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 (0.590)	5/298	0.4	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)	10 (0.990)	7/298	0.2	100%	coding (23/2850 nt)	rcsC	histidine kinase RcsC
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

CAAAAATCAGCAACGAAGAGACGCTCGTCGTGACCACGAATCGTTCGGCAAGCAACCTTTGGGAAAGCCCGGCGACTATACAGGTTATTGACCAACAAACATTGCAGAACTCCACCAATGCCTCCATAGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTT  >  NC_000913/2068732‑2069170                                                                                                                                                                                                                  |                                                                                                                                                                                                                                      cAAAAATCAGCAACGAAGAGACGCTCGTCGTGACCACGAATCGTTCGGCAAGCAACAATTGGGACCGCCCGGCGACTCTACCGGTTATTGACCCACACACATAGAAGAACTCCACCAATGCCTCAATAGCCGATAATTTGACGGCCATCCCCGGAGTCGAGATAACCGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATACATGGATGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAAc                                                                                                                                                                                              >  1:232224/1‑251 (MQ=255)                                           nttCGGCAAGCAACCTTTGGGAAAGCCCGGCGACTATACAGGTTATTGACCAACAAACATTGCAGAACTCCACCAATGCCTCCATAGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAg                                                                                                                                                                                    >  1:154661/2‑219 (MQ=255)                                              cGGCAAGCAACCTTTGGGAAAGCCCGGCGACTATACAGGTTATTGACCAACAAACATTGCAGAACTCCACCAATGCCTCCATAGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATa                                                                                                                                                  <  1:225277/250‑1 (MQ=255)                                                                                          gACCAACAAACATTGCAGAACTCCACCAATGCCTCCATAGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCg                                                                                                                      >  1:7287/1‑234 (MQ=255)                                                                                                                 caccaATGCCTCCATAGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCg                                                                              <  1:111057/251‑1 (MQ=255)                                                                                                                     aaTGCCTCCATAGCCGATAATGTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGTCCGTAAACAAATCCGCATTCGTGGCTTGATTTGCCCCTATATTGCCAGACAACTGTTAGCACTTAAGCCATTACTAGCCCGCTGCCTCAGATATCCCCGTGTCTAGCGATACCCCAGCGCACTATGCGGATGCCATTCg                                                                                                                      <  1:171154/207‑1 (MQ=25)                                                                                                                          nnncATNGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAg                                                                                                                                                                                    <  2:154661/137‑1 (MQ=255)                                                                                                                             naTAGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTg                                                                  >  1:151462/2‑251 (MQ=255)                                                                                                                                                       ccGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGAc                                                                                                                                                                                                               >  1:61883/1‑84 (MQ=255)                                                                                                                                                               gagaTAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACg                                                                                                      <  1:200670/181‑1 (MQ=255)                                                                                                                                                                 gaTAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATAGTTCCAGACATCTGTTATCACGTAAGCCATTACAAGCCCGGTGCCGGAGATATTGCCGTGGCGAGCGATAACCCAGCGGACTATTCGGATGCCATTCGTTATAATTCTCGAACGCCTCTGGAGGCTGCTTTGCAGCCGTTAACCGTTCGTGTTTGGGCATGATACTGATGTAGTCACGCTTTATCg                              <  1:167333/251‑1 (MQ=17)                                                                                                                                                                    aaCAGACAACTCCTTGGCAGGCCGTAAACAACTCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTAATCACTTAACCCATTACAAGCCCGTTGCCGCAGATATTCCAGTGGCGAGCGATAACCCAGCGCACTATGCGGCTGCCATTCGTTATAATGCTc                                                                                                           >  1:102230/1‑171 (MQ=18)                                                                                                                                                                               ccTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCTTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGctc                >  1:21693/1‑251 (MQ=255)                                                                                                                                                                                         ccGTAAACAAATCCGCATTCGTGTCTGGATGTGCCCCTATATTTCCAGACATCTGTTATCACGTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGATCGATAACCCAGCGCACTATGCGGATGCCACTCGTTATAATGCTCGAACGCCGCTGCAAGGTTCGGTGCTGCCGTTAACCCGGCTTGTTTTGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCt          <  1:142930/247‑1 (MQ=14)                                                                                                                                                                                             aaaCAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAACGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTGTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGt   <  1:248492/250‑1 (MQ=255)                                                                                                                                                                                                       gCATTCTTGGCTGTATTTGCCCCTATATTACCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCATATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGTCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTTTGTTTTGTGCATGATACTGATGTATTCTCGCTTTATCGTTTTCACGAAGCTCTCTTCTATTCCGtn  <  1:55332/241‑2 (MQ=11)                                                                                                                                                                                                         aTTCGTGGCTGGAGTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAAcn                                                                                                      <  1:47188/139‑2 (MQ=37)                                                                                                                                                                                                                  |                                                                                                                                                                                                                                      CAAAAATCAGCAACGAAGAGACGCTCGTCGTGACCACGAATCGTTCGGCAAGCAACCTTTGGGAAAGCCCGGCGACTATACAGGTTATTGACCAACAAACATTGCAGAACTCCACCAATGCCTCCATAGCCGATAATTTGCAGGACATCCCCGGAGTAGAGATAACAGACAACTCCTTGGCAGGCCGTAAACAAATCCGCATTCGTGGCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTT  >  NC_000913/2068732‑2069170

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ 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.