New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 2684222	NA (NA)	4 (0.340) +AGCACACTTTGCCAACAATCTAAATCTGTT	4/188	1.1	NA	intergenic (+166/+32)	yphH/glyA	putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
	?	NC_000913_3_pae_tpiA	= 3676286	NA (NA)					intergenic (+178/+4)	yhjE/yhjG	putative MFS transporter; membrane protein/putative inner membrane‑anchored periplasmic AsmA family protein

AAGGCGTTCACGCCGCATCCGGCATGAACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/2684192‑2684222 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAATTGCCGGATGTCTGACATCCGGCAATTAAACAGATTTAGATTGTTGGCAAAGTGTGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAATCCTTGCGAATTCA  <  NC_000913_3_pae_tpiA/3676286‑3676167                                ||||||||||||||||||||||||||||||                                                                                                                         AAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCTGACATCCGGCAATTAAACAGATT                                                                                   <  1:12470/100‑1 AAGGCGTTCACGCCGCATCCGGCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCTGACATCCGGCAATTAAACAGATT                                                                                   >  2:12470/1‑100                      GCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCTGACATCCGGCAATTAAACA                                                                                       >  1:5691/1‑75                      GCATGAACAAAGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCTGACATCCGGCAATTAAACA                                                                                       <  2:5691/75‑1                                AGCACACTTTGCCAACAATCTAAATCTGTTTAATTGCCGGATGTCTGACATCCGGCAATTAAACAGATTTAGATTGTTGGCAAAGTGTGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAATCCTTTCGAATTCA  >  4:52694/1‑150                                ||||||||||||||||||||||||||||||                                                                                                                         AAGGCGTTCACGCCGCATCCGGCATGAACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_tpiA/2684192‑2684222 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAATTGCCGGATGTCTGACATCCGGCAATTAAACAGATTTAGATTGTTGGCAAAGTGTGCTTTGTTCATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAATCCTTGCGAATTCA  <  NC_000913_3_pae_tpiA/3676286‑3676167

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