New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3666134	23 (0.120)	7 (0.040)	6/208	NT	19.2%	intergenic (‑324/+46)	gadX/gadA	acid resistance regulon transcriptional activator; autoactivator/glutamate decarboxylase A, PLP‑dependent
	?	NC_000913	= 3666147	39 (0.240)					intergenic (‑337/+33)	gadX/gadA	acid resistance regulon transcriptional activator; autoactivator/glutamate decarboxylase A, PLP‑dependent

GAACACAGGGAAATTAATAGTAAGCAAATAATCCCTTTTCGTGACATTAAAGGTAATCGCTACATTTAATAAACATTCATATAACATATATCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3665979‑3666134 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaccgaatgcccagcCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTATTAAATGTAGCGATTACCTTTAATGTCACGAAAAGGGATTATTTGC  <  NC_000913/3666147‑3666002                                                                                                                                                                                                                                                                                                                GAACACAGGGAAATTAATAGTAAGCAAATAATCCCTTTTCGTGACATTAAAGGTAATCGCTACATTTAATAAACATTCATATAACATATATCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAAT                                                                                                                                                           <  1:1025045/149‑1   ACACAGGGAAATTAATAGTAAGCAAATAATCCCTTTTCGTGACATTAAAGGTAATCGCTACATTTAATAAACAGTCATATAACATATATCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGC                                                                                                                                                         >  1:421888/1‑149              TTAATAGTAAGCAAATAATCCCTTTTCGTGACATTAAAGGTAATCGCTACATTTAATAAACATTCATATAACATATATCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGCCTTTAA                                                                                                                                              >  4:617383/1‑149                         CAAATAATCCCTTTTCGTGACATTAAAGGTAATCGCTACATTTAATAAACATTCATATAACATATATCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGCCTTTAAAAAAACAGCTG                                                                                                                                   <  3:1801476/149‑1                          AAATAATCCCTTTTCGTGACATTAAAGGTAATCGCTACATTTAATAAACATTCATATAACATATATCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGCCTTTAAAAAAACAGCTGG                                                                                                                                  <  3:617383/149‑1                                                                                           TCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTC                                                                                                                            <  1:1851946/90‑1                                                                                           TCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTC                                                                                                                            >  2:1851946/1‑90                                                                                                TCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAAC                                                                                                                                                                <  4:704033/49‑1                                                                                                TCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAAC                                                                                                                                                                >  3:704033/1‑49                                                                                                                   GCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGCCTTTAAAAAAACAGCTGG                                                                                                                                  <  4:1583340/60‑1                                                                                                                   GCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGCCTTTAAAAAAACAGCTGG                                                                                                                                  >  3:1583340/1‑60                                                                                                                                              AACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATAT                                                                >  4:794526/1‑99                                                                                                                                              AACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATAT                                                                <  3:794526/99‑1                                                                                                                                                        CCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTATTAAATGTAGCGATTAC                               <  2:1298433/122‑1                                                                                                                                                        CCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTATTAAATGTAGCGATTAC                               >  1:1298433/1‑122                                                                                                                                                        CCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTAT                                               <  3:735437/106‑1                                                                                                                                                        CCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTAT                                               >  4:735437/1‑106                                                                                                                                                         CAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTATTAAATGTAGCGATTACCTTTAATGTCACGAAAAGGGATTATTTG   >  2:1251528/1‑149                                                                                                                                                         CAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTA                                                            <  3:1464980/92‑1                                                                                                                                                         CAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTA                                                            >  4:1464980/1‑92                                                                                                                                                          AGCCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTATTAAATGTAGCGATTACCTTTAATGTCACGAAAAGGGATTATTTGC  <  1:1251528/149‑1                                                                                                                                                            CCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGA                                                                     <  3:1457923/80‑1                                                                                                                                                            CCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGA                                                                     >  4:1457923/1‑80                                                                                                                                                                                                                                                                                                                GAACACAGGGAAATTAATAGTAAGCAAATAATCCCTTTTCGTGACATTAAAGGTAATCGCTACATTTAATAAACATTCATATAACATATATCTTATCAACACGATGAATAGACAGCCAATATATTATTGCGATTAATAAGCAACCGAATGCCCAGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3665979‑3666134 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaccgaatgcccagcCTTTAAAAAAACAGCTGGGCATTCGGTTGCTTATTAATCGCAATAATATATTGGCTGTCTATTCATCGTGTTGATAAGATATATGTTATATGAATGTTTATTAAATGTAGCGATTACCTTTAATGTCACGAAAAGGGATTATTTGC  <  NC_000913/3666147‑3666002

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.