Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	3,559,357	Δ1,629 bp		[rtcR]–[glpG]	[rtcR], glpR, glpR, [glpG]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3559357	3560985	1629	42 [0]	[0] 42	[rtcR]–[glpG]	[rtcR],glpR,glpR,[glpG]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3559356	0 (0.000)	42 (1.260)	39/238	0.1	100%	coding (1089/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
	?	NC_000913	3560986 =	0 (0.000)					coding (467/831 nt)	glpG	rhomboid intramembrane serine protease

TTTGGCAGCGATCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3559207‑3559356 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCAT  >  NC_000913/3560986‑3561122                                                                                                                                                                                                                                                                                                 TTTGGCAGCGATCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCA                                                                                                                                            <  3:32461/149‑1                 AGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGG                                                                                                                            <  1:71911/149‑1                           TGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAG                                                                                                                                      >  8:93757/1‑129                           TGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAG                                                                                                                                      <  7:93757/129‑1                             ATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGC                                                                                                                >  5:111028/1‑149                             ATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATAT                                                                                                                        <  7:89127/141‑1                             ATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATAT                                                                                                                        >  8:89127/1‑141                                 TCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAG                                                                                                             >  8:24847/1‑148                                    GCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGT                                                                                                         <  6:111028/149‑1                                      TTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTG                                                                                                        >  4:73280/1‑148                                         TCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGG                                                                                                                                     >  7:24962/1‑116                                         TCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGG                                                                                                                                     <  8:24962/116‑1                                            CCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAAC                                                                                                 >  3:113821/1‑149                                                 ACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTG                                                                                            <  8:102840/149‑1                                                  CGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGG                                                                                           <  2:172794/149‑1                                                   GGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGG                                                                                          >  5:40780/1‑149                                                       CGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAA                                                                                      <  7:24847/149‑1                                                                  CCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTT                                                                                                                                   <  6:147939/93‑1                                                                  CCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTT                                                                                                                                   >  5:147939/1‑93                                                                              CGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAG                                                                                     >  2:165515/1‑127                                                                              CGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAG                                                                                     <  1:165515/127‑1                                                                                        TTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATC                                                     <  5:65584/149‑1                                                                                            GCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGC                                                                               >  5:170246/1‑119                                                                                            GCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGC                                                                               <  6:170246/119‑1                                                                                             CGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAAT                                                 <  4:585/148‑1                                                                                             CGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAAT                                                 >  3:585/1‑148                                                                                              GAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGG                                               <  6:40780/149‑1                                                                                               AAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGC                                              <  3:73280/149‑1                                                                                                       TACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAA                                                                                      <  1:40936/101‑1                                                                                                       TACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAA                                                                                      >  2:40936/1‑101                                                                                                                              CTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGC               >  8:148740/1‑149                                                                                                                               TTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTT                                                          <  7:142988/105‑1                                                                                                                               TTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTT                                                          >  8:142988/1‑105                                                                                                                               TTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCA                                                               >  3:108975/1‑100                                                                                                                               TTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCA                                                               <  4:108975/100‑1                                                                                                                                 CACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCC              <  4:113821/147‑1                                                                                                                                    CCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAA                                                                          >  3:71686/1‑84                                                                                                                                    CCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAA                                                                          <  4:71686/84‑1                                                                                                                                      TGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATT       >  2:16583/1‑149                                                                                                                                        CCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATT       <  1:16583/147‑1                                                                                                                                           GGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCAT  >  7:147307/1‑149                                                                                                                                               TACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGAT                  <  1:69329/129‑1                                                                                                                                               TACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGAT                  >  2:69329/1‑129                                                                                                                                                                                                                                                                                                 TTTGGCAGCGATCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3559207‑3559356 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCAT  >  NC_000913/3560986‑3561122

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: ‑
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.