New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 3943624	NA (NA)	5 (0.300)	5/258	1.5	56.9%	intergenic (+114/‑80)	gltU/rrlC	tRNA‑Glu/23S ribosomal RNA of rrnC operon
	?	NC_000913_3_pae_pgi	= 4037457	4 (0.230)					intergenic (+122/‑62)	alaT/rrlA	tRNA‑Ala/23S ribosomal RNA of rrnA operon

TCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGG  >  NC_000913_3_pae_pgi/4037314‑4037604                                                                                                                                                |                                                                                                                                                    tCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACCGAACAACTTTCGTTGTTCagtgtt                                                                                                                                               >  3:78236‑M2/1‑144 (MQ=255)                                        taaaAAATACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACga                                                                                                                         <  3:13973/133‑1 (MQ=33)                                        taaaAAATACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACga                                                                                                                         >  4:13973/1‑133 (MQ=32)                                                               tGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAg                                                                                       <  3:59118/144‑1 (MQ=39)                                                               tGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAg                                                                                       >  4:59118/1‑144 (MQ=39)                                                                                              aaaaaTCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCagtgtttcaattttcagcttgatccagatttttaaagagcaaatatctcaaacatcacccgaagatgagttttgagatatt                                                                    >  3:42509‑M2/1‑51 (MQ=255)                                                                                              aaaaaTCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCagtgtttcaattttcagcttgatccagatttttaaagagcaaatatctcaaacatcacccgaagatgagttttgagatatt                                                                    <  4:42509‑M2/132‑82 (MQ=255)                                                                                                                             cTGAACAACGAAAGTTGTTCagtgtttcaattttcagcttgatccagatttt                                                                                                                     >  1:45616‑M2/1‑20 (MQ=255)                                                                                                                             cTGAACAACGAAAGTTGTTCagtgtttcaattttcagcttgatccagatttt                                                                                                                     <  2:45616‑M2/52‑33 (MQ=255)                                                                                                                                          gttgttCagtgtttcaattttcagcttgatccagatttttaaagagcaaatatctcaaacatcacccgaagatgagttttgagatattaaggcaggtgactttcactcacaaaccagcaagtggcgtcccctaggggattcgaacccctg      >  3:41066‑M2/1‑7 (MQ=255)                                                                                                                                              ttCagtgtttcaattttcagcttgatccagatttttaaagagcaaatatctcaaacatcacccgaagatgagttttgagatattaaggcaggtgactttcactcacaaaccagcaagtggcgtcccctaggggttcgaatcccctagggg  >  1:10360‑M2/1‑3 (MQ=255)                                                                                                                                                |                                                                                                                                                    TCGATCCCGCATAGCTCCACCATCTCTGTAGTGATTAAATAAAAAATACTTCAGAGTGTACCTGCAAAGGTTCACTGCGAAGTTTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGG  >  NC_000913_3_pae_pgi/4037314‑4037604

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