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

CTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGA  >  NZ_CP009273/2399390‑2399557                                                                                   |                                                                                      gtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                                <  1:1066469‑M2/8‑1 (MQ=255)   ccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCg                                                                              >  1:984399‑M2/81‑90 (MQ=255)     gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtctagAAGCCAGTCGcc                                                                            >  2:312832‑M2/79‑90 (MQ=255)     gggctaatcacctcagccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                            <  2:742054‑M2/12‑1 (MQ=255)       gctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCAt                                                                          <  1:1163570‑M2/14‑1 (MQ=255)        ctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATg                                                                         <  1:1056129‑M2/15‑1 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                                <  2:809684‑M2/8‑1 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                                >  1:809684‑M2/74‑81 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                       >  2:998468‑M2/74‑90 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                       >  1:1030576‑M2/74‑90 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                       >  2:1528504‑M2/74‑90 (MQ=255)          catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                       >  1:694652‑M2/74‑90 (MQ=255)            tcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagGAGCCAGTCGCCATGGAat                                                                     >  1:609942‑M2/72‑90 (MQ=255)               tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  <  1:1089878‑M2/22‑1 (MQ=255)               tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  >  2:1389311‑M2/69‑90 (MQ=255)               tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  <  1:1177766‑M2/22‑1 (MQ=255)               tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  <  1:882920‑M2/22‑1 (MQ=255)                ctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCt                                                                 >  1:522105‑M2/68‑90 (MQ=255)                 tcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTg                                                                <  2:1453085‑M2/24‑1 (MQ=255)                    accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                               <  1:1099305‑M2/9‑1 (MQ=255)                    accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                               >  2:1099305‑M2/64‑72 (MQ=255)                       ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttat                                                          >  1:1241636‑M2/61‑90 (MQ=255)                       ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttat                                                          >  1:1287851‑M2/61‑90 (MQ=255)                            tgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGc                                                     >  1:1509355‑M2/56‑90 (MQ=255)                             gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                    <  2:1508598‑M2/36‑1 (MQ=255)                             gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                    <  2:1054262‑M2/36‑1 (MQ=255)                                 tcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  >  2:118972‑M2/51‑72 (MQ=255)                                 tcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                                  <  1:118972‑M2/22‑1 (MQ=255)                                  cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                               <  1:207127‑M2/41‑1 (MQ=255)                                          gaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCat                                       <  2:694652‑M2/49‑1 (MQ=255)                                              ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                               >  1:1195348‑M2/38‑46 (MQ=255)                                              ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                               <  2:1195348‑M2/9‑1 (MQ=255)                                              ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                   >  1:1085481‑M2/38‑90 (MQ=255)                                              ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                   >  1:36519‑M2/38‑90 (MQ=255)                                                   tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                              >  2:818307‑M2/33‑90 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  1:1089563‑M2/59‑1 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  2:341087‑M2/59‑1 (MQ=255)                                                    cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                             <  1:167565‑M2/59‑1 (MQ=255)                                                        gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTc                                                  >  2:410019‑M2/28‑65 (MQ=255)                                                        gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTc                                                  <  1:410019‑M2/38‑1 (MQ=255)                                                        gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGc                         >  1:104942‑M2/28‑90 (MQ=255)                                                         ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt                        >  1:50648‑M2/27‑90 (MQ=255)                                                            cacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAgg                     <  2:231602‑M2/67‑1 (MQ=255)                                                              cgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGat                   <  2:1197647‑M2/69‑1 (MQ=255)                                                                    gccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCa             <  2:282775‑M2/75‑1 (MQ=255)                                                                     ccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCA‑CATATCGCGAAACGGGCTAGGATCATCCAGc           <  2:1030576‑M2/76‑1 (MQ=255)                                                                      cggaagcgtcgagGAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc           <  2:609942‑M2/77‑1 (MQ=255)                                                                      cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc           <  1:1168056‑M2/77‑1 (MQ=255)                                                                             gtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACaa    >  1:736340‑M2/7‑90 (MQ=255)                                                                               cgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAaga  <  2:1314685‑M2/86‑1 (MQ=255)                                                                                   |                                                                                      CTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGA  >  NZ_CP009273/2399390‑2399557

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: ‑