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	73 [0]	[0] 73	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)	73 (1.220)	46/164	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

ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/2399377‑2399464 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  NZ_CP009273/2399472‑2399556                                                                                                                                                                               ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAA                                                                                     <  2:1063074/90‑1  CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAG                                                                                    >  1:1526587/1‑90  CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAG                                                                                    >  1:1543092/1‑90  CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAG                                                                                    >  1:302777/1‑90      GGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAG                                                                                >  2:795504/1‑90       GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGT                                                                               <  2:590940/90‑1       GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGT                                                                               >  2:1606733/1‑90        TCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGAACGAACGGCCGGAAGCGTCGAGAAGCCAGTC                                                                              <  1:227248/90‑1           GGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGGCCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCC                                                                           <  2:194969/90‑1              CTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATG                                                                        <  2:1526587/90‑1              CTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATG                                                                        <  2:775563/90‑1               TCATCATCTCAACCGGCCTTCCCGTCACGCCAAGACCGGCTTTCACTGCCGCCCGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGG                                                                       <  1:1409496/90‑1                CATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGA                                                                      >  2:1091535/1‑90                CATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGA                                                                      >  2:1597471/1‑90                CATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGA                                                                      <  1:1147940/90‑1                  TCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCTCCATGGAA                                                                     <  2:1196762/89‑1                  TCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCTCCATGGAA                                                                     >  1:1196762/1‑89                   CATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATA                                                                   <  1:782534/90‑1                   CATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATA                                                                   <  1:1382556/90‑1                     TCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATC                                                                 <  2:1721746/90‑1                      CTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCT                                                                >  1:20132/1‑90                         AACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCT                                                             <  1:1699699/90‑1                         AACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCT                                                             <  1:1100577/90‑1                          ACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTT                                                            <  2:99654/90‑1                             GGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTC                                                                              <  2:144700/69‑1                             GGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTC                                                                              >  1:144700/1‑69                              GCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATc                                                        <  1:1714497/90‑2                              GCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATT                                                        >  1:1471657/1‑90                              GCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATT                                                        <  1:795504/90‑1                                  TGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGC                                                    >  1:1456727/1‑90                                   GCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCG                                                   <  1:523551/90‑1                                    CCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGT                                                  <  2:172333/90‑1                                       TCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGC                                               <  2:987033/90‑1                                        CACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCC                                              <  1:1197852/90‑1                                        CACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCC                                              >  2:399223/1‑90                                        CACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCC                                              <  1:793803/90‑1                                           GCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGC                                           <  2:1642475/90‑1                                            CCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCA                                          <  1:1255463/90‑1                                               AGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCA                                       >  1:818733/1‑90                                                    GGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCG                                  >  2:440839/1‑90                                                    GGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCG                                  >  2:661100/1‑90                                                    GGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCG                                  >  1:1271675/1‑90                                                    GGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGA                                                                                      <  1:1365728/38‑1                                                    GGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGA                                                                                      >  2:1365728/1‑38                                                        TTCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAA                              >  1:637520/1‑90                                                         TCACTGCTGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAA                             <  1:471798/90‑1                                                         TCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAA                             <  2:819557/90‑1                                                         TCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAA                             <  2:272885/90‑1                                                         TCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTC                                                                              <  2:648923/41‑1                                                         TCACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTC                                                                              >  1:648923/1‑41                                                          CACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAC                            <  2:1119903/90‑1                                                          CACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAC                            <  1:1606733/90‑1                                                          CACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAC                            <  1:535489/90‑1                                                          CACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAC                            <  1:1704708/90‑1                                                          CACTGCCGCACGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAAC                            <  1:982128/90‑1                                                                    CGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCTCCATATCGCGAAACGGGCTAGGAT                  <  1:1525260/90‑1                                                                    CGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT                  <  2:936077/90‑1                                                                    CGAACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT                  <  2:1271675/90‑1                                                                       ACGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCAT               <  1:440839/90‑1                                                                        CGGCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATC              <  2:1637992/90‑1                                                                         GGCCGGAAGCGTCGAGAAGCCAGTCGCCATGAAATATCTGCTTTATT                                                        <  1:1310092/47‑1                                                                         GGCCGGAAGCGTCGAGAAGCCAGTCGCCATGAAATATCTGCTTTATT                                                        >  2:1310092/1‑47                                                                          GCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCA            <  1:910953/90‑1                                                                          GCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCA            <  1:828428/90‑1                                                                          GCCGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCA            <  1:585183/90‑1                                                                            CGGAAGCGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGC          <  1:483867/90‑1                                                                                  CGTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACA    >  2:1019157/1‑90                                                                                   GTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAA   >  1:512857/1‑90                                                                                   GTCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAA   >  1:1351507/1‑90                                                                                    TCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  1:1212842/1‑90                                                                                    TCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  1:451105/1‑90                                                                                    TCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCT                       >  2:1319674/1‑69                                                                                    TCGAGAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCT                       <  1:1319674/69‑1                                                                                                                                                                               ACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/2399377‑2399464 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG  >  NZ_CP009273/2399472‑2399556

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.