Additional file 22: of Ascertainment bias from imputation methods evaluation in wheat

Additional file 1: Table S1. of Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure

Maria Kabisch (820179)
Ute Hamann (89879)
Justo Lorenzo Bermejo (117602)

October 2017

Dependence of imputation accuracy (mean imputation quality scores (IQS) with corresponding 95% confi...

MET_GBS_data_crfilt_.75_allchrom.hmp.txt

Spindel, Jennifer
Begum, Hasina
Akdemir, Deniz
Virk, Parminder
Collard, Bertrand
Redoña, Edilberto
Atlin, Gary
Jannink, Jean-Luc
McCouch, Susan R.

February 2015

Post-imputation GBS data for the IRRI breeding population used in Spindel et al., 2015 and Begum and...

Data for: Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study

Jacqueline A. May

April 2023

These data files are associated with the manuscript entitled: "Approaches for handling missing value...

Additional file 21: of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Wheat GBS bin map for 50 % coverage. Markers, chromosome and position (bins) are presented as column...

Additional file 18: of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Barley SNP marker score array. Genotypes are presented as rows and SNPs as columns. (txt 278 kb

Additional file 19: of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Barley SNP marker map. Markers, chromosome and position (cM) are presented as columns. (txt 18 kb

Additional file 3: Figure S3. of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Power (PO) and false positives rate (FPR) with 25 QTL, for major and minor QTL for ascertainment bia...

Additional file 5: Figure S5. of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Power (PO) and false positives rate (FPR) with 25 QTL and 25 % missing rate, for major and minor QTL...

Ascertainment bias from imputation methods evaluation in wheat

Brandariz, Sofía P.
González Reymúndez, Agustín
Lado, Bettina
Malosetti Zunin, Marcos
Garcia, Antonio Augusto Franco
Quincke, Martín
Zitzewitz, von, Jarislav
Castro, Marina
Matus, Iván
Pozo, del, Alejandro
Castro, Ariel J.
Gutiérrez, Lucía

January 2016

Background: Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used fo...

Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references.

Hadi Alipour
Guihua Bai
Guorong Zhang
Mohammad Reza Bihamta
Valiollah Mohammadi
Seyed Ali Peyghambari

January 2019

Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged as a popular tech...

Additional file 2 of Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

Filippo Biscarini (3167496)
Nelson Nazzicari (793690)
Marco Bink (3578189)
Pere ArĂşs (4069954)
Maria JosĂŠ Aranzana (4069957)
Ignazio Verde (171060)
Sabrina Micali (793678)
Thierry Pascal (793683)
Benedicte Quilot-Turion (4069951)
Patrick Lambert (347883)
Cassia da Silva Linge (4069960)
Igor Pacheco (529836)
Daniele Bassi (529840)
Alessandra Stella (28791)
Laura Rossini (529841)

June 2017

Imputation accuracy. Statistics on imputation accuracy of missing genotypes, per cross and injected ...

Exome sequence genotype imputation in globally diverse hexaploid wheat accessions

Shi, Fan
Tibbits, Josquin
Pasam, Raj K.
Kay, Pippa
Wong, Debbie
Petkowski, Joanna
Forrest, Kerrie L.
Hayes, Ben J.
Akhunova, Alina
Davies, John
Webb, Steven
Spangenberg, German C.
Akhunov, Eduard
Hayden, Matthew J.
Daetwyler, Hans D.

July 2017

Key message: Imputing genotypes from the 90K SNP chip to exome sequence in wheat was moderately accu...

Additional file 3: Figure S3. of Accuracy of genomic selection for alfalfa biomass yield in different reference populations

Paolo Annicchiarico (1778014)
Nelson Nazzicari (793690)
Xuehui Li (508048)
Yanling Wei (508050)
Luciano Pecetti (3555941)
E. Brummer (3555944)

December 2015

Prediction accuracy for different genotype missing data imputation methods, SNP calling strategies a...

Additional file 1 of The hazards of genotype imputation when mapping disease susceptibility variants

Winston Lau (46450)
Aminah Ali (17731755)
Hannah Maude (7426886)
Toby Andrew (211073)
Dallas M. Swallow (17731758)
Nikolas Maniatis (17731761)

January 2024

Additional file 1: Table S1. Detailed output from the imputation for the three different experiments...

Supplemental Material for Nyine et al., 2018

Moses Nyine (5922203)
Shichen Wang (2618536)
Kian Kiani (5926333)
Katherine Jordan (5926328)
Shuyu Liu (5926334)
Patrick Byrne (5926337)
Scott Haley (5926339)
Stephen Baenziger (5954019)
Shiaoman Chao (5926344)
Robert Bowden (5926346)
Eduard Akhunov (5926348)

November 2018

Figure S1 is the workflow for SNP imputation in wheat. File S1.txt contains SNP HapMap used in genom...

Additional file 1: Table S1. of Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure

Maria Kabisch (820179)
Ute Hamann (89879)
Justo Lorenzo Bermejo (117602)

October 2017

Dependence of imputation accuracy (mean imputation quality scores (IQS) with corresponding 95% confi...

MET_GBS_data_crfilt_.75_allchrom.hmp.txt

Spindel, Jennifer
Begum, Hasina
Akdemir, Deniz
Virk, Parminder
Collard, Bertrand
Redoña, Edilberto
Atlin, Gary
Jannink, Jean-Luc
McCouch, Susan R.

February 2015

Post-imputation GBS data for the IRRI breeding population used in Spindel et al., 2015 and Begum and...

Data for: Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study

Jacqueline A. May

April 2023

These data files are associated with the manuscript entitled: "Approaches for handling missing value...

Additional file 21: of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Wheat GBS bin map for 50 % coverage. Markers, chromosome and position (bins) are presented as column...

Additional file 18: of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Barley SNP marker score array. Genotypes are presented as rows and SNPs as columns. (txt 278 kb

Additional file 19: of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Barley SNP marker map. Markers, chromosome and position (cM) are presented as columns. (txt 18 kb

Additional file 3: Figure S3. of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Power (PO) and false positives rate (FPR) with 25 QTL, for major and minor QTL for ascertainment bia...

Additional file 5: Figure S5. of Ascertainment bias from imputation methods evaluation in wheat

Sofía Brandariz (3565481)
Agustín González Reymúndez (3565487)
Bettina Lado (3565478)
Marcos Malosetti (654850)
Antonio Garcia (3565490)
Martín Quincke (3565493)
Jarislav von Zitzewitz (3565499)
Marina Castro (3565484)
Iván Matus (3565472)
Alejandro del Pozo (3565475)
Ariel Castro (3565496)
Lucía Gutiérrez (413373)

October 2016

Power (PO) and false positives rate (FPR) with 25 QTL and 25 % missing rate, for major and minor QTL...

Ascertainment bias from imputation methods evaluation in wheat

Brandariz, Sofía P.
González Reymúndez, Agustín
Lado, Bettina
Malosetti Zunin, Marcos
Garcia, Antonio Augusto Franco
Quincke, Martín
Zitzewitz, von, Jarislav
Castro, Marina
Matus, Iván
Pozo, del, Alejandro
Castro, Ariel J.
Gutiérrez, Lucía

January 2016

Background: Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used fo...

Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references.

Hadi Alipour
Guihua Bai
Guorong Zhang
Mohammad Reza Bihamta
Valiollah Mohammadi
Seyed Ali Peyghambari

January 2019

Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged as a popular tech...

Additional file 2 of Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

Filippo Biscarini (3167496)
Nelson Nazzicari (793690)
Marco Bink (3578189)
Pere ArĂşs (4069954)
Maria JosĂŠ Aranzana (4069957)
Ignazio Verde (171060)
Sabrina Micali (793678)
Thierry Pascal (793683)
Benedicte Quilot-Turion (4069951)
Patrick Lambert (347883)
Cassia da Silva Linge (4069960)
Igor Pacheco (529836)
Daniele Bassi (529840)
Alessandra Stella (28791)
Laura Rossini (529841)

June 2017

Imputation accuracy. Statistics on imputation accuracy of missing genotypes, per cross and injected ...

Exome sequence genotype imputation in globally diverse hexaploid wheat accessions

Shi, Fan
Tibbits, Josquin
Pasam, Raj K.
Kay, Pippa
Wong, Debbie
Petkowski, Joanna
Forrest, Kerrie L.
Hayes, Ben J.
Akhunova, Alina
Davies, John
Webb, Steven
Spangenberg, German C.
Akhunov, Eduard
Hayden, Matthew J.
Daetwyler, Hans D.

July 2017

Key message: Imputing genotypes from the 90K SNP chip to exome sequence in wheat was moderately accu...

Additional file 3: Figure S3. of Accuracy of genomic selection for alfalfa biomass yield in different reference populations

Paolo Annicchiarico (1778014)
Nelson Nazzicari (793690)
Xuehui Li (508048)
Yanling Wei (508050)
Luciano Pecetti (3555941)
E. Brummer (3555944)

December 2015

Prediction accuracy for different genotype missing data imputation methods, SNP calling strategies a...

Additional file 1 of The hazards of genotype imputation when mapping disease susceptibility variants

Winston Lau (46450)
Aminah Ali (17731755)
Hannah Maude (7426886)
Toby Andrew (211073)
Dallas M. Swallow (17731758)
Nikolas Maniatis (17731761)

January 2024

Additional file 1: Table S1. Detailed output from the imputation for the three different experiments...

Supplemental Material for Nyine et al., 2018

Moses Nyine (5922203)
Shichen Wang (2618536)
Kian Kiani (5926333)
Katherine Jordan (5926328)
Shuyu Liu (5926334)
Patrick Byrne (5926337)
Scott Haley (5926339)
Stephen Baenziger (5954019)
Shiaoman Chao (5926344)
Robert Bowden (5926346)
Eduard Akhunov (5926348)

November 2018

Figure S1 is the workflow for SNP imputation in wheat. File S1.txt contains SNP HapMap used in genom...

Additional file 1: Table S1. of Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure

Maria Kabisch (820179)
Ute Hamann (89879)
Justo Lorenzo Bermejo (117602)

October 2017

Dependence of imputation accuracy (mean imputation quality scores (IQS) with corresponding 95% confi...

MET_GBS_data_crfilt_.75_allchrom.hmp.txt

Spindel, Jennifer
Begum, Hasina
Akdemir, Deniz
Virk, Parminder
Collard, Bertrand
Redoña, Edilberto
Atlin, Gary
Jannink, Jean-Luc
McCouch, Susan R.

February 2015

Post-imputation GBS data for the IRRI breeding population used in Spindel et al., 2015 and Begum and...

Data for: Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study

Jacqueline A. May

April 2023

These data files are associated with the manuscript entitled: "Approaches for handling missing value...

Additional file 22: of Ascertainment bias from imputation methods evaluation in wheat

Abstract

Extracted data

Additional file 22: of Ascertainment bias from imputation methods evaluation in wheat

Abstract

Extracted data

Related items

Related items