New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4552017	25 (0.340)	4 (0.070)	4/182	NT	13.1%	intergenic (+67/+114)	pydA/rutR	NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family
	?	NC_002947	= 4552068	35 (0.660)					intergenic (+118/+63)	pydA/rutR	NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family

CGCGTAACCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCACCTCGC  >  NC_002947/4551922‑4552216                                                                                                                                                   |                                                                                                                                                     cgcgTACCCCCTAGCGTGGTGCGAGTTGAATCGGGTCACCGCCTGAACAGCGCACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGGGGTACAGACATCGAGGGGCCGCTTCgcg                                                                                                                                                   >  2:116934‑M2/1‑147 (MQ=255)   cgTAACCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggc                                                                                                                                                 >  1:635649‑M2/1‑145 (MQ=255)     tAACCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGAAATCGAGGGGCCGCTTCgcggccc                                                                                                                                               >  2:597230‑M2/1‑143 (MQ=255)             aCCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgat                                                                                                                                            <  1:626764‑M2/145‑11 (MQ=255)             aCCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgat                                                                                                                                            >  2:626764‑M2/1‑135 (MQ=255)                                                            ccccTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatcgcgacacaagg                                                                                                                                >  1:115063‑M2/1‑88 (MQ=255)                                                            ccccTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatcgcgacacaagg                                                                                                                                <  2:115063‑M2/110‑23 (MQ=255)                                                                         ggCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCa                                                                                                            >  2:1896982/1‑117 (MQ=255)                                                                         ggCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCa                                                                                                            <  1:1896982/117‑1 (MQ=255)                                                                          gCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAg                                                                                                                >  1:720003/1‑112 (MQ=255)                                                                          gCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAg                                                                                                                <  2:720003/112‑1 (MQ=255)                                                                           ccTTGTGTCGCGATCGGGCCGCACAGCGGCCCCCGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGCTCGCGACACAACGCCGCTCCCACAAAAAGACCACGTACACCTGCAACGCCGGATCACGGCCCCAGccc                                                                         >  2:337880/1‑150 (MQ=38)                                                                           ccTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTGCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCCCCAGccc                                                                         >  1:1701081/1‑150 (MQ=255)                                                                            cTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACg                                                                                   >  2:1543334/1‑139 (MQ=255)                                                                            cTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACg                                                                                   <  1:1543334/139‑1 (MQ=255)                                                                             ttGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatcgcgacacaaggccgctcccacaggggccgcgtcagctgttcaggcggtgacccgcttcaactg                                                                            >  1:212583‑M2/1‑71 (MQ=255)                                                                             ttGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatcgcgacacaaggccgctcccacaggggccgcgtcagctgttcaggcggtgacccgcttcaactg                                                                            <  2:212583‑M2/145‑75 (MQ=255)                                                                               gtgtCGCGATCGGGCCGCACAGCGGCCCAAGAAGTCTTTGCCGCGATACAGACATCGAGGGCCCGCTTCGCGGCATCTACGCTACACAAGGCCATTCTCTGTTCTTCAGCACTGCTACCTGTAGTGCCGGATCACGGCTCCAGCCCGATc                                                                     <  1:337880/150‑1 (MQ=255)                                                                                tgtCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACACGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATcc                                                                    >  2:1363334/1‑150 (MQ=255)                                                                                 atctcgATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATccc                                                                   >  1:1827785/5‑150 (MQ=255)                                                                                    gcgATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACACAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCg                                                                >  1:1339440/1‑150 (MQ=255)                                                                                         ggggCCGCTGTGCGG‑CCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGAt                                                          <  1:1816606/149‑1 (MQ=39)                                                                                          gggCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGAt                                                          >  1:168491/1‑150 (MQ=255)                                                                                            gCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCTGTTGCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCa                                                        >  1:355004/1‑150 (MQ=255)                                                                                              cGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatc                                                                                                                                           <  1:199994‑M2/65‑12 (MQ=255)                                                                                              cGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatc                                                                                                                                           >  2:199994‑M2/1‑54 (MQ=255)                                                                                              cGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACg                                                      >  2:935241/1‑150 (MQ=255)                                                                                               gCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGAACGCCACACAAGGCCACTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGc                                                     >  2:328509/1‑150 (MQ=255)                                                                                               gCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGACCGATAGCGACACAAGGCCGCTACAACAAAAAGAACACTGCCACCTCGGAAGCCCGAGGTGTACGGCAGGCCGGTCCCCCGCAACATCACGc                                                     >  2:804103/1‑150 (MQ=255)                                                                                                 acaGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatcgcgacacaaggccgctcccacaggggccgcgtcagctgttcaggcggtgacccgcttcaactggcctcacggtaggggttacgc                                                       >  1:1436759‑M2/1‑51 (MQ=255)                                                                                                 acaGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCgcggcccgatcgcgacacaaggccgctcccacaggggccgcgtcagctgttcaggcggtgacccgcttcaactggcctcacggtaggggttacgc                                                       <  2:1436759‑M2/146‑96 (MQ=255)                                                                                                          ccAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATccccc                                                                 <  2:1296246/127‑1 (MQ=255)                                                                                                          ccAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATccccc                                                                 >  1:1296246/1‑127 (MQ=255)                                                                                                            agcagTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATc                                                                     >  2:1623875/1‑121 (MQ=255)                                                                                                            agcagTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATc                                                                     <  1:1623875/121‑1 (MQ=255)                                                                                                              cagTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTc                                                                               >  2:357980/1‑109 (MQ=255)                                                                                                              cagTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTc                                                                               <  1:357980/109‑1 (MQ=255)                                                                                                                       ccGCGATACAGACATCGAGGGGCCGCTTCGCGGGCCGATCGCGAGACGAAACCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGGTCCCCCGCAAGATCACGCTGGTGACCGTCTGCACCGGATtct                             >  1:547357/1‑150 (MQ=255)                                                                                                                       ccGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtct                             <  2:168491/150‑1 (MQ=255)                                                                                                                       ccGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtct                             >  2:1641659/1‑150 (MQ=255)                                                                                                                        cgcgATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGCTCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtctc                            <  2:1827785/150‑1 (MQ=255)                                                                                                                                aGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCa                    >  1:1091289/1‑150 (MQ=255)                                                                                                                                aGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCa                    >  2:951474/1‑150 (MQ=255)                                                                                                                                aGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCAGATCACGGATCCAGCCCAATCCCCCGCAAGATCACGGTGGTCACCCTTTGCACCGGAGTCTCCAAgccaa                    >  2:819291/1‑146 (MQ=38)                                                                                                                                 caCATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGGCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCAt                   <  2:1514070/149‑1 (MQ=255)                                                                                                                                  aCATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATg                  >  2:1768195/1‑150 (MQ=255)                                                                                                                                  aCATCGAGGGGCCGCTTCGCGGCCCGANCGCGACACAAGGNCGCTCCNACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATg                  >  1:1514070/1‑150 (MQ=255)                                                                                                                                          gggCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAg          >  2:1028101/1‑150 (MQ=255)                                                                                                                                            gCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCa        >  2:9635/1‑150 (MQ=255)                                                                                                                                            gCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCACCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCa        <  1:9635/150‑1 (MQ=255)                                                                                                                                               gCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGaa                         <  1:546060/130‑1 (MQ=255)                                                                                                                                               gCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGaa                         >  2:546060/1‑130 (MQ=255)                                                                                                                                                cTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCACCTc    >  2:380623/1‑150 (MQ=255)                                                                                                                                                  acgccgcCCGATCGCGACACAAGGCCTCTCCCACAAACAGGCCACGCCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCACCTcgc  <  2:547357/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                     CGCGTAACCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCACCTCGC  >  NC_002947/4551922‑4552216

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ 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.