New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973115 =	16 (0.600)	15 (0.560)	15/276	NT	48.4%	intergenic (‑661/‑119)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 3577555	NA (NA)					intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E

AAGAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973254‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTC  <  CP009273/3577555‑3577412                                                                                                                                                                                                                                                                                               AAGAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGGGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGGCAAACAGGTAAATATTCGTCTGATCATTAGTAAAGATAAGGTAATGAC                                                                                                                                          >  1:391861/1‑149                  TCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACGCCCACTTATTAATAGT                                                                                                                         >  1:443004/1‑149                            TTCCTTATTCTGTGAACTTCAGGAGACAGTAAAGCTTTACTCCTAATGGAGAAGCGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                               >  1:257943/1‑149                                tgATTCTGTGAACTTCAGGTTACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTCCAGCTACGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGA                                                                                                           <  1:417477/147‑1                                        TGAACGTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTTTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                                                                                                   <  1:115987/149‑1                                             TTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGA                                                                                              >  2:182141/1‑149                                                       ATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATG                                                                                    >  2:154355/1‑149                                                                    TCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGAGTATTAGTAAAGATAAGGTAATGACTCCAACTTGTTGATAGTGTTTTATGTTCTGATAATGCCCGATGACTCTGCAATGAATGCTCCACgct                                                                       >  2:2836/1‑146                                                                            GAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCCTGCA‑GCTCCACCGGTTTTGGGAA                                                              >  1:190341/1‑149                                                                                    ACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGAGAACGACAGCG                                                      <  2:318840/149‑1                                                                                                             GTAAATATTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTGATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCGCCTATGTTGAGAACGACAGCGGCTTCCGGCCCAGCCGCGCCAGGTG                             >  2:256818/1‑149                                                                                                                    TTAGTCTGATTATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTC                      <  1:182141/149‑1                                                                                                                            ATTATTAGTAAAGATAAGGTAATGACTCCAACTTCTTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAG              <  1:59798/149‑1                                                                                                                              TATTAGTAAAGATAAGGTAATGACTCCAACTTTTTGATAGTGTTTTATGTTCGGTTAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGTGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGT            <  2:257943/149‑1                                                                                                                              TATTAGTAAAGATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCAATTTTGAGAACGCCAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGT            >  1:196583/1‑149                                                                                                                                        GATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATACCGCTC  >  2:344557/1‑149                                                                                                                                        GATAAGGTAATGACTCCAACTTATTGATAGTGTTTTATGCTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGCTTCAGGTTATACCGCTC  >  2:191724/1‑149                                                                                                                                                                                                                                                                                               AAGAATATTGCTATAGCTCATAACCTGTTCCTTATTCTGTGAACTTCAGGTGACATTAAAGCTTTACTCCTAATGGAGAAACGACGCAATCCCAACTCGGTCAAACAGGTAAATATTAGTCTGATTATTAGTAAAGATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1973254‑1973115 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCA‑GCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTC  <  CP009273/3577555‑3577412

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.