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)	17 (1.200)	16/310	0.0	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)	18 (1.270)	15/310	0.1	100%	coding (23/2850 nt)	rcsC	histidine kinase RcsC
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

CTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAG  >  NC_000913/2997470‑2997941                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                            ctggctgCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCt                                                                                                                                                                                                                               >  1:12365/1‑251 (MQ=255)        ctACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGaa                                                                                                                                                                                                                          >  1:50258/1‑249 (MQ=255)            acCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACACTTGCGATCTTTTCCTGTGTGGTACGCCGTCTGTGTTTCTACGGCCCTACGCAATCAATCATCTGC‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGAttt                                                                                                                                                                                                                    >  1:294897/1‑251 (MQ=14)                              gAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACAtt                                                                                                                                                                                                   >  1:224683/1‑250 (MQ=255)                                      ccGTCATCCCCTGTTCAAAGCTCTGCTGAACAAGTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTAGTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGgtg                                                                                                                                                                                                                                      <  1:176323/207‑1 (MQ=255)                                             ccccGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATc                                                                                                                                                                                    <  1:107493/250‑1 (MQ=255)                                                     cAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTCAGACATCAATCATCTGT‑TCTCCACTGACTAGTCTAAAAACTAGTATTAAGTCTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTctct                                                                                                                                                                           >  1:155418/1‑251 (MQ=255)                                                                    nanTTNNGATCNTTGCCTGGGGGGTACACCGTCTGCNTTTCTCCGGCCCTAAGACATCAAGCAGC‑GTGNCNCCAATGACTAGTCGAAAAACGAGTATTAAGACTATCACTTATTTAAGTNATATTGGGTGNCTGNNGATTNANGNGGCCAGGCTAAACTGGCTCTTTTCTTC‑TGNTGTTTATCGTTGAAAGATTTGTANNATNNNTANNATTaa                                                                                                                                                                                                 <  2:242983/213‑1 (MQ=17)                                                                                   ccTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACAGCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTCAAGGCATATTGGTTGTCTGGAGATTCAGGTGGCCAGTCTAAACTTGCTCTTTTCTTCATGG‑GTGTATCTTTGAAAGAGGGGTATTATAAATATCATTAAGTATAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTg                                                                                                                                              <  1:300792/250‑1 (MQ=18)                                                                                           gTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGTCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGata                                                                                                                                                                                                            <  1:326514/180‑1 (MQ=255)                                                                                             aCGCCGTCTGCGTTTCTCCCGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTccc                                                                                                                                   >  1:252795/1‑251 (MQ=255)                                                                                               gCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTAGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTccccc                                                                                                                                 <  1:21768/251‑1 (MQ=255)                                                                                                              ccGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATGTAATTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TTGTGTTTATCTTTGAAAGATTTGTATGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTCATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTg                                                                                                                     <  1:226549/248‑1 (MQ=255)                                                                                                                ggCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTATGACTCTCACTTCTTTAAGTGATATTGGTTGTCTGGAGCTTCAGGGGGCCAGTCTACAATTGCTATTTTATTC‑TGGTGTTTATCTTTGAACGCTTTGTAGGATAACTAACATTCAGTACCGCAGAATCGGCTTCTCTGTACTGTCTATCTTTTTCCCGATAACCTGGGGATTCTCCCCCTAACTCAAGCTGTAACg                                                                                                                >  1:187290/1‑251 (MQ=18)                                                                                                                   ccTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGtt                                                                                                              >  1:97889/1‑250 (MQ=255)                                                                                                                                                                         gACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGtt                                                        <  1:306924/251‑1 (MQ=255)                                                                                                                                                                           cTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCNGTANNNNNTannnnnnnnnn                                                                                                                                                       >  2:192298/1‑144 (MQ=37)                                                                                                                                                                             aTCACTTAAATAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGNAATNNNNNTcnnnnnnnnnn                                                                                                                                                     >  2:193128/1‑144 (MQ=38)                                                                                                                                                                               cACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTATGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTTTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATcc                                                  <  1:130671/251‑1 (MQ=255)                                                                                                                                                                                   tATTTGAGGGATATTGGTTGTCGGGAGATTCAGGGGGCCAGTCTAAACGTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTAGCTTTTGCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGGAACGTTATTCTTGCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAg                                                <  1:223798/249‑1 (MQ=255)                                                                                                                                                                                                      gTCTGGCGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCCTC‑TGGTGTTTATCTTTGCACGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGCAATGTTTATCTTTTTACAGATAACCTGCGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAACGAGTTTCATCCAGTTCATTGACTTTAGCTTcgcg                           >  1:300381/1‑251 (MQ=255)                                                                                                                                                                                                          ngagaTTNNGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGc                                                                                                                                                                                 <  2:12365/96‑1 (MQ=255)                                                                                                                                                                                                           gagaTTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTACGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTc                                                                                                                                                         >  1:211629/1‑120 (MQ=255)                                                                                                                                                                                                                             cTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCtt                                                                                                        >  1:177806/1‑151 (MQ=255)                                                                                                                                                                                                                               aaaCTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACagag  <  1:7576/251‑1 (MQ=255)                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                            CTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGT‑TCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTC‑TGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAG  >  NC_000913/2997470‑2997941

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.