Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add per-chromosome mutation rates to C. reinhardtii and update refs #950

Merged
merged 1 commit into from
May 31, 2021
Merged

Add per-chromosome mutation rates to C. reinhardtii and update refs #950

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
48 changes: 23 additions & 25 deletions stdpopsim/catalog/ChlRei/species.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,13 @@

from . import genome_data

# IMPORTANT: these are recombination rate values with the rate of sex
# IMPORTANT: These are recombination rate values with the rate of sex
# incorporated - e.g. they are lower than the physical recombination rates on account
# of being the 'realized' recombination rates in nature, since C. reinhardtii only
# undergoes sex/recombination once every ~840 generations (Hasan and Ness 2020).
# when simulating natural populations with these values, the infrequency
# of sex should be implicitly taken into account. otherwise, to get estimates
# of physical rates, divide all values by 0.001194. see Discussion of Hasan
# When simulating natural populations with these values, the infrequency
# of sex should be implicitly taken into account. Otherwise, to get estimates
# of physical rates, divide all values by 0.001194. See Discussion of Hasan
# and Ness 2020 for more details
_recombination_rate = {
"1": 1.21e-10,
Expand All @@ -30,26 +30,24 @@
"17": 1.83e-10,
}

_overall_rate = 9.63 * 1e-10 # SNM rate
# there is also an indel mutation rate in Ness 2015 if that is eventually supported
_mutation_rate = {
"1": _overall_rate,
"2": _overall_rate,
"3": _overall_rate,
"4": _overall_rate,
"5": _overall_rate,
"6": _overall_rate,
"7": _overall_rate,
"8": _overall_rate,
"9": _overall_rate,
"10": _overall_rate,
"11": _overall_rate,
"12": _overall_rate,
"13": _overall_rate,
"14": _overall_rate,
"15": _overall_rate,
"16": _overall_rate,
"17": _overall_rate,
"1": 9.74e-10,
"2": 8.62e-10,
"3": 9.5e-10,
"4": 9.66e-10,
"5": 1.17e-9,
"6": 9.12e-10,
"7": 9.14e-10,
"8": 8.98e-10,
"9": 9.17e-10,
"10": 9.27e-10,
"11": 1.03e-9,
"12": 9.55e-10,
"13": 7.56e-10,
"14": 8.96e-10,
"15": 6.91e-10,
"16": 9.59e-10,
"17": 1.05e-9,
}

_genome = stdpopsim.Genome.from_data(
Expand All @@ -66,13 +64,13 @@
stdpopsim.Citation(
author="Hasan and Ness",
year=2020,
doi="https://doi.org/10.1093/gbe/evaa057",
doi="https://doi.org/10.6084/m9.figshare.14608239.v1",
reasons={stdpopsim.CiteReason.REC_RATE},
),
stdpopsim.Citation(
author="Ness et al",
year=2015,
doi="https://doi.org/10.1101/gr.191494.115",
doi="https://doi.org/10.6084/m9.figshare.14700156.v1",
reasons={stdpopsim.CiteReason.MUT_RATE},
),
],
Expand Down