New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	3409928 =	63 (0.920)	5 (0.080)	4/328	NT	6.0%	intergenic (‑494/‑42)	PP_3022/PP_3024	Transcriptional regulator, AraC family/conserved protein of unknown function
	?	AE015451	= 3450711	95 (1.430)					intergenic (‑125/+258)	PP_5558/PP_3069	putative transcriptional xre family of phage origin/Outer membrane autotransporter

GCTGTTTTGCAATGCGCTTATGCCGAAGGTAGTAGTCTTTTTTTAAAAGCTTCACATGATATCCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/3410123‑3409928 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggttACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTTCATGCATACAGTATAGCGAGTAGTGACCATGACGGCCGACATCATTACCTTCCCGACACCGACCATGGAAGAAG  <  AE015451/3450711‑3450535                                                                                                                                                                                                                                                                                                                                                                                       GCTGTTTTGCAATGCGCTTATGCCGAAGGTAGTAGTCTTTTTTTAAAAGCTTCACATGATATCCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCC                                                                                                                                            <  2:206462/235‑1           AATGCGCTTATGTCGAAGGTAGTAGTCTTTTTTTAAAAGCTTCACATGATATCCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCT                                                                                                                                  <  1:465867/235‑1                                                               CCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTCATATTGTCAGTCGCTAGG                                                                                                                                                                                      >  2:480178/1‑131                                                                cgTTCAATGCGTCGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCGGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCC                                                                                                                                            <  2:145848/170‑1                                                                      cTGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCACTTTGCCTCTGTTCGCCTGCTGAGTAAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTT                                                                            <  1:354057/229‑1                                                                                                                                               GGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTTACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTTCATGCATACAGTATAGCGAGTAGTGACCATGACGGCCGACATCATTACCTTCTCGACACCGACCATGGAAGAAG  >  1:412273/1‑231                                                                                                                                                                                                                                                                                                                                                                                       GCTGTTTTGCAATGCGCTTATGCCGAAGGTAGTAGTCTTTTTTTAAAAGCTTCACATGATATCCATTCAATGCGCAGGTGATTTGTAAGTACGACAAGCGTGGCAATTTGCCTCTGTTCGCCTGCTGAGTCAATGCATGGAGGGTTGATACCAATTTACCCTGAAGCTAGAGTTTATATTGTCAGTCGCTAGGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/3410123‑3409928 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggttACCTAGCGACTGATAATATAATTTTTAGAATAACCACCCTCCTGCCCCTAAGCAGGCCTTGATCCGTATACATTGCTTAAGATGGCTTTCTCGCTATACTGTTCATGCATACAGTATAGCGAGTAGTGACCATGACGGCCGACATCATTACCTTCCCGACACCGACCATGGAAGAAG  <  AE015451/3450711‑3450535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ 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.