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	68 [0]	[0] 69	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)	63 (1.260)	32/118	0.1	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

GTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCTGCGGCAGCAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTATCGGAC  >  CP009273/2399970‑2400104                                                                    |                                                                    caacgagttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagca                                                                     >  1:4700722‑M2/68‑68 (MQ=255)   acgagttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcaaa                                                                   <  1:4272111‑M2/3‑1 (MQ=255)    cgagttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcaaaa                                                                  >  1:482482‑M2/65‑68 (MQ=255)      tgttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAgt                                                                <  1:3668522‑M2/6‑1 (MQ=255)      agttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAgt                                                                <  1:1701994‑M2/6‑1 (MQ=255)      agttgttccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAgt                                                                <  1:5258137‑M2/6‑1 (MQ=255)             ccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGa                                                         <  1:1400107‑M2/13‑1 (MQ=255)             ccagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGa                                                         >  1:1424183‑M2/56‑68 (MQ=255)              cagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGAt                                                        <  1:421356‑M2/14‑1 (MQ=255)              cagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGAt                                                        >  1:4822454‑M2/55‑68 (MQ=255)              cagacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGAt                                                        <  1:4429084‑M2/14‑1 (MQ=255)                gacgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCg                                                      <  1:2010486‑M2/16‑1 (MQ=255)                 ccgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:1699562‑M2/52‑68 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:4698687‑M2/52‑68 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:3177397‑M2/52‑68 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:4288905‑M2/52‑68 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:4112767‑M2/52‑68 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:2296996‑M2/52‑68 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:1106851‑M2/52‑68 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     <  1:801719‑M2/17‑1 (MQ=255)                 acgctgcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCgg                                                     >  1:5163354‑M2/52‑68 (MQ=255)                      gcatttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaaca                                                <  1:1498939‑M2/22‑1 (MQ=255)                        atttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagc                                              >  1:2765416‑M2/45‑68 (MQ=255)                         tttgctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagca                                             >  1:305751‑M2/44‑68 (MQ=255)                           tgctgacttacggcggactgagtacgccacccagcggctgcAAAAGTGTTCAGATcggccccagcacc                                           >  1:4971408‑M2/42‑66 (MQ=255)                            gctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagcaaca                                          <  1:4780131‑M2/28‑1 (MQ=255)                            gctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagcaaca                                          <  1:4711952‑M2/28‑1 (MQ=255)                            gctgacttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGgcaacagcaaca                                          <  1:4600440‑M2/28‑1 (MQ=255)                               gacttacggcggactgagtacgccacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAAt                                       >  1:3141659‑M2/38‑68 (MQ=255)                                acttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATg                                      >  1:92927‑M2/37‑68 (MQ=255)                                 cttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGt                                     <  1:1833037‑M2/33‑1 (MQ=255)                                 cttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGt                                     >  1:1531041‑M2/36‑68 (MQ=255)                                 cttacggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGt                                     >  1:550143‑M2/36‑68 (MQ=255)                                      ggcggactgagtacgacacacagcgggagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGATCTca                                >  1:4895921‑M2/31‑68 (MQ=255)                                      ggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTca                                <  1:5166650‑M2/38‑1 (MQ=255)                                      ggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTca                                >  1:4680571‑M2/31‑68 (MQ=255)                                      ggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTca                                >  1:724174‑M2/31‑68 (MQ=255)                                      ggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTca                                >  1:1200138‑M2/31‑68 (MQ=255)                                      ggcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTca                                <  1:5030300‑M2/38‑1 (MQ=255)                                       gcggactgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACTGCAACAAATGTTCTcag                               >  1:4328085‑M2/30‑68 (MQ=255)                                       gcggactgagtacgacacacagcggcagcAAAAGAGTTCAGATCGGCAACAGCAACAAATGTTCTcag                               >  1:954831‑M2/30‑68 (MQ=255)                                           actgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGa                           <  1:4124512‑M2/43‑1 (MQ=255)                                           actgagtacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGa                           <  1:1037095‑M2/43‑1 (MQ=255)                                                 tacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgcgg                     >  1:3542841‑M2/20‑68 (MQ=255)                                                 tacgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgagg                     >  1:1519987‑M2/20‑68 (MQ=255)                                                  acgacacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggt                    >  1:3030071‑M2/19‑68 (MQ=255)                                                     acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCGACAAATGTTCTCAGCAGAtcgaggtcga                 >  1:1521582‑M2/16‑68 (MQ=255)                                                     acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                 >  1:1946662‑M2/16‑68 (MQ=255)                                                     acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                 >  1:5575894‑M2/16‑68 (MQ=255)                                                     acacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcga                 >  1:3791932‑M2/16‑68 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag                <  1:1326068‑M2/54‑1 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag                <  1:906104‑M2/54‑1 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag                <  1:1220978‑M2/54‑1 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag                <  1:68384‑M2/54‑1 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag                <  1:2734409‑M2/54‑1 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgag                <  1:4536256‑M2/54‑1 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtagag                <  1:1838919‑M2/54‑1 (MQ=255)                                                      cacacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggacgag                <  1:4045103‑M2/54‑1 (MQ=255)                                                       acacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGAtcgaggtcgagg               <  1:3547069‑M2/55‑1 (MQ=255)                                                       acacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCACAGCAGAtcgaggtcgagg               >  1:3291542‑M2/14‑68 (MQ=255)                                                        cacagcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATcgaggtcgaggt              <  1:3024762‑M2/56‑1 (MQ=255)                                                         acagcggcagcAAAAGTGTTCAGCTCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGtt             >  1:1578234‑M2/12‑68 (MQ=255)                                                           agcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCCAGGTTaa           >  1:3741309‑M2/10‑68 (MQ=255)                                                            gcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAAt          >  1:3173057‑M2/9‑68 (MQ=255)                                                            gcggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAAt          <  1:4017672‑M2/60‑1 (MQ=255)                                                             cggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAAtt         <  1:2099234‑M2/61‑1 (MQ=255)                                                              ggcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTa        >  1:4908780‑M2/7‑68 (MQ=255)                                                               gcagcAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTAt       >  1:2639316‑M2/6‑68 (MQ=255)                                                                    aaaaGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTATCGGAc  <  1:1857078/68‑1 (MQ=255)                                                                    |                                                                    GTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCTGCGGCAGCAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAGGTTAATTATCGGAC  >  CP009273/2399970‑2400104

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑