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	39 [0]	[0] 39	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)	39 (1.200)	22/164	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

CCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACA  >  NZ_CP009273/2399385‑2399554                                                                                        |                                                                                   cgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAg                                                                                  >  1:765069‑M2/88‑90 (MQ=255)    aggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCa                                                                               >  2:557009‑M2/85‑90 (MQ=255)       tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                            <  1:864765‑M2/9‑1 (MQ=255)       tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                            <  2:578044‑M2/9‑1 (MQ=255)       tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                            <  1:451938‑M2/9‑1 (MQ=255)        ccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCg                                                                           >  1:642545‑M2/81‑90 (MQ=255)            gctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCAt                                                                       <  2:30629‑M2/14‑1 (MQ=255)              tcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATgg                                                                     <  1:882679‑M2/16‑1 (MQ=255)               catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                    >  1:582759‑M2/74‑90 (MQ=255)               catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                    >  1:639634‑M2/74‑90 (MQ=255)               catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                    >  2:290706‑M2/74‑90 (MQ=255)               catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                    >  2:11766‑M2/74‑90 (MQ=255)                  catctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAata                                                                 <  1:37560‑M2/20‑1 (MQ=255)                  catctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAata                                                                 <  2:581644‑M2/20‑1 (MQ=255)                    tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  1:470654‑M2/22‑1 (MQ=255)                    tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  2:294720‑M2/22‑1 (MQ=255)                    tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  1:658488‑M2/22‑1 (MQ=255)                    tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  2:582759‑M2/22‑1 (MQ=255)                         accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                          >  1:380613‑M2/64‑90 (MQ=255)                            ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttat                                                       >  2:306777‑M2/61‑90 (MQ=255)                                 tgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGc                                                  >  1:533807‑M2/56‑90 (MQ=255)                                  gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                 <  1:277439‑M2/36‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                            <  2:639634‑M2/41‑1 (MQ=255)                                       cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                            >  1:8218‑M2/50‑90 (MQ=255)                                                   ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                >  2:460746‑M2/38‑90 (MQ=255)                                                   ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                >  1:169036‑M2/38‑90 (MQ=255)                                                   ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                                >  1:238498‑M2/38‑90 (MQ=255)                                                        tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                           <  1:306777‑M2/58‑1 (MQ=255)                                                         ccctgccgcacgaacggccggaagcgtggagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  1:103303‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  2:481012‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  1:460746‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  2:700370‑M2/59‑1 (MQ=255)                                                         cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  2:913816‑M2/59‑1 (MQ=255)                                                              ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt                     <  2:238498‑M2/64‑1 (MQ=255)                                                              ccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt                     <  2:961610‑M2/64‑1 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc        <  2:765069‑M2/77‑1 (MQ=255)                                                                           cggaagcgtcgagAAGCCAGCCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc        <  2:719037‑M2/77‑1 (MQ=255)                                                                                gcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATAc   <  1:557009‑M2/82‑1 (MQ=255)                                                                                 cgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACa  >  1:605146‑M2/8‑90 (MQ=255)                                                                                        |                                                                                   CCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACA  >  NZ_CP009273/2399385‑2399554

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑