Fig. 2
From: The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos
Strategy for robust distinction of trans-homolog from cis contacts. a Homolog misassignment can arise from sequencing errors, false SNVs, or sample heterogeneity (lines, Hi-C molecules; red, maternal fragment (M); blue, paternal fragment (P); stars, errors). b Contact frequency plotted against genome separation using ≥ 1 SNV per read. Arrows, change in contact frequency between short-range trans-homolog contacts and either long-range (>1 Mb) trans-homolog (orange) or trans-heterolog (black) contacts. Shaded area over the trans-homolog curve, enrichment of contact frequency due to homolog-misassigned “dangling ends” (shaded area over cis curve). c Contact frequency for inward only read pairs with at least two SNVs per read, with no sequence mismatches allowed (PHM = 0.01%). d Contact frequency for inward only read pairs with at least one SNV per read (PHM = 0.17%). e Fraction of homolog-misassigned cis contacts among trans-homolog pairs as a function of genomic separation. b–d Contact frequencies for chromosomes 2 and 3 normalized by cis contact frequency at 1 kb. Dashed black line, average trans-heterolog contact frequency; HM, homolog misassignment; PHm, probability of homolog misassignment
