New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1423471 =	39 (0.450)	10 (0.120)	6/168	NT	18.1%	pseudogene (271/444 nt)	rzpR	pseudogene, Rac prophage; Bacteriophage Rz lysis protein family;Phage or Prophage Related; putative Rac prophage endopeptidase; completely contained in another CDS
	?	NC_000913	1423543 =	54 (0.660)					pseudogene (343/444 nt)	rzpR	pseudogene, Rac prophage; Bacteriophage Rz lysis protein family;Phage or Prophage Related; putative Rac prophage endopeptidase; completely contained in another CDS

CCCGGAGGGTGAAATAATCCCGTTCAGCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1423573‑1423471 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagacACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAGGTGCTCAGCAATACATAACCGAGCAGTGTTTAAA  >  NC_000913/1423543‑1423640                                                                                                                                                                                                           CCCGGAGGGTGAAATAATCCCGTTCAGCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACA                                                                                                       <  2:758663/100‑1  CCGGAGGGTGAAATAATCCCGTTCAGCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAG                                                                                                      >  2:777020/1‑100   CGGAGGGTGAAATAATCCCGTTCAGCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGA                                                                                                     <  2:154080/100‑1    GGAGGGTGAAATAATCCCGTTCAGCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGAC                                                                                                    <  2:1025330/100‑1    GGAGGGTGAAATAATCCCGTTCAGCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGAC                                                                                                    <  1:582484/100‑1                           GCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCAC                                                                             >  1:171518/1‑100                           GCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCCGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCAC                                                                             >  2:1503628/1‑100                            CGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCCGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACC                                                                            >  2:1102115/1‑100                             GGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACCC                                                                           >  1:1854941/1‑100                             GGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACCC                                                                           >  1:1594210/1‑100                             GGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACC                                                                            >  1:1101631/1‑99                                GTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACCCTCC                                                                        >  2:1717204/1‑100                                  CTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACCCTCCGG                                                                      >  1:360915/1‑100                                   TGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACCCTCCGGG                                                                     >  2:2139549/1‑100                                           GGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTG                                                             >  1:149654/1‑100                                                                                                   CAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAGGTGCTCAGCAATACATAACCGAGCAGTGTTT     >  1:1954566/1‑100                                                                                                   CAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAGGTGCTCAGCAATACATAACCGAGCAGTGTTT     >  1:643039/1‑100                                                                                                      ACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAGGTGCTCAGCAATACATAACCGAGCAGTGTTTAAA  <  2:2097166/100‑1                                                                                                                                                                                                           CCCGGAGGGTGAAATAATCCCGTTCAGCGGTGTCTGCCAGTCGGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGGTGGCTTCACGCACTGACTGACAGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1423573‑1423471 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagacACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAGGTGCTCAGCAATACATAACCGAGCAGTGTTTAAA  >  NC_000913/1423543‑1423640

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.