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	75 [0]	[0] 75	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)	75 (1.200)	41/162	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

TCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATAC  >  NZ_CP009273/2399384‑2399553                                                                                         |                                                                                  acgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagaa                                                                                  <  1:1262953‑M2/2‑1 (MQ=255)  cgcaggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAg                                                                                 >  1:656846‑M2/88‑90 (MQ=255)     aggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCa                                                                              <  1:256093‑M2/6‑1 (MQ=255)     aggtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCa                                                                              <  1:707005‑M2/6‑1 (MQ=255)       gtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                            >  1:1687683‑M2/83‑90 (MQ=255)       gtccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                            >  2:1498296‑M2/83‑90 (MQ=255)        tccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                           <  2:1343869‑M2/9‑1 (MQ=255)         ccgggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCg                                                                          <  2:1760686‑M2/10‑1 (MQ=255)           gggctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGcc                                                                        <  1:199040‑M2/12‑1 (MQ=255)              ctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATg                                                                     <  2:1267416‑M2/15‑1 (MQ=255)              ctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATg                                                                     <  1:1255128‑M2/15‑1 (MQ=255)              ctcatcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATg                                                                     <  1:1651385‑M2/15‑1 (MQ=255)                catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:687358‑M2/74‑90 (MQ=255)                catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:1429774‑M2/74‑90 (MQ=255)                catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:1514253‑M2/74‑90 (MQ=255)                catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:332238‑M2/74‑90 (MQ=255)                catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:1252307‑M2/74‑90 (MQ=255)                catcatctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:1712668‑M2/74‑90 (MQ=255)                   catctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAata                                                                <  2:931895‑M2/20‑1 (MQ=255)                    atctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAatat                                                               <  2:606994‑M2/21‑1 (MQ=255)                     tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                              <  1:738137‑M2/22‑1 (MQ=255)                     tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                              <  1:1640067‑M2/22‑1 (MQ=255)                     tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                              <  1:1886076‑M2/22‑1 (MQ=255)                     tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                              >  1:1146329‑M2/69‑90 (MQ=255)                     tctcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                              <  1:493210‑M2/22‑1 (MQ=255)                     tctcaaccggccgtgccggcaggccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATc                                                              <  2:1791963‑M2/22‑1 (MQ=255)                       tcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTg                                                            <  2:1089124‑M2/24‑1 (MQ=255)                       tcaaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTg                                                            <  2:1429775‑M2/24‑1 (MQ=255)                        caaccggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGc                                                           <  1:1032232‑M2/25‑1 (MQ=255)                          accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                         >  1:1572516‑M2/64‑90 (MQ=255)                          accggccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCtt                                                         <  2:1127772‑M2/27‑1 (MQ=255)                              gccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGc                                                                         >  1:308384‑M2/60‑70 (MQ=255)                              gccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGc                                                                         <  2:308384‑M2/11‑1 (MQ=255)                              gccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttatt                                                     <  2:903347‑M2/31‑1 (MQ=255)                               ccttgccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTttatta                                                    >  2:768757‑M2/59‑90 (MQ=255)                                   gccgtcacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCg                                                <  1:768757‑M2/36‑1 (MQ=255)                                        cacgccaaggccggctttcactgccgcacgaccggccggaagggtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                           <  1:453226‑M2/41‑1 (MQ=255)                                        cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                            <  2:1309867‑M2/8‑1 (MQ=255)                                        cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                            >  1:1309866‑M2/50‑57 (MQ=255)                                        cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                           <  1:1598437‑M2/41‑1 (MQ=255)                                        cacgccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                           <  1:1188345‑M2/41‑1 (MQ=255)                                           gccaagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGc                                        <  2:1572517‑M2/44‑1 (MQ=255)                                             caagaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCAc                                      <  2:279746‑M2/46‑1 (MQ=255)                                               agaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCa                                    <  2:1229668‑M2/48‑1 (MQ=255)                                                taccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                            >  2:694725‑M2/42‑49 (MQ=255)                                                gaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGt                                                                            <  1:694725‑M2/8‑1 (MQ=255)                                                gaccggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCat                                   >  1:1721490‑M2/42‑90 (MQ=255)                                                 accggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCata                                  <  2:820190‑M2/50‑1 (MQ=255)                                                    ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                           <  1:1692296‑M2/9‑1 (MQ=255)                                                    ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTc                                                                           >  2:1692297‑M2/38‑46 (MQ=255)                                                    ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                           >  2:462751‑M2/38‑78 (MQ=255)                                                    ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGcc                                           <  1:462751‑M2/41‑1 (MQ=255)                                                    ggctttcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATcg                               >  1:515244‑M2/38‑90 (MQ=255)                                                         tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                          <  1:1669285‑M2/58‑1 (MQ=255)                                                         tcactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGaaa                          <  2:440290‑M2/58‑1 (MQ=255)                                                          cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCTCCAGCACCATATCGCGAAAc                         <  2:23024‑M2/59‑1 (MQ=255)                                                          cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                         <  1:564983‑M2/59‑1 (MQ=255)                                                          cactgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                         <  2:515244‑M2/59‑1 (MQ=255)                                                           actgccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACg                        <  1:769059‑M2/60‑1 (MQ=255)                                                              gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   <  2:1630084‑M2/17‑1 (MQ=255)                                                              gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   <  2:1678641‑M2/17‑1 (MQ=255)                                                              gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:1678640‑M2/28‑44 (MQ=255)                                                              gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGa                                                                   >  1:1630083‑M2/28‑44 (MQ=255)                                                              gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                         <  1:560152‑M2/59‑1 (MQ=255)                                                              gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAc                         >  2:560152‑M2/28‑86 (MQ=255)                                                              gccgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGc                     >  1:1920373‑M2/28‑90 (MQ=255)                                                                cgcacgaacggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTa                   >  1:808695‑M2/26‑90 (MQ=255)                                                                       acggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGatcat            <  1:1469653‑M2/72‑1 (MQ=255)                                                                       acggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGatcat            <  2:687358‑M2/72‑1 (MQ=255)                                                                       acggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGatcat            <  2:1712669‑M2/72‑1 (MQ=255)                                                                        cggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGatcatc           >  1:132578‑M2/18‑90 (MQ=255)                                                                        cggccggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGatcatc           >  1:1124478‑M2/18‑90 (MQ=255)                                                                            cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc       <  2:332238‑M2/77‑1 (MQ=255)                                                                            cggaagcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGc       <  1:1409274‑M2/77‑1 (MQ=255)                                                                                 gcgtcgagAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATAc  <  1:295420‑M2/82‑1 (MQ=255)                                                                                         |                                                                                  TCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATAC  >  NZ_CP009273/2399384‑2399553

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑