Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,319,850	IS2 (+) +5 bp	coding (23‑27/2850 nt)	rcsC ←	histidine kinase RcsC

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2068941 =	NA (NA)	15 (1.150)	12/290	0.1	100%	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	2319850 =	0 (0.000)					coding (27/2850 nt)	rcsC	histidine kinase RcsC
*	?	NC_000913	= 2319854	0 (0.000)	15 (1.150)	11/290	0.1	100%	coding (23/2850 nt)	rcsC	histidine kinase RcsC
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

GCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACT  >  NC_000913/2997476‑2997905                                                                                                                                                                                                                        |                                                                                                                                                                                                                       gctACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAACGCTCTGCTGACCAATTGCGCTCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAATAACTAGTATTCAGACTATCACTTATTTCAGTGATATTGGTTGTCTGGCGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaa                                                                                                                                                                                      >  1:328908/1‑250 (MQ=14)                                  gTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGTAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCg                                                                                                                                                    <  1:224518/251‑1 (MQ=255)                                                aaaGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAAGCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTg                                                                                                                                      <  1:223519/251‑1 (MQ=255)                                                                   gCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGACCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCg                                                                                                                                               <  1:190040/223‑1 (MQ=255)                                                                   gCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAAATAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTcc                                                                                                                    >  1:291053/1‑250 (MQ=255)                                                                                gtgtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGAGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATGAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTggg                                                                                                        <  1:318578/249‑1 (MQ=255)                                                                                                                  gACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGTCTTCTCTGTAATGTTTATCTTTTGCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCtt                                                                    <  1:115556/251‑1 (MQ=255)                                                                                                                                            cTAGTCTAAAAACTATTATCAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTNTTTNCTTCNGGNGTTTAGCAGTGAAAGNTTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCGNNANNNTNGATCtttt                                                                                                                       <  2:222066/174‑1 (MQ=21)                                                                                                                                                        cTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTAAGGGGGCCAGTCTACACTTGCTCTTTTCTTCTGGAGTTTATCTTTGAAAGATTTGTAGGCTAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATc                                                                                                                           >  1:312947/1‑158 (MQ=37)                                                                                                                                                                                    tGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGATTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACt  >  1:137989/1‑251 (MQ=255)                                                                                                                                                                                                        ttCAGGGGGCCAGTCTAAACTTGCTCTTTGCTTCTGGTGTTTATCTTTGAAAGAGTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAAGCAAGCTGTAACGt                                                                           <  1:101978/158‑1 (MQ=255)                                                                                                                                                                                                            gggggCCAGTCTAAACTTGCTCTTTTNTTCTGGNNTTNATCTTTGAAAGATTTGTAGNATNNNTNNNANTAAGTNAANNCGCATCGGCNTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCNAGCTGTAACNNTATTCTTTCATAACCtttctcntttnntnnanctc                                        >  2:77833/1‑172 (MQ=255)                                                                                                                                                                                                            gggggCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAggtg                                             <  1:77833/184‑1 (MQ=255)                                                                                                                                                                                                                gCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGACAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTACATCa                                                                                      >  1:234661/1‑139 (MQ=255)                                                                                                                                                                                                                gCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGNAGGNTAAANAANATTAAGTAAAGCCGCNTCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGANNCNNNCNCTAAATCa                                                                                      <  2:234661/139‑1 (MQ=255)                                                                                                                                                                                                                 ccAGTCGAAACTGGCTCGGTACTTCTGGTTTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAATTAAAGCCGCAt                                                                                                                                                 <  2:27551/79‑1 (MQ=255)                                                                                                                                                                                                                        |                                                                                                                                                                                                                       GCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACT  >  NC_000913/2997476‑2997905

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ 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.