TPR vs FDR curves for deletion and duplication predictions of CONGA.

Here, we use Mota, Saqqaq and Yamnaya genomes down-sampled to various depths from their original coverages of 9.6×, 13.1× and 23.3×, respectively. The numbers inside boxes show the down-sampled coverage values. We calculated TPR and FDR for down-sampled genomes assuming that our CONGA-based predicti...

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Main Authors:	Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)
Format:	Still Image
Language:	unknown
Published:	2022
Subjects:	Genetics Evolutionary Biology Ecology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified systematic cnv analyses single nucleotide polymorphisms sampling experiments suggest nine different laboratories copy number variants technical challenges posed ancient genome analyses conga thus paves ascertained deletions across technical factors genotyped deletions genotype deletions ancient shotgun ancient genomes xlink "> used conga snps ) sequenced genomes read length present conga population origin major contributor largely confined homozygous states highly correlated heterogenous set genotype 10 evolutionary adaptation effectively applied coverages ranging 121 bps 1 kbps 002 outgroup 000 years &# 8805 Saqqaq
Online Access:	https://doi.org/10.1371/journal.pcbi.1010788.g004

id	ftunivfreestate:oai:figshare.com:article/21727837
record_format	openpolar
spelling	ftunivfreestate:oai:figshare.com:article/21727837 2023-05-15T18:15:05+02:00 TPR vs FDR curves for deletion and duplication predictions of CONGA. Arda Söylev (14259721) Sevim Seda Çokoglu (14259724) Dilek Koptekin (4591300) Can Alkan (9984) Mehmet Somel (133767) 2022-12-14T18:43:06Z https://doi.org/10.1371/journal.pcbi.1010788.g004 unknown https://figshare.com/articles/figure/TPR_vs_FDR_curves_for_deletion_and_duplication_predictions_of_CONGA_/21727837 doi:10.1371/journal.pcbi.1010788.g004 CC BY 4.0 CC-BY Genetics Evolutionary Biology Ecology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified systematic cnv analyses single nucleotide polymorphisms sampling experiments suggest nine different laboratories copy number variants technical challenges posed ancient genome analyses conga thus paves ascertained deletions across technical factors genotyped deletions genotype deletions ancient shotgun ancient genomes xlink "> used conga snps ) sequenced genomes read length present conga population origin major contributor largely confined homozygous states highly correlated heterogenous set genotype 10 evolutionary adaptation effectively applied coverages ranging 121 bps 1 kbps 002 outgroup 000 years &# 8805 Image Figure 2022 ftunivfreestate https://doi.org/10.1371/journal.pcbi.1010788.g004 2022-12-16T00:20:09Z Here, we use Mota, Saqqaq and Yamnaya genomes down-sampled to various depths from their original coverages of 9.6×, 13.1× and 23.3×, respectively. The numbers inside boxes show the down-sampled coverage values. We calculated TPR and FDR for down-sampled genomes assuming that our CONGA-based predictions with the original genomes (full data) reflect the ground truth. These predictions, in turn, were made using modern-day CNVs as candidate CNV list. The purpose of the experiment was to evaluate accuracy at lower coverage relative to the full data, as well as to compare performance across different real genomes ( Methods ). Still Image Saqqaq KovsieScholar Repository (University of the Free State - UFS UV)
institution	Open Polar
collection	KovsieScholar Repository (University of the Free State - UFS UV)
op_collection_id	ftunivfreestate
language	unknown
topic	Genetics Evolutionary Biology Ecology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified systematic cnv analyses single nucleotide polymorphisms sampling experiments suggest nine different laboratories copy number variants technical challenges posed ancient genome analyses conga thus paves ascertained deletions across technical factors genotyped deletions genotype deletions ancient shotgun ancient genomes xlink "> used conga snps ) sequenced genomes read length present conga population origin major contributor largely confined homozygous states highly correlated heterogenous set genotype 10 evolutionary adaptation effectively applied coverages ranging 121 bps 1 kbps 002 outgroup 000 years &# 8805
spellingShingle	Genetics Evolutionary Biology Ecology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified systematic cnv analyses single nucleotide polymorphisms sampling experiments suggest nine different laboratories copy number variants technical challenges posed ancient genome analyses conga thus paves ascertained deletions across technical factors genotyped deletions genotype deletions ancient shotgun ancient genomes xlink "> used conga snps ) sequenced genomes read length present conga population origin major contributor largely confined homozygous states highly correlated heterogenous set genotype 10 evolutionary adaptation effectively applied coverages ranging 121 bps 1 kbps 002 outgroup 000 years &# 8805 Arda Söylev (14259721) Sevim Seda Çokoglu (14259724) Dilek Koptekin (4591300) Can Alkan (9984) Mehmet Somel (133767) TPR vs FDR curves for deletion and duplication predictions of CONGA.
topic_facet	Genetics Evolutionary Biology Ecology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified systematic cnv analyses single nucleotide polymorphisms sampling experiments suggest nine different laboratories copy number variants technical challenges posed ancient genome analyses conga thus paves ascertained deletions across technical factors genotyped deletions genotype deletions ancient shotgun ancient genomes xlink "> used conga snps ) sequenced genomes read length present conga population origin major contributor largely confined homozygous states highly correlated heterogenous set genotype 10 evolutionary adaptation effectively applied coverages ranging 121 bps 1 kbps 002 outgroup 000 years &# 8805
description	Here, we use Mota, Saqqaq and Yamnaya genomes down-sampled to various depths from their original coverages of 9.6×, 13.1× and 23.3×, respectively. The numbers inside boxes show the down-sampled coverage values. We calculated TPR and FDR for down-sampled genomes assuming that our CONGA-based predictions with the original genomes (full data) reflect the ground truth. These predictions, in turn, were made using modern-day CNVs as candidate CNV list. The purpose of the experiment was to evaluate accuracy at lower coverage relative to the full data, as well as to compare performance across different real genomes ( Methods ).
format	Still Image
author	Arda Söylev (14259721) Sevim Seda Çokoglu (14259724) Dilek Koptekin (4591300) Can Alkan (9984) Mehmet Somel (133767)
author_facet	Arda Söylev (14259721) Sevim Seda Çokoglu (14259724) Dilek Koptekin (4591300) Can Alkan (9984) Mehmet Somel (133767)
author_sort	Arda Söylev (14259721)
title	TPR vs FDR curves for deletion and duplication predictions of CONGA.
title_short	TPR vs FDR curves for deletion and duplication predictions of CONGA.
title_full	TPR vs FDR curves for deletion and duplication predictions of CONGA.
title_fullStr	TPR vs FDR curves for deletion and duplication predictions of CONGA.
title_full_unstemmed	TPR vs FDR curves for deletion and duplication predictions of CONGA.
title_sort	tpr vs fdr curves for deletion and duplication predictions of conga.
publishDate	2022
url	https://doi.org/10.1371/journal.pcbi.1010788.g004
genre	Saqqaq
genre_facet	Saqqaq
op_relation	https://figshare.com/articles/figure/TPR_vs_FDR_curves_for_deletion_and_duplication_predictions_of_CONGA_/21727837 doi:10.1371/journal.pcbi.1010788.g004
op_rights	CC BY 4.0
op_rightsnorm	CC-BY
op_doi	https://doi.org/10.1371/journal.pcbi.1010788.g004
_version_	1766188132910235648

TPR vs FDR curves for deletion and duplication predictions of CONGA.

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