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

ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCA  >  NZ_CP009273/2399377‑2399546                                                                                        |                                                                                   acGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaa                                                                                  <  1:1262953‑M1/90‑3 (MQ=255)  cGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaag                                                                                 >  1:656846‑M1/1‑87 (MQ=255)     aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcca                                                                              <  1:256093‑M1/90‑7 (MQ=255)     aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcca                                                                              <  1:707005‑M1/90‑7 (MQ=255)       gTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                            >  1:1687683‑M1/1‑82 (MQ=255)       gTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                            >  2:1498296‑M1/1‑82 (MQ=255)        tCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                           <  2:1343869‑M1/90‑10 (MQ=255)         ccGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcg                                                                          <  2:1760686‑M1/90‑11 (MQ=255)           gggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcc                                                                        <  1:199040‑M1/90‑13 (MQ=255)              cTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                     <  2:1267416‑M1/90‑16 (MQ=255)              cTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                     <  1:1255128‑M1/90‑16 (MQ=255)              cTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatg                                                                     <  1:1651385‑M1/90‑16 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:687358‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:1429774‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:1514253‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:332238‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:1252307‑M1/1‑73 (MQ=255)                catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:1712668‑M1/1‑73 (MQ=255)                   catcTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaata                                                                <  2:931895‑M1/90‑21 (MQ=255)                    atcTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatat                                                               <  2:606994‑M1/90‑22 (MQ=255)                     tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  1:738137‑M1/90‑23 (MQ=255)                     tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  1:1640067‑M1/90‑23 (MQ=255)                     tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  1:1886076‑M1/90‑23 (MQ=255)                     tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              >  1:1146329‑M1/1‑68 (MQ=255)                     tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  1:493210‑M1/90‑23 (MQ=255)                     tctcAACCGGCCGTGCCGGCAGGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  2:1791963‑M1/90‑23 (MQ=255)                       tcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctg                                                            <  2:1089124‑M1/90‑25 (MQ=255)                       tcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctg                                                            <  2:1429775‑M1/90‑25 (MQ=255)                        cAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgc                                                           <  1:1032232‑M1/90‑26 (MQ=255)                          aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                         >  1:1572516‑M1/1‑63 (MQ=255)                          aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                         <  2:1127772‑M1/90‑28 (MQ=255)                              gCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttatt                                                     <  2:903347‑M1/90‑32 (MQ=255)                              gCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgc                                                                         >  1:308384‑M1/1‑59 (MQ=255)                              gCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgc                                                                         <  2:308384‑M1/70‑12 (MQ=255)                               ccTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttatta                                                    >  2:768757‑M1/1‑58 (MQ=255)                                   gCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcg                                                <  1:768757‑M1/90‑37 (MQ=255)                                        cACGCCAAGGCCGGCTTTCACTGCCGCACGACCGGCCGGAAGGGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                           <  1:453226‑M1/90‑42 (MQ=255)                                        cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                           <  1:1598437‑M1/90‑42 (MQ=255)                                        cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                           <  1:1188345‑M1/90‑42 (MQ=255)                                        cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                            <  2:1309867‑M1/57‑9 (MQ=255)                                        cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                            >  1:1309866‑M1/1‑49 (MQ=255)                                           gCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagc                                        <  2:1572517‑M1/90‑45 (MQ=255)                                             cAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcac                                      <  2:279746‑M1/90‑47 (MQ=255)                                               aGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcacca                                    <  2:1229668‑M1/90‑49 (MQ=255)                                                tacCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                            >  2:694725‑M1/2‑41 (MQ=255)                                                gACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccat                                   >  1:1721490‑M1/1‑41 (MQ=255)                                                gACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagt                                                                            <  1:694725‑M1/49‑9 (MQ=255)                                                 aCCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccata                                  <  2:820190‑M1/90‑51 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                               >  1:515244‑M1/1‑37 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                           >  2:462751‑M1/1‑37 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                           <  1:462751‑M1/78‑42 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                           <  1:1692296‑M1/46‑10 (MQ=255)                                                    ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                           >  2:1692297‑M1/1‑37 (MQ=255)                                                         tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                          <  1:1669285‑M1/90‑59 (MQ=255)                                                         tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                          <  2:440290‑M1/90‑59 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtctccagcaccatatcgcgaaac                         <  2:23024‑M1/90‑60 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:564983‑M1/90‑60 (MQ=255)                                                          cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:515244‑M1/90‑60 (MQ=255)                                                           aCTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacg                        <  1:769059‑M1/90‑61 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggc                     >  1:1920373‑M1/1‑27 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:560152‑M1/86‑60 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         >  2:560152‑M1/1‑27 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   <  2:1630084‑M1/44‑18 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   <  2:1678641‑M1/44‑18 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:1678640‑M1/1‑27 (MQ=255)                                                              gCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:1630083‑M1/1‑27 (MQ=255)                                                                cGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggcta                   >  1:808695‑M1/1‑25 (MQ=255)                                                                       aCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcat            <  1:1469653‑M1/90‑73 (MQ=255)                                                                       aCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcat            <  2:687358‑M1/90‑73 (MQ=255)                                                                       aCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcat            <  2:1712669‑M1/90‑73 (MQ=255)                                                                        cGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatc           >  1:132578‑M1/1‑17 (MQ=255)                                                                        cGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatc           >  1:1124478‑M1/1‑17 (MQ=255)                                                                            cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc       <  2:332238‑M1/90‑78 (MQ=255)                                                                            cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc       <  1:1409274‑M1/90‑78 (MQ=255)                                                                                 gCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatac  <  1:295420‑M1/90‑83 (MQ=255)                                                                                        |                                                                                   ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCA  >  NZ_CP009273/2399377‑2399546

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: ‑