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	48 [1]	[0] 48	[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	1 (0.020)	45 (1.100)	35/244	0.3	98.9%	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

GGCAGCGATCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3559210‑3559356 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCATGGCAATAAAC  >  NC_000913/3560986‑3561132                                                                                                                                                                                                                                                                                                        GGCAGCGATCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGA                                                                                                                                                    <  2:77600/148‑1  GCAGCGATCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAG                                                                                                                                                   >  8:59251/1‑148         TCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTA                                                                                                                                            >  5:15753/1‑148                     CAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCA                                                                                                                               >  7:74860/1‑149                            TTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGC                                                                                                                          >  2:43301/1‑147                                AGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAG                                                                                                                    >  3:151010/1‑149                                 GCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGT                                                                                                                   >  2:209920/1‑149                                     ATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGC                                                                                                                 <  1:43301/147‑1                                     ATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGC                                                                                                                 <  4:151010/147‑1                                         CCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAAC                                                                                                           <  8:74860/149‑1                                                 GTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGT                                                                                                   <  3:4620/149‑1                                                     GCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGC                                                                                                         <  3:147761/139‑1                                                     GCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGC                                                                                                         >  4:147761/1‑139                                                     GCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGA                                                                                                                                                    >  3:133455/1‑96                                                     GCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGA                                                                                                                                                    <  4:133455/96‑1                                                         TTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGC                                                                                                                          >  2:50771/1‑118                                                         TTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGC                                                                                                                          <  1:50771/118‑1                                                         TTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATAT                                                                                                                                  >  3:106496/1‑110                                                         TTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATAT                                                                                                                                  <  4:106496/110‑1                                                         TTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACC‑TCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCAGCAGCGAGCAGTGCATTAACGCGTGGGTGAAGTAACG                                                                                          >  4:29746/1‑149                                                                CAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAA                                                                                    <  6:15753/149‑1                                                                   CTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTC                                                                                 <  1:209920/149‑1                                                                       TTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAAT                                                                             <  7:59251/149‑1                                                                           CGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAGTTT                                                                           >  5:183771/1‑147                                                                           CGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTT                                                                           >  5:38549/1‑147                                                                              AGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTG                                                                      >  4:38184/1‑149                                                                                GCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTT                                                                    >  2:178442/1‑149                                                                                GCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGA                                                                                                                                        >  4:124586/1‑81                                                                                GCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGA                                                                                                                                        <  3:124586/81‑1                                                                                  AAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAA                                                                                                                     >  6:1722/1‑98                                                                                         GCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAA                                                            <  1:178442/148‑1                                                                                         GCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGA                                                                                                                                        >  4:55572/1‑72                                                                                         GCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGA                                                                                                                                        <  3:55572/72‑1                                                                                         GCGAAGATCTGTACGCGCGGATCAATCTCTGGACC‑TCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGAGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATG                                                          <  3:29746/149‑1                                                                                            AAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAA                                                                                    <  5:6841/121‑1                                                                                            AAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAA                                                                                    >  6:6841/1‑121                                                                                                                 ATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATC                                                               <  3:105493/121‑1                                                                                                                 ATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATC                                                               >  4:105493/1‑121                                                                                                                        GACCTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCT                               <  6:183771/146‑1                                                                                                                           CTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGC                         >  2:177338/1‑149                                                                                                                           CTTCACCCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGC                         >  1:217408/1‑149                                                                                                                                 CCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCATTTCC                                <  5:86187/136‑1                                                                                                                                 CCTGCCGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCATTTCC                                >  6:86187/1‑136                                                                                                                                      CGGGTCTACGCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGC              <  6:38549/149‑1                                                                                                                                               GCCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCATGGCAAT      >  5:50223/1‑148                                                                                                                                                CCAGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCATGGCAATA     >  5:55355/1‑148                                                                                                                                                  AGAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCATGGCAATAAAC  <  2:217408/149‑1                                                                                                                                                                                                                                                                                                        GGCAGCGATCGCCAGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3559210‑3559356 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccagAGCAGGTTAAAGAGGATATGCATCAGCGAGAAGTGCATTAACGCGTGGGTGAAGTAACGCCAGAACTCAAATTTCAGTGTTGGATCGAATGGCCAGGCCAGCCATAACATCACTTCCTGATCGCCGAGAATTTGCATGGCAATAAAC  >  NC_000913/3560986‑3561132

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.