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	35 [0]	[0] 35	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)	35 (1.130)	25/172	0.2	100%	coding (657/939 nt)	lrhA	transcriptional regulator LrhA
	?	NZ_CP009273	2399472 =	0 (0.000)					coding (649/939 nt)	lrhA	transcriptional regulator LrhA

GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACA  >  NZ_CP009273/2399383‑2399554                                                                                          |                                                                                   cacgcagggccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggacgcgtcgagaa                                                                                   >  2:530764‑M2/90‑91 (MQ=255)        gtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                            <  2:222660‑M2/9‑1 (MQ=255)          ccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGc                                                                          >  2:856575‑M2/81‑91 (MQ=255)           cgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                         <  2:243547‑M2/12‑1 (MQ=255)            gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCa                                                                        >  1:309631‑M2/79‑91 (MQ=255)            gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCa                                                                        >  1:673551‑M2/79‑91 (MQ=255)             ggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCAt                                                                       <  1:184572‑M2/14‑1 (MQ=255)              gctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggatgcgtcgagAAGCCAGTCGCCATg                                                                      <  1:554593‑M2/15‑1 (MQ=255)                 catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGaa                                                                   >  2:863523‑M2/74‑91 (MQ=255)                 catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGaa                                                                   >  2:767393‑M2/74‑91 (MQ=255)                   tcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAata                                                                 <  1:57868‑M2/20‑1 (MQ=255)                     atctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  2:369325‑M2/22‑1 (MQ=255)                     atctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  2:590913‑M2/22‑1 (MQ=255)                     atctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                               <  2:346568‑M2/22‑1 (MQ=255)                      tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCt                                                              >  1:26126‑M2/69‑91 (MQ=255)                         caaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCt                                                           <  1:827163‑M2/26‑1 (MQ=255)                              ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttatt                                                      >  2:393504‑M2/61‑91 (MQ=255)                              ggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcatcgagAAGCCAGTCGCCATGGAATATCTGCTttatt                                                      >  1:740965‑M2/61‑91 (MQ=255)                                        tcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                            <  2:853152‑M2/41‑1 (MQ=255)                                         cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCa                                           >  2:204784‑M2/50‑91 (MQ=255)                                                agaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCat                                    >  1:337889‑M2/43‑91 (MQ=255)                                                     ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcgc                               >  2:76415‑M2/38‑91 (MQ=255)                                                          tcactgccgcacggacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  1:655911‑M2/59‑1 (MQ=255)                                                          tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATCTCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  1:832638‑M2/59‑1 (MQ=255)                                                          tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  2:162429‑M2/59‑1 (MQ=255)                                                          tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  2:389458‑M2/59‑1 (MQ=255)                                                          tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                          <  1:450219‑M2/59‑1 (MQ=255)                                                           cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACg                         >  2:658505‑M2/32‑91 (MQ=255)                                                               gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                 <  1:622762‑M2/36‑1 (MQ=255)                                                               gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                 >  2:622762‑M2/28‑63 (MQ=255)                                                               gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt                     <  2:309631‑M2/64‑1 (MQ=255)                                                               gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCt                     <  1:445995‑M2/64‑1 (MQ=255)                                                                       aacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGatcat             >  1:221986‑M2/20‑91 (MQ=255)                                                                         cggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATcc           <  1:508228‑M2/74‑1 (MQ=255)                                                                                  gcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACa  >  2:177875‑M2/9‑91 (MQ=255)                                                                                          |                                                                                   GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACA  >  NZ_CP009273/2399383‑2399554

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑