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update the describe to add pages and tables in detail
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AprilYUZhang committed Jan 29, 2025
1 parent dea86c6 commit b8c0d34
Showing 1 changed file with 3 additions and 7 deletions.
10 changes: 3 additions & 7 deletions stdpopsim/catalog/SusScr/species.py
Original file line number Diff line number Diff line change
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)
# This is the per-chromosome recombination rate, typically the mean
# rate along the chromosome.
# Values in this dictionary are set to -1 by default, so you have
# to update each one. These should be derived from the most reliable
# data and how they were obtained should be documented here.
# The appropriate citation must be added to the list of
# recombination_rate_citations in the Genome object.
# X recombination rate is mean of autosomes because it is not in paper.
# The data sourced from Johnsson et al., Additional file 4: Table S3
_recombination_rate = {
"1": 5.335247608983185e-09,
"2": 8.6057260999254e-09,
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"MT": 0,
}

# the de novo mutation rate is inferred by Zhang et al 2022,
# which was used for the PSMC demographic inference
# the de novo mutation rate is inferred by Zhang et al., p. 1040 Genomics Proteomics Bioinformatics,
# which was used for the PSMC demographic inference
_overall_rate = 3.6e-9
_mutation_rate = {
"1": _overall_rate,
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