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)	6 (0.810)	4/316	0.3	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)	11 (1.480)	9/316	0.0	100%	coding (23/2850 nt)	rcsC	histidine kinase RcsC
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

GCGATTTTCGGCGATGTACTTCAGCTCTTTCATCACATCAGAGGTGCGTTGAATAAAGCGCTGAGCCTGATCGGAACTCAGATTAAATTCCTGACGAATTTCCGATTCTCGCTGATGTAACGCATTAACGATGTAAAAAACGGATGAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACGAAAAGAAGCAAGGTATTTCAAAGGGGCGAAGCTCCGCCTCAGGTGACCGATGGAGTGTGGTTAAGGTAGCGGTAAAAGCGTGTTACCGCAATGTTCTCTCTTCTCTGGAATATGATACACCGCCGAGAAATCATCACCTTAACCTCTGATAATCGTCATATACCGGACAAGACTAGTGGATTTCAGCATGCATTATATGAAGTGGATTTATCCACGCCGCTTACGCAATCAAATGATCCTGAT  >  NC_000913/2319637‑2320098                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                         gCGATTTTCGGCGATGTACTTCAGATCTTTCATCACAACAGAGGTGCGTTGAATAAAGCGCTGAGCCTGATCGGAACTCAGATTAAATTCCTGACGAATTTCCGATTCTCGCTGATGTAACGCATTAACGATGTCAAAAACGGATGAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggccccctgaatctccagacaaccaat                                                                                                                                                                                                                     >  1:164089‑M1/1‑218 (MQ=255)                      nagCTCTTTCATCACATCAGAGGTGCGTTGAATAAAGCGCTGAGCCTGATCGGAACTCAGATTAAATTCCTGACGAATTTCCGATTCTCGCTGATGTAACGCATTAACGATGTAAAAAACGGATGAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagt                                                                                                                                                                                                >  1:33498‑M1/2‑197 (MQ=255)                                               ccagacgggttaacggcagcaaagaaccttgcagaggcgttcgagcattataacgaatggcatccgcatagtgcgctgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaTGTACGAAAAGAAGCAAGGTATTTCAAAGGGGCGAAGCTCCGCCTCAGGTGACCGATGGAGTGTGGTTAAGGTAGCGGTaaa                                                                                                                                                                         >  1:12283‑M2/168‑249 (MQ=255)                                                          aacggcagcaaagaaccttgcagaggcgttcgagcattataacgaatggcatccgcatagtgcgctgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaTGTACGAAAAGAAGCAAGGTATTTCAAAGGGGCGAAGCTCCGCCTCAGGTGACCGATGGAGTGTGGTTAAGGTAGCGGTAAAAGCGTGTTACCg                                                                                                                                                             <  1:119487‑M2/94‑1 (MQ=255)                                                                 gCCTGATCGGAACTCAGATTAAATTCCTGACGAATTTCCGATTCTCGCTGATGTAACGCATTAACGATGTAAAAAACGGATGAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgatt                                                                                                                                                     >  1:7684‑M1/1‑154 (MQ=255)                                                                 gCCTGATCGGAACTCAGATTAAATTCCTGACGAATTTCCGATTCTCGCTGATGTAACGCATTAACGATGTAAAAAACGGATGAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgatt                                                                                                                                                     >  1:141902‑M1/1‑154 (MQ=255)                                                                    tGATCGGAACTCAGATTAAATTCCTGACGAATTTCCGATTCTCGCTGACGTAAAGCATTAACGATATAAAAAACGGATGAAAAAGAAATCAACAGACCGAGCACTAACGCCCATGCTATGAACATGTAGCGCGCGGCTTTAAGAGTTGCACtagactggccacctgaatctccagaa                                                                                                                                                                                                                            >  1:171564‑M1/1‑151 (MQ=255)                                                                                                       cGATTCTCGCTGATGTAACGCATTAACGATGTAAAAAACGGATGAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccac                                                                                                               >  1:143349‑M1/1‑116 (MQ=255)                                                                                                                                                  gAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGTACATGTAGCGTGAGGCTTTCAGGGTTGTACtagactggccccctgaatctccagacaaccaatatcacttaaagaagttatagtcttaatactagtttttagactagtcagtggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtacc                                                                                                                 <  1:159317‑M1/206‑134 (MQ=255)                                                                                                                                                       gcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaTGTACGACAAGAAGCAAGGTATTTCGACGGGGCGAAGCTCCGCCTCAGGTGACCGATGGAGTGTGGTTAAGGTAGCGGTAAAAGCGTGTTACCGCAATg                                                                                                                                                        >  1:89095‑M2/64‑162 (MQ=255)                                                                                                                                                       aGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggccccctgaatctccagacaaccaatatcactgaaagaagtgatagtcttaatacttgtttttagactagtcattggagaacagatgattgatg                                                                                                                                                 <  1:98253‑M1/169‑102 (MQ=255)                                                                                                                                                         cAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggcccctgaatctccanncaacca                                                                                                                                                                                                                        >  2:12451‑M1/1‑66 (MQ=255)                                                                                                                                                         cAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACtagactggcccctgaatctccagacaaccaatatcacttaaataagtgatagtc                                                                                                                                                                                                <  1:12451‑M1/120‑55 (MQ=255)                                                                                                                                                              agggcttgtaatgggttaagtgataacagatgtctggcaatatagcggcaaatccaTGTACGACATGCAGAAAGGTATTTCAAAGGGGCGAAGCTGCGCCTAAGGTGACCGATGGCGTGTGGTTAAGGTAGCGGTAAAAGCGTGTTACCGCAATGTTCTCTCTTCTCTGGAATATGATAAACCGCCGAGAAATCCTCACCTTAACCTCTGATAATCGTCATATACCGGACAAGACTAGTGGATTTCAgcat                                                        >  1:125772‑M2/57‑251 (MQ=255)                                                                                                                                                                ngcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaTGTACGAAAAGAAGCAAGGTATTTCAAAGGGGCGAAGCTCCGCCTCAGGTGACCGATGGAGTGTGGTTAAGGTAGCGGTAAAAGCGTGTTACCGCAATGTTCTCTCTTCTCTGGAATATGAt                                                                                                                                 >  1:20474‑M2/55‑176 (MQ=255)                                                                                                                                                                ggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaTGTACGAAAAGAAGCAAGGTATTTAAAAGGGGCGAAGCTCCGCCTCAGGTGACCGATGGAGTGTGGTTAAGGTAGCGGTAAAAGCGTGTTACCGCAATGTTCTCTCTTCTCTGGAATATGATACACCGCCGAGAAATCATCACCTTAACCTCTGATAATCGTCATATACCGGACAAGACTAGTGGATTTCAg                                                           >  1:129048‑M2/55‑246 (MQ=255)                                                                                                                                                                                                                    gTTGTACtagactgtcccccagaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgagtgatgtcgtagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcagagctttgatccgtggagtacgttcttcctctttgcccggcaacatggtgtagcagccagccagttatttctctggcgtaag  <  1:118433‑M1/251‑245 (MQ=255)                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                         GCGATTTTCGGCGATGTACTTCAGCTCTTTCATCACATCAGAGGTGCGTTGAATAAAGCGCTGAGCCTGATCGGAACTCAGATTAAATTCCTGACGAATTTCCGATTCTCGCTGATGTAACGCATTAACGATGTAAAAAACGGATGAAAAAGCAATCAACAGCCAGAGCACTAACGCCAATGCTCTGAACATGTAGCGCGAGGCTTTCAGGGTTGTACGAAAAGAAGCAAGGTATTTCAAAGGGGCGAAGCTCCGCCTCAGGTGACCGATGGAGTGTGGTTAAGGTAGCGGTAAAAGCGTGTTACCGCAATGTTCTCTCTTCTCTGGAATATGATACACCGCCGAGAAATCATCACCTTAACCTCTGATAATCGTCATATACCGGACAAGACTAGTGGATTTCAGCATGCATTATATGAAGTGGATTTATCCACGCCGCTTACGCAATCAAATGATCCTGAT  >  NC_000913/2319637‑2320098

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ 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.