New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1378545	59 (0.900)	4 (0.060)	4/248	NT	7.5%	coding (6/1647 nt)	opuD_1	Glycine betaine transporter OpuD
	?	USA300TCH1516_ALE	= 1378579	42 (0.670)					coding (40/1647 nt)	opuD_1	Glycine betaine transporter OpuD

TTATTCAAGAAAATTTGATTATCGCAAAGACCTTTGTTATCCTATAAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1378404‑1378545 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgaatACTTCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTCAATTCTATATTTAATTTTATGTAGTAGAATAAAAATATTATCTAAACATTTTATTCAATAACTCACGCACCTTTATAGGAT  <  USA300TCH1516_ALE/1378579‑1378442                                                                                                                                                                                                                                                                                          TTATTCAAGAAAATTTGATTATCGCAAAGACCTTTGTTATCCTATAAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGA                                                                                                                                              <  2:542815/140‑1                                                                                                       AAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATACTTCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTCAATTCTATATTTAATTT                                                                  <  1:739953/114‑1                                                                                                       AAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATACTTCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTCAATTCTATATTTAATTT                                                                  >  2:739953/1‑114                                                                                                           TAAATATAGAATTGAAGGGAGTAATTAATTATGAATACTTCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTCAATTCTATATTTA                                                                      <  1:656899/106‑1                                                                                                           TAAATATAGAATTGAAGGGAGTAATTAATTATGAATACTTCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTCAATTCTATATTTA                                                                      >  2:656899/1‑106                                                                                                                                           cacTACGTCTTGTCAGTTGGATTTTGTCGTGAAGCAGAATGCATAATTAATTACTCCCTTCAATTCTATATTTCCTGTTATGTAGTAGAATAAAAATATTATCTAAACATTTTATTCAATAACTCACGCACCTTTATAGG    <  2:582634/137‑1                                                                                                                                           GAATACTGCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTCAATTCTATATTTAATTTTATGTAGTAGAATAAAAATATTATCTAAACATTTTATTCAATAACTCACGCACCTTTATAGG    <  1:743314/140‑1                                                                                                                                             ATACTTCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTAACTTCTATATTTAATCTTATGTAGTAGAATATAATAATTACATAAACATTTTATTAAATACAGCACGCACCTTTCTAGGAT  >  2:89787/1‑140                                                                                                                                                                                                                                                                                          TTATTCAAGAAAATTTGATTATCGCAAAGACCTTTGTTATCCTATAAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1378404‑1378545 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgaatACTTCTTTCCATTTGGATTCTCTGGTGAAGAAGAATTCATAATTAATTACTCCCTTCAATTCTATATTTAATTTTATGTAGTAGAATAAAAATATTATCTAAACATTTTATTCAATAACTCACGCACCTTTATAGGAT  <  USA300TCH1516_ALE/1378579‑1378442

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.