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

AGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCG  >  NC_000913/3559223‑3559493                                                                                                                                      |                                                                                                                                          aGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagagg                                                                                                                            <  1:71911‑M1/149‑16 (MQ=255)           tGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcag                                                                                                                                      >  8:93757‑M1/1‑124 (MQ=255)           tGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcag                                                                                                                                      <  7:93757‑M1/129‑6 (MQ=255)             aTTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagc                                                                                                                >  5:111028‑M1/1‑122 (MQ=255)             aTTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatat                                                                                                                        <  7:89127‑M1/141‑20 (MQ=255)             aTTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatat                                                                                                                        >  8:89127‑M1/1‑122 (MQ=255)                 tCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgag                                                                                                             >  8:24847‑M1/1‑118 (MQ=255)                    gCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagt                                                                                                         <  6:111028‑M1/149‑35 (MQ=255)                      ttATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtg                                                                                                        >  4:73280‑M1/1‑113 (MQ=255)                         tCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcagg                                                                                                                                     <  8:24962‑M1/116‑7 (MQ=255)                         tCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcagg                                                                                                                                     >  7:24962‑M1/1‑110 (MQ=255)                            ccGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaac                                                                                                 >  3:113821‑M1/1‑107 (MQ=255)                                 aCGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtg                                                                                            <  8:102840‑M1/149‑48 (MQ=255)                                  cGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgg                                                                                           <  2:172794‑M1/149‑49 (MQ=255)                                   ggTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtggg                                                                                          >  5:40780‑M1/1‑100 (MQ=255)                                       cgcgATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaa                                                                                      <  7:24847‑M1/149‑54 (MQ=255)                                                  ccAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggtt                                                                                                                                   >  5:147939‑M1/1‑85 (MQ=255)                                                  ccAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggtt                                                                                                                                   <  6:147939‑M1/93‑9 (MQ=255)                                                              cGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaag                                                                                     >  2:165515‑M1/1‑73 (MQ=255)                                                              cGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaag                                                                                     <  1:165515‑M1/127‑55 (MQ=255)                                                                        tttCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatc                                                     <  5:65584‑M1/149‑87 (MQ=255)                                                                            gcgAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgc                                                                               >  5:170246‑M1/1‑59 (MQ=255)                                                                            gcgAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgc                                                                               <  6:170246‑M1/119‑61 (MQ=255)                                                                             cgAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaat                                                 <  4:585‑M1/148‑91 (MQ=255)                                                                             cgAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaat                                                 >  3:585‑M1/1‑58 (MQ=255)                                                                              gAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatgg                                               <  6:40780‑M1/149‑93 (MQ=255)                                                                               aaGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggc                                              <  3:73280‑M1/149‑94 (MQ=255)                                                                                       tACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaa                                                                                      <  1:40936‑M1/101‑54 (MQ=255)                                                                                       tACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaa                                                                                      >  2:40936‑M1/1‑48 (MQ=255)                                                                                                              cTTCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggccaggccagccataacatcacttcctgatcgc               >  8:148740‑M1/1‑25 (MQ=255)                                                                                                               ttCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgtt                                                          <  7:142988‑M1/105‑82 (MQ=255)                                                                                                               ttCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgtt                                                          >  8:142988‑M1/1‑24 (MQ=255)                                                                                                               ttCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttca                                                               <  4:108975‑M1/100‑77 (MQ=255)                                                                                                               ttCACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttca                                                               >  3:108975‑M1/1‑24 (MQ=255)                                                                                                                 cACCCTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggccaggccagccataacatcacttcctgatcgcc              <  4:113821‑M1/147‑126 (MQ=255)                                                                                                                    ccTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaa                                                                          >  3:71686‑M1/1‑19 (MQ=255)                                                                                                                    ccTGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaa                                                                          <  4:71686‑M1/84‑66 (MQ=255)                                                                                                                      tGCCGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggccaggccagccataacatcacttcctgatcgccgagaatt       >  2:16583‑M1/1‑17 (MQ=255)                                                                                                                        ccGGGTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggccaggccagccataacatcacttcctgatcgccgagaatt       <  1:16583‑M1/147‑133 (MQ=255)                                                                                                                           ggTCTACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggccaggccagccataacatcacttcctgatcgccgagaatttgcat  >  7:147307‑M1/1‑12 (MQ=255)                                                                                                                               tACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggccaggccagccataacatcacttcctgat                  <  1:69329‑M1/129‑122 (MQ=255)                                                                                                                               tACGCCAGagcaggttaaagaggatatgcatcagcgagaagtgcattaacgcgtgggtgaagtaacgccagaactcaaatttcagtgttggatcgaatggccaggccagccataacatcacttcctgat                  >  2:69329‑M1/1‑8 (MQ=255)                                                                                                                                      |                                                                                                                                          AGGTGAGCAGTGATTTTCAGCTTATCGCCGGAACGGTGCGCGATTTGCGCCAGCTGGTTGCCGAAGGCAAATTTCGCGAAGATCTGTACGCGCGGATCAATCTCTGGACCTTCACCCTGCCGGGTCTACGCCAGCGCCAGGAAGATATTGAACCGAACCTGGATTATGAAGTGGAGCGCCACGCCTCACTCACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCG  >  NC_000913/3559223‑3559493

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: ‑