009273/2399375‑2399550

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: ‑