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

CAACGAGTTGTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCTGCGGCAGCAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAG  >  CP009273/2399961‑2400090                                                                   |                                                                cAACGAGTTGTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCa                                                                >  1:4700722‑M1/1‑67 (MQ=255)   aCGAGTTGTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaa                                                              <  1:4272111‑M1/68‑4 (MQ=255)    cGAGTTGTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaa                                                             >  1:482482‑M1/1‑64 (MQ=255)      tgttgttcCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagt                                                           <  1:3668522‑M1/67‑7 (MQ=255)      aGTTGTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagt                                                           <  1:5258137‑M1/68‑7 (MQ=255)      aGTTGTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagt                                                           <  1:1701994‑M1/68‑7 (MQ=255)             ccAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcaga                                                    <  1:1400107‑M1/68‑14 (MQ=255)             ccAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcaga                                                    >  1:1424183‑M1/1‑55 (MQ=255)              cAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagat                                                   <  1:421356‑M1/68‑15 (MQ=255)              cAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagat                                                   <  1:4429084‑M1/68‑15 (MQ=255)              cAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagat                                                   >  1:4822454‑M1/1‑54 (MQ=255)                gACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcg                                                 <  1:2010486‑M1/68‑17 (MQ=255)                 ccgCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:1699562‑M1/2‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:2296996‑M1/1‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:1106851‑M1/1‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:3177397‑M1/1‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:4698687‑M1/1‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:4112767‑M1/1‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:4288905‑M1/1‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                >  1:5163354‑M1/1‑51 (MQ=255)                 aCGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcgg                                                <  1:801719‑M1/68‑18 (MQ=255)                      gCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaaca                                           <  1:1498939‑M1/68‑23 (MQ=255)                        aTTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagc                                         >  1:2765416‑M1/1‑44 (MQ=255)                         tttGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagca                                        >  1:305751‑M1/1‑43 (MQ=255)                           tGCTGACTTACGGCGGACTGAGTACGCCACCCAGCGGCTGCaaaagtgttcagatcggccccagcacc                                      >  1:4971408‑M1/1‑41 (MQ=255)                            gCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaaca                                     <  1:4780131‑M1/68‑29 (MQ=255)                            gCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaaca                                     <  1:4711952‑M1/68‑29 (MQ=255)                            gCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaaca                                     <  1:4600440‑M1/68‑29 (MQ=255)                               gACTTACGGCGGACTGAGTACGCCACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaat                                  >  1:3141659‑M1/1‑37 (MQ=255)                                aCTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatg                                 >  1:92927‑M1/1‑36 (MQ=255)                                 cTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgt                                >  1:1531041‑M1/1‑35 (MQ=255)                                 cTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgt                                >  1:550143‑M1/1‑35 (MQ=255)                                 cTTACGGCGGACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgt                                <  1:1833037‑M1/68‑34 (MQ=255)                                      ggcggACTGAGTACGACACACAGCGGGAGCaaaagtgttcagatcggcaacagcaacaaatgatctca                           >  1:4895921‑M1/1‑30 (MQ=255)                                      ggcggACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctca                           >  1:724174‑M1/1‑30 (MQ=255)                                      ggcggACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctca                           >  1:4680571‑M1/1‑30 (MQ=255)                                      ggcggACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctca                           <  1:5030300‑M1/68‑39 (MQ=255)                                      ggcggACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctca                           <  1:5166650‑M1/68‑39 (MQ=255)                                      ggcggACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctca                           >  1:1200138‑M1/1‑30 (MQ=255)                                       gcggACTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaactgcaacaaatgttctcag                          >  1:4328085‑M1/1‑29 (MQ=255)                                       gcggACTGAGTACGACACACAGCGGCAGCaaaagagttcagatcggcaacagcaacaaatgttctcag                          >  1:954831‑M1/1‑29 (MQ=255)                                           aCTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcaga                      <  1:4124512‑M1/68‑44 (MQ=255)                                           aCTGAGTACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcaga                      <  1:1037095‑M1/68‑44 (MQ=255)                                                 tACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgcgg                >  1:3542841‑M1/1‑19 (MQ=255)                                                 tACGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgagg                >  1:1519987‑M1/1‑19 (MQ=255)                                                  aCGACACACAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggt               >  1:3030071‑M1/1‑18 (MQ=255)                                                     acacacAGCGGCAGCaaaagtgttcagatcggcaacagcgacaaatgttctcagcagatcgaggtcga            >  1:1521582‑M1/1‑15 (MQ=255)                                                     acacacAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcga            >  1:1946662‑M1/1‑15 (MQ=255)                                                     acacacAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcga            >  1:5575894‑M1/1‑15 (MQ=255)                                                     acacacAGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcga            >  1:3791932‑M1/1‑15 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgag           <  1:1326068‑M1/68‑55 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgag           <  1:906104‑M1/68‑55 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgag           <  1:1220978‑M1/68‑55 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgag           <  1:68384‑M1/68‑55 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgag           <  1:2734409‑M1/68‑55 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgag           <  1:4536256‑M1/68‑55 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtagag           <  1:1838919‑M1/68‑55 (MQ=255)                                                      cacacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggacgag           <  1:4045103‑M1/68‑55 (MQ=255)                                                       acacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgagg          <  1:3547069‑M1/68‑56 (MQ=255)                                                       acacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttcacagcagatcgaggtcgagg          >  1:3291542‑M1/1‑13 (MQ=255)                                                        cacaGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgaggt         <  1:3024762‑M1/68‑57 (MQ=255)                                                         acaGCGGCAGCaaaagtgttcagctcggcaacagcaacaaatgttctcagcagatcgaggtcgaggtt        >  1:1578234‑M1/1‑11 (MQ=255)                                                           aGCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtccaggttaa      >  1:3741309‑M1/1‑9 (MQ=255)                                                            gCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgaggttaat     >  1:3173057‑M1/1‑8 (MQ=255)                                                            gCGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgaggttaat     <  1:4017672‑M1/68‑61 (MQ=255)                                                             cGGCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgaggttaatt    <  1:2099234‑M1/68‑62 (MQ=255)                                                              ggCAGCaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgaggttaatta   >  1:4908780‑M1/1‑6 (MQ=255)                                                               gcagcaaaagtgttcagatcggcaacagcaacaaatgttctcagcagatcgaggtcgaggttaattat  >  1:2639316‑M1/1‑5 (MQ=255)                                                                   |                                                                CAACGAGTTGTTCCAGACGCTGCATTTGCTGACTTACGGCGGACTGAGTACGACACACAGCGGCAGCTGCGGCAGCAAAAGTGTTCAGATCGGCAACAGCAACAAATGTTCTCAGCAGATCGAGGTCGAG  >  CP009273/2399961‑2400090

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: ‑