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	31 [0]	[0] 31	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)	31 (1.080)	24/166	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

CCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  NZ_CP009273/2399385‑2399556                                                                                        |                                                                                     cgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAg                                                                                    >  1:184086‑M2/88‑90 (MQ=255)       tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                              <  2:833721‑M2/9‑1 (MQ=255)          gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                           >  1:536220‑M2/79‑90 (MQ=255)           ggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCa                                                                          <  1:193101‑M2/13‑1 (MQ=255)             ctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATg                                                                        <  2:493897‑M2/15‑1 (MQ=255)               catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                      >  2:175705‑M2/74‑90 (MQ=255)                         accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                            <  1:688864‑M2/27‑1 (MQ=255)                         accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                            >  1:689818‑M2/64‑90 (MQ=255)                            ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttat                                                         >  1:514253‑M2/61‑90 (MQ=255)                                     gtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCg                                                <  2:514254‑M2/39‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGc                                                              >  2:814246‑M2/50‑74 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGc                                                              <  1:814245‑M2/25‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                              <  1:396363‑M2/41‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                              <  2:149847‑M2/41‑1 (MQ=255)                                              agaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCa                                       >  1:198550‑M2/43‑90 (MQ=255)                                                        tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                             <  2:640390‑M2/58‑1 (MQ=255)                                                        tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                             <  2:496432‑M2/58‑1 (MQ=255)                                                        tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                             <  1:100890‑M2/58‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgttgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  2:433298‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  2:520145‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  2:9325‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  2:198550‑M2/59‑1 (MQ=255)                                                          actgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACg                           <  2:143258‑M2/60‑1 (MQ=255)                                                              ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt                       <  1:655512‑M2/64‑1 (MQ=255)                                                                   cgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGat                  <  1:175705‑M2/69‑1 (MQ=255)                                                                       cggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGatcatc              >  2:389755‑M2/18‑90 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            >  2:594508‑M2/14‑72 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                            <  1:594507‑M2/59‑1 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc          <  2:689819‑M2/77‑1 (MQ=255)                                                                                gcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATAc     <  2:683101‑M2/82‑1 (MQ=255)                                                                                   tcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAag  >  1:329314‑M2/6‑90 (MQ=255)                                                                                        |                                                                                     CCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  NZ_CP009273/2399385‑2399556

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑