Table 2 Genomic features investigated in the present study
From: A genome-wide view of mutation rate co-variation using multivariate analyses
Feature | Measurement (per Mb) | Source |
|---|---|---|
GC content | Percentage of G and C bases | 'GC Percent' track from the UCSC Genome Browser |
CpG islands | Count | 'CpG island' track from the UCSC Genome Browser |
Non-CG methyl-cytosines | Count | [16] |
LINE | Count | 'RepeatMasker' track from the UCSC Genome Browser |
SINE | Count | 'RepeatMasker' track from the UCSC Genome Browser |
Nuclear lamina | Number of LaminB1 interaction sites with positive intensity | 'NKI LaminB1' track from the UCSC Genome Browser |
Telomere | Distance in bp | 'Gap' track from the UCSC Genome Browser |
Female recombination rate (1 Mb) | Centimorgan (cM) | 'Recomb rate' track from the UCSC Genome Browser |
Male recombination rate (1 Mb) | Centimorgan (cM) | 'Recomb rate' track from the UCSC Genome Browser |
Recombination rate (0.5 Mb and 0.1 Mb) | Centimorgan (cM) | [82] |
SNP | Count | 'SNPs 129' track from the UCSC Genome Browser |
Replication timing | Time through S-phase | [33] |
Nucleosome-free regions | Coverage | [17] |
Coding exons | Coverage | 'UCSC Genes' track from the UCSC Genome Browser |
Conserved elements | Coverage | '28-way most conserved' track from the UCSC Genome Browser |