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	50 [0]	[0] 50	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)	50 (0.910)	32/166	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

GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAA  >  NZ_CP009273/2399383‑2399550                                                                                  |                                                                                       gTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                                <  1:1066469‑M1/90‑9 (MQ=255)   ccGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcg                                                                              >  1:984399‑M1/1‑80 (MQ=255)     gggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCTAGaagccagtcgcc                                                                            >  2:312832‑M1/1‑78 (MQ=255)     gggCTAATCACCTCAGCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcc                                                                            <  2:742054‑M1/90‑13 (MQ=255)       gCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccat                                                                          <  1:1163570‑M1/90‑15 (MQ=255)        cTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                         <  1:1056129‑M1/90‑16 (MQ=255)          catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                       >  2:998468‑M1/1‑73 (MQ=255)          catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                       >  2:1528504‑M1/1‑73 (MQ=255)          catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                       >  1:1030576‑M1/1‑73 (MQ=255)          catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                       >  1:694652‑M1/1‑73 (MQ=255)          catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                                >  1:809684‑M1/1‑73 (MQ=255)          catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                                <  2:809684‑M1/81‑9 (MQ=255)            tcatcTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGgagccagtcgccatggaat                                                                     >  1:609942‑M1/1‑71 (MQ=255)               tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  1:1089878‑M1/90‑23 (MQ=255)               tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  >  2:1389311‑M1/1‑68 (MQ=255)               tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  1:1177766‑M1/90‑23 (MQ=255)               tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  1:882920‑M1/90‑23 (MQ=255)                ctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatct                                                                 >  1:522105‑M1/1‑67 (MQ=255)                 tcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctg                                                                <  2:1453085‑M1/90‑25 (MQ=255)                    aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                               <  1:1099305‑M1/72‑10 (MQ=255)                    aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                               >  2:1099305‑M1/1‑63 (MQ=255)                       ggCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttat                                                          >  1:1241636‑M1/1‑60 (MQ=255)                       ggCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttat                                                          >  1:1287851‑M1/1‑60 (MQ=255)                            tGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagc                                                     >  1:1509355‑M1/1‑55 (MQ=255)                             gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                    <  2:1508598‑M1/90‑37 (MQ=255)                             gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                    <  2:1054262‑M1/90‑37 (MQ=255)                                 tCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  >  2:118972‑M1/1‑50 (MQ=255)                                 tCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                                  <  1:118972‑M1/72‑23 (MQ=255)                                  cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                               <  1:207127‑M1/90‑42 (MQ=255)                                          gACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccat                                       <  2:694652‑M1/90‑50 (MQ=255)                                              ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                                   >  1:1085481‑M1/1‑37 (MQ=255)                                              ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                                   >  1:36519‑M1/1‑37 (MQ=255)                                              ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                               >  1:1195348‑M1/1‑37 (MQ=255)                                              ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                               <  2:1195348‑M1/46‑10 (MQ=255)                                                   tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                              >  2:818307‑M1/1‑32 (MQ=255)                                                    cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:1089563‑M1/90‑60 (MQ=255)                                                    cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  2:341087‑M1/90‑60 (MQ=255)                                                    cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                             <  1:167565‑M1/90‑60 (MQ=255)                                                        gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggc                         >  1:104942‑M1/1‑27 (MQ=255)                                                        gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtc                                                  <  1:410019‑M1/65‑39 (MQ=255)                                                        gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtc                                                  >  2:410019‑M1/1‑27 (MQ=255)                                                         ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                        >  1:50648‑M1/1‑26 (MQ=255)                                                            cACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctagg                     <  2:231602‑M1/90‑68 (MQ=255)                                                              cGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggat                   <  2:1197647‑M1/90‑70 (MQ=255)                                                                    gCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatcca             <  2:282775‑M1/90‑76 (MQ=255)                                                                     ccGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcacatatcgcgaaacgggctaggatcatccagc            <  2:1030576‑M1/90‑77 (MQ=255)                                                                      cGGAAGCGTCGAGgagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           <  2:609942‑M1/90‑78 (MQ=255)                                                                      cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc           <  1:1168056‑M1/90‑78 (MQ=255)                                                                             gTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaa    >  1:736340‑M1/1‑6 (MQ=255)                                                                               cGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatacaaga  <  2:1314685‑M1/90‑87 (MQ=255)                                                                                  |                                                                                       GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAA  >  NZ_CP009273/2399383‑2399550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑