Predicted genome-wide chromatin contact differences among 71 bonobos and chimpanzees
Data files
Nov 01, 2023 version files 744.28 MB
Abstract
This file contains predicted chromatin contact differences in HFF cells using Akita among pairs of 71 bonobos and chimpanzees at 4,420 ~ 1 Mb genomic windows in the panTro6 genome. Each entry corresponds to a pairwise comparison at a given window. Data per comparison includes the individual IDs in the pairwise comparison, lineages represented, chromosome, position, window ID, mean squared error, Spearman correlation, divergence (1 - Spearman correlation), and the number of nucleotide differences for the pair at the given window.
README
This file contains descriptions of the column headers for "HFF_comparisons.txt".
- ind1 = individual 1 in comparison
- ind2 = individual 2 in comparison
- lineages = lineages represented in comparison (ppn = bonobo, pte = Nigeria-Cameroon chimpanzee, pts = eastern chimpanzee, ptt = central chimpanzee, ptv = western chimpanzee)
- chr = chromosome
- window_start = 0-based position in panTro6 coordinates
- window = window ID
- mse = mean squared error between contact maps for individual 1 and individual 2
- spearman = Spearman correlation between contact maps for individual 1 and individual 2
- divergence = 1 - Spearman correlation between contact maps for individual 1 and individual 2
- seq_diff = the number of nucleotide differences between individual 1 and individual 2 for the window
Methods
All data in this file were generated using publicly available datasets (see below). Variants were filtered using bcftools to retain high-quality sites and high-quality genotypes. The dataframe was created using Pandas in a Python Jupyter notebook.
Data used to generate these predictions:
- chimpanzee reference sequence (https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/)
- Illumina short reads for 71 bonobos and chimpanzees (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA189439, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB15086)