New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	3651929 =	172 (4.470)	4 (0.100)	4/314	NT	2.3%	coding (204/528 nt)	gadE	gad regulon transcriptional activator
	?	CP009273	4487998 =	NA (NA)					intergenic (+241/‑91)	intB/insC1	pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA
Rejected: Frequency below/above cutoff threshold.

ATTTTTCAGAATCAGTTGCATAATTTTGAACTGATTATGTGAAAAACATAATTGTGAATTCTTATGGGGCAAGTGTTTACCATAAGTAATCTCAAGAAGATTTTTGATACTTTCTTTGCGGCTAACAAAATAAATAGGCGCTTTAGCTTTTAGTTTACTGATGTGATAAGGTGCCAAAACAATAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/3652115‑3651929 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATG  >  CP009273/4487998‑4488206                                                                                                                                                                                                                                                                                                                                                                                                              ATTTTTCAGAATCAGTTGTATAATTTTTAACTGATTATGTGAAAAACATAATTGTGAATTCTTATGGGGCAAGTGTTTACCATAAGTAATTNCAAGAAGATTTTTGATACTATCTTTGCGGCTAACAAAATAAATAGGCGCTTTAGCTGTTAGTTTACTGATGTGATAAGGTGCCAAAACAATAATTTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAA                                                                                                                           <  1:565752/275‑1                                            AAACATAATTGTGAAATCTTATGTAGCATGTGTTTACCATAAGTAATCTCAAGAAGATTTTTGATACTTTCTTTGCGGCTAACAAAATAAATAGGCGCTTTAGCTTTTAGTTTACTGATGTGATAAGGTGCCAAAACAATAATTTt                                                                                                                                                                                                                 >  1:486050/1‑145                                                    TTGTGAATTCTTATGGGGCAAGTGTTTACCATAAGTAATCTCAAGAAGATTTTTGATACTTTCTTTGCGGCTAACAAAATAAATAGGCGCTTTAGCTTTTAGTTTACTGATGTGATAAGGTGCCAAAACAATAATTTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAA                                                                                                                                                                     >  1:245338/1‑182                                                        GAATTCTTATGTGGCAAGTGTTTACCATAAGTAATCTCAAGAAGATTTTTGATACTTTCTTTGCGGCTAACAAAATAAATAGGCGCTTTAGCTTTTAGTTTACTGATGTGATAAGGTGCCAAAACAATAATTTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGA                                                                                                                                                                 <  2:245333/182‑1                                                                                                                         GCTAACAAAATAAATAGGCGCTTTAGCTTTTAGTTTACT‑ATGTGATAAGGTGCCAAAACAATAATTTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTACCACGGCAACATa  >  2:34368/1‑274                                                                                                                                                                                                                                                                                                                                                                                                              ATTTTTCAGAATCAGTTGCATAATTTTGAACTGATTATGTGAAAAACATAATTGTGAATTCTTATGGGGCAAGTGTTTACCATAAGTAATCTCAAGAAGATTTTTGATACTTTCTTTGCGGCTAACAAAATAAATAGGCGCTTTAGCTTTTAGTTTACTGATGTGATAAGGTGCCAAAACAATAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/3652115‑3651929 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATG  >  CP009273/4487998‑4488206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ 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.