Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,317,225	IS2 (–) +5 bp	coding (2648‑2652/2850 nt)	rcsC ←	histidine kinase RcsC

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1651548	NA (NA)	41 (1.130)	37/488	0.1	93.0%	noncoding (706/706 nt)	IS2	repeat region
	?	NC_000913	= 2317229	3 (0.080)					coding (2648/2850 nt)	rcsC	histidine kinase RcsC
*	?	NC_000913	2317225 =	3 (0.080)	37 (1.020)	34/488	0.2	92.3%	coding (2652/2850 nt)	rcsC	histidine kinase RcsC
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

TACGCCAGAGAAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAAT  >  NC_000913/2997450‑2997924                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                          tACGCCAGCGAAATAACTGGCTGGATGCTACACCATGTTGCCGGGCAAAGAGGGAGACCGTCATCAGCGGTTCAAAGCTATGATGTACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGAGTTTCTCCGGCCATACGACATCAATCATCTGTTCTCCAATGCATAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAATAGATATATGTTGTCTGGCTATTCAGGGGGCCATGATAAACTTGctc                                                                                                                                                                                                                                  >  2:314755/1‑251 (MQ=11)     ccAGAGAAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCtttt                                                                                                                                                                                                                              >  1:242025/1‑251 (MQ=33)          gaAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATGCAGGGGGCCAGTCTAAACTTGCTCTTTtcttct                                                                                                                                                                                                                         <  1:149223/251‑1 (MQ=25)                aCTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGtt                                                                                                                                                                                                                   <  1:178749/251‑1 (MQ=39)                   ggctggctGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGttt                                                                                                                                                                                                                  <  1:69527/249‑1 (MQ=40)                        gctgctACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTg                                                                                                                                                                                                           >  1:364563/1‑251 (MQ=255)                           gctACACCATGTTGCCGGGCAACTAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGaa                                                                                                                                                                                                         <  2:364563/250‑1 (MQ=255)                                                   aGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACtt                                                                                                                                                                                                                                      >  1:371221/1‑197 (MQ=31)                                                       agaCCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGACAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGTTTTGTAGGTTAAATAACATTAAGTa                                                                                                                                                                             >  2:119908/1‑250 (MQ=255)                                                                  cccGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCgg                                                                                                                                                                 <  1:404843/251‑1 (MQ=255)                                                                     ggTTCAAAGCTCTGCTGAACAATTGCGATCTTGTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGATATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCtt                                                                                                                                                              <  1:190696/251‑1 (MQ=255)                                                                           aatctctGATGAACAAGTGCGATCATTTTCTGTGTAGTACGCCGTAGGCGTTGAGCCGGACCTAAGACATCAATCATCTGTTCTACAAGGACGAGTATAAAAGCTAGTATTGATACTATCTCTTATTTAAGTGATATTGGTTGGCTGGAGATGCAGGGGGAGTGTCTAAACTTGATCGTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCAAGGGCTGCTCTGt                                                                                                                                                        <  2:360390/248‑1 (MQ=255)                                                                            aGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGG‑CCAGTCTAAACTTGCTCTTTTCTTATGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAACCGCATCGGCTTCTCTGTa                                                                                                                                                       >  2:374451/1‑250 (MQ=255)                                                                                                         tgtgtgGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtctc                                                                                                                                                           >  1:452904/1‑218 (MQ=255)                                                                                                         tgtgtgGTACGCCGGCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTAGCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCATGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTTTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTtctc                                                                                                                                                           <  2:452904/218‑1 (MQ=255)                                                                                                            gtgGTACGCCGTCTGTGTTTCTACGGCCCTAAGACATCAATCATCAGTTCTCCAGTGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGTGCCAGTCTAAAATTGCTCTTTTCTTCTGGTGTTTCTATTTGAACGATTTGTAGGATCAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCAAGATAACCTGGGGAtt                                                                                                                       >  2:237368/1‑251 (MQ=21)                                                                                                               gTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATtctc                                                                                                                    <  1:150286/251‑1 (MQ=255)                                                                                                                                                        cttttgtcCAATGTCTAGTCTAAAAACTAGTATTTAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTTAAAGATTTTTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCtt                                                                             <  2:241669/243‑1 (MQ=255)                                                                                                                                                            tctcCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCt                                                                        <  1:160839/250‑1 (MQ=255)                                                                                                                                                                cAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAg                                                                   <  1:329296/251‑1 (MQ=255)                                                                                                                                                                        aGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTc                                                            >  1:448360/1‑250 (MQ=255)                                                                                                                                                                             aaaaaCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTc                                                      >  1:438207/1‑251 (MQ=255)                                                                                                                                                                                aaCTAGTATTAAGACTATCACTTATTTAAGTGAGATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCgtt                                                   <  1:349898/251‑1 (MQ=255)                                                                                                                                                                                 aCTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCgttg                                                  <  1:358818/251‑1 (MQ=255)                                                                                                                                                                                    aGTATTAAGACTATCACTTATTTAAGTGATATTGGATGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGttgttg                                               <  1:14317/251‑1 (MQ=255)                                                                                                                                                                                       atttaGACTAGCGCTTATTCAAGTGCTATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCAGCGGCTTCTCTGTTATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCTCCTAAATCAAGCTGTATCGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGaaa                                            <  2:138375/247‑1 (MQ=255)                                                                                                                                                                                          aaGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAagag                                         <  1:127742/251‑1 (MQ=255)                                                                                                                                                                                            aaCTATCACTTAGTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCCCTTTTCTTCTGGAGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGACTTCTCGGTAATGTTTATCTTTTTCCAGATAACCTGTGGATTCTCCCCCGAAATCAAGCTGTAACGTTATTCTGGCATAACCTTTATCATTGAGGTGTTTCAACCTCGTTGTTGAAAGAGtt                                       <  2:158617/250‑1 (MQ=255)                                                                                                                                                                                                     ttATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTATTTTCTTCTGGTGTTTATATTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTATTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGt                              >  1:256143/1‑251 (MQ=255)                                                                                                                                                                                                       aTTTAAGTGATATTGGTTGTCTTGAGATTTAGGGGGCCAGTTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGATTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACTTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGtt                             <  2:437223/250‑1 (MQ=255)                                                                                                                                                                                                           aaGTGATATTTGGTGTCTGGAGAGTCAGGGGGCCAGGTTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTTAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACTTTATTCTGTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTg                        <  2:165198/251‑1 (MQ=255)                                                                                                                                                                                                                        tGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCTGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCAGTGACTTTAGCTTcg            <  2:438207/250‑1 (MQ=255)                                                                                                                                                                                                                                 aTTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAAt  >  1:172598/1‑251 (MQ=255)                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                          TACGCCAGAGAAATAACTGGCTGGCTGCTACACCATGTTGCCGGGCAACGAGGGAGACCGTCATCCCCGGTTCAAAGCTCTGCTGAACAATTGCGATCTTTTCCTGTGTGGTACGCCGTCTGCGTTTCTCCGGCCCTAAGACATCAATCATCTGTTCTCCAATGACTAGTCTAAAAACTAGTATTAAGACTATCACTTATTTAAGTGATATTGGTTGTCTGGAGATTCAGGGGGCCAGTCTAAACTTGCTCTTTTCTTCTGGTGTTTATCTTTGAAAGATTTGTAGGATAAATAACATTAAGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAAT  >  NC_000913/2997450‑2997924

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.