Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	CP009273	2,400,028	Δ9 bp	coding (85‑93/939 nt)	lrhA ←	transcriptional repressor of flagellar, motility and chemotaxis genes

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	2400028	2400036	9	75 [0]	[0] 75	lrhA	transcriptional repressor of flagellar, motility and chemotaxis genes

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 2400027	0 (0.000)	69 (1.120)	33/118	0.2	100%	coding (94/939 nt)	lrhA	transcriptional repressor of flagellar, motility and chemotaxis genes
	?	CP009273	2400037 =	0 (0.000)					coding (84/939 nt)	lrhA	transcriptional repressor of flagellar, motility and chemotaxis genes

TCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCTGCGGCAGCAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTATCGGA  >  CP009273/2399972‑2400103                                                                  |                                                                   acgagttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcaaa                                                                  <  1:4847823‑M2/3‑1 (MQ=255) acgagttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcaaa                                                                  <  1:5041085‑M2/3‑1 (MQ=255)  cgagttgttccagacgctgcatttgctgacttacggcggactgagtacgacacaccgcggcagcaaaa                                                                 >  1:6011384‑M2/65‑68 (MQ=255)   gagttgttccagacgctgcatttgctgacttacggcggactgagtccgacacacaggggcagcATAAg                                                                >  1:5396101‑M2/64‑68 (MQ=255)    tgttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAgt                                                               <  1:2052810‑M2/6‑1 (MQ=255)    agttgttccagacgctgcatttcctgacttacggcggactgagtacgacacacagcggcagcAAAAgt                                                               <  1:4613021‑M2/6‑1 (MQ=255)      ttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAgtgt                                                             <  1:776861‑M2/8‑1 (MQ=255)      ttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAgtgt                                                             <  1:3416096‑M2/8‑1 (MQ=255)         ttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCa                                                          <  1:4441446‑M2/11‑1 (MQ=255)         ttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCa                                                          <  1:5213571‑M2/11‑1 (MQ=255)          tccagacgctgcatttgctgacttacggcggactgagtacgacacccagcggccgcAAAAGTGGTCAg                                                         >  1:2013605‑M2/57‑68 (MQ=255)          tccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGttcct                                                         >  1:6213507‑M2/57‑66 (MQ=255)          tccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAg                                                         >  1:1456996‑M2/57‑68 (MQ=255)            cagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGAt                                                       <  1:364054‑M2/14‑1 (MQ=255)             agacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATc                                                      >  1:1982705‑M2/54‑68 (MQ=255)               acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                    >  1:5222445‑M2/52‑68 (MQ=255)               acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                    >  1:2403680‑M2/52‑68 (MQ=255)               acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                    >  1:120324‑M2/52‑68 (MQ=255)               acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                    <  1:3224317‑M2/17‑1 (MQ=255)               acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                    >  1:2641925‑M2/52‑68 (MQ=255)               acgctgcatttgctgacttacggcggactgagtacgaaacacagcggccgcAAAAGTGTTCAGATCgg                                                    >  1:5644303‑M2/52‑68 (MQ=255)                cgctgcatttgctgactttcggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgc                                                   >  1:653036‑M2/51‑68 (MQ=255)                    tcatttgctgacttactgcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaaca                                               <  1:2848302‑M2/22‑1 (MQ=255)                    gcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaaca                                               <  1:1503637‑M2/22‑1 (MQ=255)                       tttgctgacttacggcggactgagtacgacacacagcggcagcAAATGTGTTCAGATCGgcaacagca                                            <  1:3259790‑M2/25‑1 (MQ=255)                          gctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagcaaca                                         <  1:513647‑M2/28‑1 (MQ=255)                          gctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagcaaca                                         <  1:4943701‑M2/28‑1 (MQ=255)                          gctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagcaaca                                         <  1:3525701‑M2/28‑1 (MQ=255)                               cttacggcggactgagtacgacacacagcggcagcAAAAGTGTTTAGATCGGCAACAGCAACAAATGt                                    <  1:1223020‑M2/33‑1 (MQ=255)                               cttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGt                                    <  1:2854313‑M2/33‑1 (MQ=255)                               cttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGt                                    <  1:2107194‑M2/33‑1 (MQ=255)                                 tacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTtc                                  <  1:5291191‑M2/35‑1 (MQ=255)                                   cggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTtctc                                <  1:508462‑M2/37‑1 (MQ=255)                                    ggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTca                               >  1:6175600‑M2/31‑68 (MQ=255)                                    ggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTca                               >  1:310907‑M2/31‑68 (MQ=255)                                      cggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTcagc                             >  1:5261884‑M2/29‑68 (MQ=255)                                      cggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTcagc                             >  1:4794289‑M2/29‑68 (MQ=255)                                       ggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTcagca                            <  1:133175‑M2/41‑1 (MQ=255)                                         actgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGa                          <  1:2733838‑M2/43‑1 (MQ=255)                                         actgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGa                          >  1:1224343‑M2/26‑68 (MQ=255)                                         actgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGa                          <  1:1946592‑M2/43‑1 (MQ=255)                                         actgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGa                          >  1:282503‑M2/26‑68 (MQ=255)                                         actgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGa                          <  1:2602019‑M2/43‑1 (MQ=255)                                              gtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgag                     >  1:4016360‑M2/21‑68 (MQ=255)                                               tacgtcacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgagg                    <  1:3267500‑M2/49‑1 (MQ=255)                                                acgacacactgcggcagcAAAAGTGTTCAGATCGGCAACTGCAACAAATGTTCTCAGCAGAtcgaggt                   <  1:2163954‑M2/50‑1 (MQ=255)                                                acgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggt                   <  1:4075086‑M2/50‑1 (MQ=255)                                                acgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggt                   <  1:2448509‑M2/50‑1 (MQ=255)                                                   acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                >  1:5407933‑M2/16‑68 (MQ=255)                                                   acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                >  1:2916416‑M2/16‑68 (MQ=255)                                                   acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                >  1:4654186‑M2/16‑68 (MQ=255)                                                   acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                >  1:4627973‑M2/16‑68 (MQ=255)                                                   acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                >  1:155093‑M2/16‑68 (MQ=255)                                                   acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                <  1:77051‑M2/53‑1 (MQ=255)                                                   acacacagcggcagcAAAAGAGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                >  1:4241904‑M2/16‑68 (MQ=255)                                                    ctcacagcggcagcAAAAGTGTTCAGATCGGCTACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag               <  1:420427‑M2/54‑1 (MQ=255)                                                    cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag               <  1:5311909‑M2/54‑1 (MQ=255)                                                     acacagcggcagcAAAAGTGTTCAGATCGGCAACAGCACCAAATGTTCTCAGGAGAtcgaggtcgagg              >  1:2066041‑M2/14‑68 (MQ=255)                                                     acacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgagg              >  1:2809509‑M2/14‑68 (MQ=255)                                                     acacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgagggcgagg              <  1:3375522‑M2/55‑1 (MQ=255)                                                      caccgcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATcgaggtcgaggt             <  1:1447407‑M2/56‑1 (MQ=255)                                                      cacagcggcaggAATAGTGTTCAGTTCGGCATCAGCTACAAATGTTCTCAGCAGATcgaggtcgaggt             <  1:4427379‑M2/56‑1 (MQ=255)                                                      cacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATcgaggtcgaggt             <  1:3256718‑M2/56‑1 (MQ=255)                                                      cacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATcgaggtcgaggt             <  1:4573826‑M2/56‑1 (MQ=255)                                                      cacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATcgaggtcgaggt             <  1:2837830‑M2/56‑1 (MQ=255)                                                      cacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATcgaggtcgaggt             <  1:3909170‑M2/56‑1 (MQ=255)                                                      agcagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATcgaggtcgaggt             <  1:232029‑M2/56‑1 (MQ=255)                                                       acagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCGGCAGATCGAGGTCGAGGtt            >  1:2614280‑M2/12‑68 (MQ=255)                                                       acagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAgatcgaggtcgaggat            >  1:2309572‑M2/12‑66 (MQ=255)                                                          gcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTTAt         >  1:2427586‑M2/9‑68 (MQ=255)                                                           cggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAAtt        <  1:2873540‑M2/61‑1 (MQ=255)                                                            ggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTa       >  1:2225706‑M2/7‑68 (MQ=255)                                                             gcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTAt      >  1:1460803‑M2/6‑68 (MQ=255)                                                                 cAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTATCGGa  <  1:1435978‑M2/67‑1 (MQ=255)                                                                 cAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTATCGGa  <  1:4721266‑M2/67‑1 (MQ=255)                                                                  |                                                                   TCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCTGCGGCAGCAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTATCGGA  >  CP009273/2399972‑2400103

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑