New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4322620 =	32 (0.890)	5 (0.140)	5/276	4.3	12.8%	pseudogene (111/372 nt)	phnE	defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily
	?	NC_000913_3_pae_tpiA	4322653 =	37 (1.050)					pseudogene (78/372 nt)	phnE	defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTGAGCCCGGCCCGGTGGAAGGCATTCGCGCCACCGGTGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/4322660‑4322620 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gccGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAATGG  >  NC_000913_3_pae_tpiA/4322653‑4322800                                                                                                                                                                                               TTGAGCCCGGCCCGGTGGAAGGCATTCGCGCCACCGGTGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACG                                          >  1:36291/1‑149       CCGGCCCGGTGGAAGGCATTCGCGCCACCGGTGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACC                                    >  1:235456/1‑149         GGCCCGGTGGAAGGCATTCGCGCCACCGGTGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCAGGACCGCACGCCACCGAACGGACCGAGGCTGACGGCGACCcc                                  >  1:175930/1‑147          GCCCGGTGGAAGGCATTCGCGCCACCGGTGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCC                                                                                >  1:360198/1‑102          GCCCGGTGGAAGGCATTCGCGCCACCGGTGCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCC                                                                                <  2:360198/102‑1                                       GCCGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAAT    <  2:417999/149‑1                                         CGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAATGG  >  1:409553/1‑149                                                                                                                                                                                               TTGAGCCCGGCCCGGTGGAAGGCATTCGCGCCACCGGTGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/4322660‑4322620 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gccGGGCTCAATCGCTTCCACCGCTTCGGAAAGCAGCTTGGAGAGCACGCCGGTGGTGTGGATAAACAGCGCCAGCACGCCAGCACGCCAGCGAACGGGCCGAGGCCGACGGCGACCACGAACAGCATGGCGAAGACCATTTCGTTAATGG  >  NC_000913_3_pae_tpiA/4322653‑4322800

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.