New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	3949028 =	58 (1.510)	14 (0.380)	7/298	NT	24.1%	coding (338/1545 nt)	ilvA	L‑threonine dehydratase, biosynthetic; also known as threonine deaminase
	?	CP009273	3949257 =	33 (0.900)					coding (567/1545 nt)	ilvA	L‑threonine dehydratase, biosynthetic; also known as threonine deaminase

CCGACTGGCACAAATACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/3949253‑3949028 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtcggcggCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATGAAGGATTTATTC  >  CP009273/3949257‑3949524                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                acagCTGGCACAAATACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCCGCGCCAGCGTGCCTTGCCCGGCAATCACCNTAGGATGGNCGAACGTCGGCATCCAGGTGAACCCCTGCTGCTGTGACAGTTCGAGCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGTGGCGGTCTGGCTTCTGGCGTGGCGGTGCTGATAAAACAACTGATGCC                                                                                                                                                                                                                              <  1:477393/270‑1              ATACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAAACAAAATGA                                                                                                                                                                                                                >  1:321096/1‑275               TACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGCCTTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGg                                                                                                                                                                                                                  >  1:30562/1‑271               TACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGT                                                                                                                                                                                                                  >  1:254182/1‑272                ACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATC                                                                                                                                                                                                              >  1:342695/1‑275                ACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTAGACTTTGATGTCGGCGGCGGCGGTCGGGCTGCTGGCGTGGCGGGGCTGGTCAAACAACTGATGACGAAAATAAAAATGATa                                                                                                                                                                                                              >  1:422793/1‑274                ACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGATCGCGCCGTGNAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGCGGCGGTCTGGCGGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGGGAaa                                                                                                                                                                                                              >  1:660656/1‑273                ACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCACGTGAACCCCTGCTGCTCTGCCAGTTCCATCGCTTTGGCTTTCGCTTCATCCAAGTCCCCGCCGTGTAGCAGCCCTCCGCCGCCGCAGCCGCGCCCCGCGTCG‑CCTTGCTGTCGGCGTCGGCGGTCTGGCTGCTGGCGTCGCGGTGCGGCGCAGACAACCGCTGCCGCAAGTCAAAGgtaag                                                                                                                                                                                                              >  2:115953/1‑269                                                                          aaaaacaaagCGGGTGGTCGCACGGGGGAAGCGAGGGGAACCCCGGCTGCTGTGACAGTTCGGTCGCTTTGGCTGTCGCGTCATCAAAGGTCGCGCCGTGGAGCAGCACGTCGCCGCCGAAGCCGCGCACCGCGTCGACGTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCC                                                                                                                                                      <  2:342689/263‑1                                                                                                                                      CGATCGCTTTGGCTTTCGCTTCATCAAATTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGG                                                                                                                                                                                                                                                                                 >  1:563259/1‑90                                                                                                                                                                                              CCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGTGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGT                                                                                                                                                                                                                  >  2:585331/1‑97                                                                                                                                                                                              CCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGAAAGCGAT                                >  1:583787/1‑275                                                                                                                                                                                              CCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGT                                                                                                                                                                                                                  >  2:542142/1‑97                                                                                                                                                                                                  AGCCGCGCACCGCGTCGACTTTGATGTCGGCGGTGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATC                                                                                                                                                                                                              <  1:585340/97‑1                                                                                                                                                                                                  AGCCGCGCACCGCGTCGACTTTGATGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATC                                                                                                                                                                                                              <  1:542151/97‑1                                                                                                                                                                                                                           GTCGGCCGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAA                                                                                     >  2:426639/1‑193                                                                                                                                                                                                                            TCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGACGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCTCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACCTCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATGAAGGATTTATTC  <  1:165151/275‑1                                                                                                                                                                                                                            TCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCGGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGT                                                                                                               <  2:684823/166‑1                                                                                                                                                                                                                               GCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTT                                                                                 <  1:426646/193‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                CCGACTGGCACAAATACGCGGTCGAGATGGGCGTCCTGCTGGAGCAGTTCCAGCGCCAGCGTGCCTTGCCCGGCAATCACCATCGGATGGTCGAACGGCGGCACCCAGGTGAACCCCTGCTGCTGTGACAGTTCGATCGCTTTGGCTTTCGCTTCATCAAAGTTCGCGCCGTGGAGCAGCACTTCGCCGCCGAAGCCGCGCACCGCGTCGACTTTGATGTCGGCGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/3949253‑3949028 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtcggcggCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATGAAGGATTTATTC  >  CP009273/3949257‑3949524

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ 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.