Title: Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci
Authors: last_name: Lilue
first_name: Jingtao
name: Jingtao Lilue
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
notes: Joint first authors
last_name: Doran
first_name: Anthony G.
name: Anthony G. Doran
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
notes: Joint first authors
last_name: Fiddes
first_name: Ian T.
name: Ian T. Fiddes
affiliations: label: 3
institution: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz
country: USA
name: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz , CA 95064, USA
notes: Joint first authors
last_name: Abrudan
first_name: Monica
name: Monica Abrudan
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Armstrong
first_name: Joel
name: Joel Armstrong
affiliations: label: 3
institution: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz
country: USA
name: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz , CA 95064, USA
last_name: Bennett
first_name: Ruth
name: Ruth Bennett
affiliations: label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
last_name: Chow
first_name: William
name: William Chow
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Collins
first_name: Joanna
name: Joanna Collins
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Collins
first_name: Stephan
name: Stephan Collins
affiliations: label: 4
institution: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg
country: France
name: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg , 67404 Illkirch , France
label: 5
institution: Centre des Sciences du Goût et de l’Alimentation, University of Bourgogne Franche-Comté
country: France
name: Centre des Sciences du Goût et de l’Alimentation, University of Bourgogne Franche-Comté , 21000 Dijon , France
last_name: Czechanski
first_name: Anne
name: Anne Czechanski
affiliations: label: 6
institution: The Jackson Laboratory
country: USA
name: The Jackson Laboratory , 600 Main Street, Bar Harbor, ME 04609, USA
last_name: Danecek
first_name: Petr
name: Petr Danecek
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Diekhans
first_name: Mark
name: Mark Diekhans
affiliations: label: 3
institution: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz
country: USA
name: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz , CA 95064, USA
last_name: Dolle
first_name: Dirk-Dominic
name: Dirk-Dominic Dolle
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Dunn
first_name: Matt
name: Matt Dunn
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Durbin
first_name: Richard
name: Richard Durbin
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Earl
first_name: Dent
name: Dent Earl
affiliations: label: 3
institution: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz
country: USA
name: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz , CA 95064, USA
last_name: Ferguson-Smith
first_name: Anne
name: Anne Ferguson-Smith
affiliations: label: 7
institution: Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH
country: UK
name: Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH , UK
last_name: Flicek
first_name: Paul
name: Paul Flicek
affiliations: label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
last_name: Flint
first_name: Jonathan
name: Jonathan Flint
affiliations: label: 8
institution: Brain Research Institute, University of California, 695 Charles E Young Dr S, Los Angeles
country: USA
name: Brain Research Institute, University of California, 695 Charles E Young Dr S, Los Angeles , CA 90095, USA
last_name: Frankish
first_name: Adam
name: Adam Frankish
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
last_name: Fu
first_name: Beiyuan
name: Beiyuan Fu
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Gerstein
first_name: Mark
name: Mark Gerstein
affiliations: label: 9
institution: Yale Computational Biology and Bioinformatics, Yale University
country: USA
name: Yale Computational Biology and Bioinformatics, Yale University , New Haven , CT 06520, USA
last_name: Gilbert
first_name: James
name: James Gilbert
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Goodstadt
first_name: Leo
name: Leo Goodstadt
affiliations: label: 10
institution: The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN
country: UK
name: 10 The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN , UK
last_name: Harrow
first_name: Jennifer
name: Jennifer Harrow
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Howe
first_name: Kerstin
name: Kerstin Howe
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Kolmogorov
first_name: Mikhail
name: Mikhail Kolmogorov
affiliations: label: 11
institution: Department of Computer Science and Engineering, University of California
country: USA
name: 11 Department of Computer Science and Engineering, University of California , 9500 Gilman Drive La Jolla, San Diego, CA 92093 USA
last_name: Köenig
first_name: Stefanie
name: Stefanie Köenig
affiliations: label: 12
institution: Institute of Mathematics and Computer Science, University of Greifswald
country: Germany
name: 12 Institute of Mathematics and Computer Science, University of Greifswald , Domstraβe 11, 17489 Greifswald , Germany
last_name: Lelliott
first_name: Chris
name: Chris Lelliott
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Loveland
first_name: Jane
name: Jane Loveland
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
last_name: Mathews
first_name: Clayton E.
name: Clayton E. Mathews
affiliations: label: 13
institution: Department of Pathology, Immunology, and Laboratory Medicine, University of Florida
country: USA
name: 13 Department of Pathology, Immunology, and Laboratory Medicine, University of Florida , Gainesville, FL , USA
last_name: Mott
first_name: Richard
name: Richard Mott
affiliations: label: 14
institution: Genetics Institute, University College London, Gower Street
country: UK
name: 14 Genetics Institute, University College London, Gower Street , London WC1E 6BT , UK
last_name: Muir
first_name: Paul
name: Paul Muir
affiliations: label: 9
institution: Yale Computational Biology and Bioinformatics, Yale University
country: USA
name: Yale Computational Biology and Bioinformatics, Yale University , New Haven , CT 06520, USA
last_name: Navarro
first_name: Fabio
name: Fabio Navarro
affiliations: label: 9
institution: Yale Computational Biology and Bioinformatics, Yale University
country: USA
name: Yale Computational Biology and Bioinformatics, Yale University , New Haven , CT 06520, USA
last_name: Odom
first_name: Duncan
name: Duncan Odom
affiliations: label: 15
institution: Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way
country: UK
name: 15 Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way , Cambridge , CB2 0RE, UK
last_name: Park
first_name: Naomi
name: Naomi Park
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Pelan
first_name: Sarah
name: Sarah Pelan
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Phan
first_name: Son K
name: Son K Phan
affiliations: label: 16
institution: LOG-G Department, Salk Institute for Biological Studies
country: USA
name: 16 LOG-G Department, Salk Institute for Biological Studies , 10010 North Torrey Pines Rd, San Diego, CA 92037, USA .
last_name: Quail
first_name: Michael
name: Michael Quail
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Reinholdt
first_name: Laura
name: Laura Reinholdt
affiliations: label: 6
institution: The Jackson Laboratory
country: USA
name: The Jackson Laboratory , 600 Main Street, Bar Harbor, ME 04609, USA
last_name: Romoth
first_name: Lars
name: Lars Romoth
affiliations: label: 12
institution: Institute of Mathematics and Computer Science, University of Greifswald
country: Germany
name: 12 Institute of Mathematics and Computer Science, University of Greifswald , Domstraβe 11, 17489 Greifswald , Germany
last_name: Shirley
first_name: Lesley
name: Lesley Shirley
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Sisu
first_name: Cristina
name: Cristina Sisu
affiliations: label: 9
institution: Yale Computational Biology and Bioinformatics, Yale University
country: USA
name: Yale Computational Biology and Bioinformatics, Yale University , New Haven , CT 06520, USA
last_name: Sjoberg-Herrera
first_name: Marcela
name: Marcela Sjoberg-Herrera
affiliations: label: 17
institution: Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile
country: Chile
name: 17 Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile
last_name: Stanke
first_name: Mario
name: Mario Stanke
affiliations: label: 12
institution: Institute of Mathematics and Computer Science, University of Greifswald
country: Germany
name: 12 Institute of Mathematics and Computer Science, University of Greifswald , Domstraβe 11, 17489 Greifswald , Germany
last_name: Steward
first_name: Charles
name: Charles Steward
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Thomas
first_name: Mark
name: Mark Thomas
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Threadgold
first_name: Glen
name: Glen Threadgold
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Thybert
first_name: David
name: David Thybert
affiliations: label: 18
institution: Earlham Institute, Norwich Research Park
country: UK
name: 18 Earlham Institute, Norwich Research Park , Norwich NR4 7UZ, UK
last_name: Torrance
first_name: James
name: James Torrance
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Wong
first_name: Kim
name: Kim Wong
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Wood
first_name: Jonathan
name: Jonathan Wood
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Yalcin
first_name: Binnaz
name: Binnaz Yalcin
affiliations: label: 4
institution: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg
country: France
name: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg , 67404 Illkirch , France
last_name: Yang
first_name: Fengtang
name: Fengtang Yang
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Adams
first_name: David J.
name: David J. Adams
corresponding: yes
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
last_name: Paten
first_name: Benedict
name: Benedict Paten
corresponding: yes
affiliations: label: 3
institution: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz
country: USA
name: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz , CA 95064, USA
last_name: Keane
first_name: Thomas M.
name: Thomas M. Keane
corresponding: yes
affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
Affiliations: label: 1
institution: Wellcome Trust Sanger Institute, Wellcome Genome Campus
country: UK
name: Wellcome Trust Sanger Institute, Wellcome Genome Campus , Hinxton , CB10 1SA, UK
label: 2
institution: European Bioinformatics Institute, Wellcome Genome Campus
country: UK
name: European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, UK
label: 3
institution: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz
country: USA
name: Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz , CA 95064, USA
label: 4
institution: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg
country: France
name: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg , 67404 Illkirch , France
label: 5
institution: Centre des Sciences du Goût et de l’Alimentation, University of Bourgogne Franche-Comté
country: France
name: Centre des Sciences du Goût et de l’Alimentation, University of Bourgogne Franche-Comté , 21000 Dijon , France
label: 6
institution: The Jackson Laboratory
country: USA
name: The Jackson Laboratory , 600 Main Street, Bar Harbor, ME 04609, USA
label: 7
institution: Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH
country: UK
name: Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH , UK
label: 8
institution: Brain Research Institute, University of California, 695 Charles E Young Dr S, Los Angeles
country: USA
name: Brain Research Institute, University of California, 695 Charles E Young Dr S, Los Angeles , CA 90095, USA
label: 9
institution: Yale Computational Biology and Bioinformatics, Yale University
country: USA
name: Yale Computational Biology and Bioinformatics, Yale University , New Haven , CT 06520, USA
label: 10
institution: The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN
country: UK
name: 10 The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN , UK
label: 11
institution: Department of Computer Science and Engineering, University of California
country: USA
name: 11 Department of Computer Science and Engineering, University of California , 9500 Gilman Drive La Jolla, San Diego, CA 92093 USA
label: 12
institution: Institute of Mathematics and Computer Science, University of Greifswald
country: Germany
name: 12 Institute of Mathematics and Computer Science, University of Greifswald , Domstraβe 11, 17489 Greifswald , Germany
label: 13
institution: Department of Pathology, Immunology, and Laboratory Medicine, University of Florida
country: USA
name: 13 Department of Pathology, Immunology, and Laboratory Medicine, University of Florida , Gainesville, FL , USA
label: 14
institution: Genetics Institute, University College London, Gower Street
country: UK
name: 14 Genetics Institute, University College London, Gower Street , London WC1E 6BT , UK
label: 15
institution: Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way
country: UK
name: 15 Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way , Cambridge , CB2 0RE, UK
label: 16
institution: LOG-G Department, Salk Institute for Biological Studies
country: USA
name: 16 LOG-G Department, Salk Institute for Biological Studies , 10010 North Torrey Pines Rd, San Diego, CA 92037, USA .
label: 17
institution: Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile
country: Chile
name: 17 Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , Santiago 8331150, Chile
label: 18
institution: Earlham Institute, Norwich Research Park
country: UK
name: 18 Earlham Institute, Norwich Research Park , Norwich NR4 7UZ, UK
Field: Biochemistry, Genetics and Molecular Biology
Document type: preprint
Year: 2018