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	69 [0]	[0] 68	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)	68 (1.060)	35/166	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

ACACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCA  >  NZ_CP009273/2399375‑2399546                                                                                          |                                                                                   acacGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAg                                                                                    <  2:1746351/90‑1 (MQ=255)       aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcca                                                                              >  2:503055‑M1/1‑84 (MQ=255)       aGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagcca                                                                              >  1:1675169‑M1/1‑84 (MQ=255)          tCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                           <  2:930892‑M1/90‑10 (MQ=255)          tCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                           <  1:1226399‑M1/90‑10 (MQ=255)          tCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtc                                                                           <  1:659910‑M1/90‑10 (MQ=255)           ccGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcg                                                                          <  1:1546415‑M1/90‑11 (MQ=255)             gggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcc                                                                        <  2:273896‑M1/90‑13 (MQ=255)             gggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcc                                                                        <  1:1829084‑M1/90‑13 (MQ=255)              ggCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcca                                                                       >  1:1863036‑M1/1‑77 (MQ=255)                 tcatcaTCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgg                                                                    <  1:589157‑M1/90‑17 (MQ=255)                  catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:852380‑M1/1‑73 (MQ=255)                  catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  2:1133032‑M1/1‑73 (MQ=255)                  catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcca                                                                       >  1:178958‑M1/1‑73 (MQ=255)                  catcatCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgcca                                                                       <  2:178958‑M1/86‑14 (MQ=255)                       tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              >  2:1721984‑M1/1‑68 (MQ=255)                       tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  1:1592256‑M1/90‑23 (MQ=255)                       tctcAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  1:862849‑M1/90‑23 (MQ=255)                          cAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgc                                                           >  2:101046‑M1/1‑65 (MQ=255)                            aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                         <  1:1536289‑M1/90‑28 (MQ=255)                            aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                         >  1:1704174‑M1/1‑63 (MQ=255)                            aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                         >  2:1642912‑M1/1‑63 (MQ=255)                            aCCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctt                                                         <  2:1785697‑M1/90‑28 (MQ=255)                              cGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgcttta                                                       >  2:1522130‑M1/1‑61 (MQ=255)                               ggCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttat                                                      >  2:1443871‑M1/1‑60 (MQ=255)                                gCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttatt                                                     >  1:408868‑M1/1‑59 (MQ=255)                                 ccTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttatta                                                    >  2:1026931‑M1/1‑58 (MQ=255)                                          cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                           <  1:1841505‑M1/90‑42 (MQ=255)                                          cACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgcc                                           <  1:1847643‑M1/90‑42 (MQ=255)                                             gCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagc                                        <  1:1034147‑M1/90‑45 (MQ=255)                                             gCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagc                                        <  1:1536636‑M1/90‑45 (MQ=255)                                             gCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   >  1:589561‑M1/1‑46 (MQ=255)                                             gCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatgga                                                                   <  2:589561‑M1/63‑18 (MQ=255)                                               cAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcac                                      >  1:1691139‑M1/1‑44 (MQ=255)                                                      ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                               >  2:410781‑M1/1‑37 (MQ=255)                                                      ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcg                               >  1:1246530‑M1/1‑37 (MQ=255)                                                      ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              <  1:1490156‑M1/59‑23 (MQ=255)                                                      ggCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatc                                                              >  2:1490156‑M1/1‑37 (MQ=255)                                                           tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                          <  1:646328‑M1/90‑59 (MQ=255)                                                           tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                          <  1:1522130‑M1/90‑59 (MQ=255)                                                           tCACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaa                          <  1:998122‑M1/90‑59 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:1878119‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:1226657‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:1704174‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:1675169‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:162435‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:433679‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:1478538‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:1379309‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:1896289‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:1291479‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:1271366‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:355014‑M1/90‑60 (MQ=255)                                                            cACTGCCGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:1182793‑M1/90‑60 (MQ=255)                                                                 ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                    <  1:1396738‑M1/90‑65 (MQ=255)                                                                 ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                    >  2:1543720‑M1/1‑26 (MQ=255)                                                                 ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggct                    <  1:503055‑M1/90‑65 (MQ=255)                                                                 ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         >  2:938363‑M1/1‑26 (MQ=255)                                                                 ccGCACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  1:938363‑M1/85‑60 (MQ=255)                                                                    cACGAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctagg                 <  2:1011489‑M1/90‑68 (MQ=255)                                                                       gAACGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatc              <  2:1120647‑M1/90‑71 (MQ=255)                                                                         aCGGCCGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcat            <  2:1691139‑M1/90‑73 (MQ=255)                                                                              cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc       <  2:1466296‑M1/90‑78 (MQ=255)                                                                              cGGAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagc       <  2:1863036‑M1/90‑78 (MQ=255)                                                                                gAAGCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaa     <  1:338765‑M1/90‑80 (MQ=255)                                                                                 aaGCGTCGAGaggccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaat    <  1:222394‑M1/90‑81 (MQ=255)                                                                                   gCGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaacgggctaggatcatccagcaatac  <  1:1133032‑M1/90‑83 (MQ=255)                                                                                    cGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         <  2:1120532‑M1/66‑60 (MQ=255)                                                                                    cGTCGAGaagccagtcgccatggaatatctgctttattaagcgtcgccagcaccatatcgcgaaac                         >  1:1120532‑M1/1‑7 (MQ=255)                                                                                          |                                                                                   ACACGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCA  >  NZ_CP009273/2399375‑2399546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑