New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2442821	45 (0.870)	5 (0.110)	5/228	NT	11.6%	intergenic (+18/+40)	glvR/USA300HOU_RS12585	HTH‑type transcriptional regulator GlvR/hypothetical protein
	?	USA300TCH1516_ALE	= 2442838	37 (0.810)					intergenic (+35/+23)	glvR/USA300HOU_RS12585	HTH‑type transcriptional regulator GlvR/hypothetical protein

CGTCTATGTATCCAGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2442668‑2442821 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaaggaagttatgatAGGCTCAAGGCCATTAAATCATAACTTCCTTTTTTCTAATTTGAAATATCATTATGTAGTAAATACTCATTATATTTTCTTACAAGTGTTTCAAAGAATATATGATAACTGATGAAGCTAGAATAGTCTGT  <  USA300TCH1516_ALE/2442838‑2442708                                                                                                                                                                                                                                                                                               CGTCTATGTATCCAGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAA                                                                                                                                                  >  2:599294/1‑141    CTATGTATCCAGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGG                                                                                                                                               <  2:562743/141‑1              AGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGAT                                                                                                                                     <  1:36227/141‑1                               AACTAATGGTACCGACCATTCTAGCTTTATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTATTACATAATGATATTTCAAATTATATAAAAGGAAGTTATGATAGGCTCAAGGCCATTAA                                                                                                                    <  1:40815/141‑1                                                 TTCTAGCTCCATTAGTTATCATATATACCTTGAAACCCTTGTAAGAAAATATAAGGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATAGTCTCAAGGCCATTCAATCATAACTTCCTTTTTT                                                                                                  <  2:272561/141‑1                                                                   TCATATATTCTTTGAAACACTTGTAAAAAAATATAATGAGTATTTATTACATAATGATATTTCAAATTAGAAAAAA‑GAAGTTATGATAGGCTCAAGGCCATTAAATCATAACTTCCTTTTTTCTAATTTGAAATATCATTA                                                                               <  2:31997/141‑1                                                                              TTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATAGGCTCAAGGCCATTAAATCATAACTTCCTTTTTTCTAATTTGAAATATCATTATGTAGTAAAT                                                                     >  2:156228/1‑141                                                                                                            ATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATAGGCTCAAGGCCATTAAATCATAACTTCCTTTTTTCTAATTTGAAATATCATTATGTAGTAAATACTCATTATATTTTCTTACAAGTGTTTCAA                                       <  1:156228/141‑1                                                                                                                                            AAAGGAAGTTATGATAGGCTCAAGGCCAGTAAATCATAACTTCCTTTTTTCTAATTTGATAATTCTTTATGTAGTAAATACGCAGTATATTTTCTTACAAGTGTTTCAAAGAATATATGATAACTGATGAAGCTAGAATAG       <  2:218520/141‑1                                                                                                                                                 aatTTATGATAGGCTCAAGGCCATTAAATCATAACTTCCTTTTTTCTAATTTGAAATATCATTATGTAGTAAATACTCATTATATTTTCTTACAAGTGTTTCAAAGAATATATGATAACTGATGAAGCTAGAATAGTCTGT  <  1:576655/138‑1                                                                                                                                                                                                                                                                                               CGTCTATGTATCCAGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2442668‑2442821 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaaggaagttatgatAGGCTCAAGGCCATTAAATCATAACTTCCTTTTTTCTAATTTGAAATATCATTATGTAGTAAATACTCATTATATTTTCTTACAAGTGTTTCAAAGAATATATGATAACTGATGAAGCTAGAATAGTCTGT  <  USA300TCH1516_ALE/2442838‑2442708

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.