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Assembly Rnor_5.0

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Rnor_5.0 assembly

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ACI/EurMcwi (KNAW)

Sample ID:	731
Strain RGD ID	7364991
Secondary Analysis:	GATK

ACI/EurMcwi (MCW)

Sample ID:	711
Strain RGD ID	7364991
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14

ACI/N (KNAW)

Sample ID:	730
Strain RGD ID	10000
Secondary Analysis:	GATK

BBDP/WorN (KNAW)

Sample ID:	732
Strain RGD ID	1598798
Secondary Analysis:	GATK

BDIX.Cg-Tal/NemOda (KyushuU)

Sample ID:	781
Strain RGD ID	2304314
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

BDIX/NemOda (KyushuU)

Sample ID:	779
Strain RGD ID	2304285
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

BN-Lx/Cub (KNAW)

Sample ID:	734
Strain RGD ID	61117
Secondary Analysis:	GATK

BN-Lx/CubPrin (KNAW)

Sample ID:	735
Strain RGD ID	5131094
Secondary Analysis:	GATK

BN/SsN (KNAW)

Sample ID:	733
Strain RGD ID	61115
Secondary Analysis:	GATK

BN/SsNSlc (KyushuU)

Sample ID:	772
Strain RGD ID	1302631
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

BUF/MNa (KyushuU)

Sample ID:	766
Strain RGD ID	61118
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

BUF/N (KNAW)

Sample ID:	736
Strain RGD ID	60986
Secondary Analysis:	GATK

COP/CrCrl (MCW & UW)

Sample ID:	712
Strain RGD ID	1358153
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v2.3-5
Breeder:	Charles River Laboratories
Grant Information:	NIH (CA77876)

Crl:SD (UDEL)

Sample ID:	764
Strain RGD ID	737891
Secondary Analysis:	GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)

DA/BklArbNsi (KNAW)

Sample ID:	737
Strain RGD ID	1600340
Secondary Analysis:	GATK

DOB/Oda (KyushuU)

Sample ID:	780
Strain RGD ID	2304305
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

European Variation Archive Release 4

Sample ID:	31
Strain RGD ID	0

F344/DuCrlCrlj (KyushuU)

Sample ID:	768
Strain RGD ID	69643
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

F344/Jcl (KyushuU)

Sample ID:	778
Strain RGD ID	1547866
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

F344/NCrl (KNAW)

Sample ID:	739
Strain RGD ID	737926
Secondary Analysis:	GATK

F344/NHsd (KNAW)

Sample ID:	740
Strain RGD ID	61109
Secondary Analysis:	GATK

F344/NRrrc (Illumina) (KNAW)

Sample ID:	757
Strain RGD ID	70509
Platform:	Illumina
Secondary Analysis:	GATK

F344/NRrrc (SOLiD) (KNAW)

Sample ID:	738
Strain RGD ID	70509
Platform:	SOLID
Secondary Analysis:	GATK

F344/NSlc (KyushuU)

Sample ID:	771
Strain RGD ID	1302627
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

F344/Stm (KyushuU)

Sample ID:	775
Strain RGD ID	1302686
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

FHH/EurMcwi (KNAW)

Sample ID:	741
Strain RGD ID	629509
Secondary Analysis:	GATK

FHH/EurMcwi (MCW)

Sample ID:	713
Strain RGD ID	629509
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14

FHL/EurMcwi (KNAW)

Sample ID:	742
Strain RGD ID	1581626
Secondary Analysis:	GATK

FHL/EurMcwi (MCW)

Sample ID:	714
Strain RGD ID	1581626
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14

GH/OmrMcwi (MCW)

Sample ID:	715
Strain RGD ID	1579686
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v2.3-5

GK/Ox (KNAW)

Sample ID:	743
Strain RGD ID	4889464
Secondary Analysis:	GATK

HTX/Kyo (KyushuU)

Sample ID:	770
Strain RGD ID	1302600
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

HWY/Slc (KyushuU)

Sample ID:	776
Strain RGD ID	1302718
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

IS-Tlk/Kyo (KyushuU)

Sample ID:	774
Strain RGD ID	1302668
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

IS/Kyo (KyushuU)

Sample ID:	765
Strain RGD ID	10018
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

KFRS3B/Kyo (KyushuU)

Sample ID:	782
Strain RGD ID	2314377
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

LE/OrlBarth (UDEL)

Sample ID:	763
Strain RGD ID	10047391
Secondary Analysis:	GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)

LE/Stm (Illumina) (KNAW)

Sample ID:	744
Strain RGD ID	629485
Secondary Analysis:	GATK

LE/Stm (KyushuU)

Sample ID:	769
Strain RGD ID	629485
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

LE/Stm (SOLiD) (KNAW)

Sample ID:	745
Strain RGD ID	629485
Secondary Analysis:	GATK

LEC/Tj (KyushuU)

Sample ID:	777
Strain RGD ID	1302721
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

LEW/Crl (KNAW)

Sample ID:	746
Strain RGD ID	737932
Secondary Analysis:	GATK

LEW/NCrl (KNAW)

Sample ID:	747
Strain RGD ID	61104
Secondary Analysis:	GATK

LH/MavRrrc (KNAW)

Sample ID:	721
Strain RGD ID	60990
Secondary Analysis:	GATK

LL/MavRrrc (KNAW)

Sample ID:	722
Strain RGD ID	68077
Secondary Analysis:	GATK

LN/MavRrrc (KNAW)

Sample ID:	723
Strain RGD ID	61015
Secondary Analysis:	GATK

M520/N (KNAW)

Sample ID:	748
Strain RGD ID	10024
Secondary Analysis:	GATK

MHS/Gib (KNAW)

Sample ID:	724
Strain RGD ID	10025
Secondary Analysis:	GATK

MNS/Gib (KNAW)

Sample ID:	749
Strain RGD ID	10028
Secondary Analysis:	GATK

MR/N (KNAW)

Sample ID:	725
Strain RGD ID	70449
Secondary Analysis:	GATK

NIG-III/Hok (KyushuU)

Sample ID:	767
Strain RGD ID	68104
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

RCS/Kyo (KyushuU)

Sample ID:	773
Strain RGD ID	1302660
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

SBH/Ygl (KNAW)

Sample ID:	750
Strain RGD ID	631572
Secondary Analysis:	GATK

SBH/Ygl (MCW)

Sample ID:	716
Strain RGD ID	631572
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA-0.5.8c, GATK-v1.0.6001, samtools, Picard
Breeder:	Medical College of Wisconsin

SBN/Ygl (KNAW)

Sample ID:	751
Strain RGD ID	631573
Secondary Analysis:	GATK

SBN/Ygl (MCW)

Sample ID:	717
Strain RGD ID	631573
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA-0.5.8c, GATK-v1.0.6001, samtools, Picard
Breeder:	Medical College of Wisconsin

SDLEF7/Barth (UDEL)

Sample ID:	762
Strain RGD ID	10047393
Secondary Analysis:	GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)

SHR/NCrlPrin (KNAW)

Sample ID:	752
Strain RGD ID	9586448
Secondary Analysis:	GATK

SHR/NHsd (KNAW)

Sample ID:	753
Strain RGD ID	724574
Secondary Analysis:	GATK

SHR/OlaIpcv (KNAW)

Sample ID:	754
Strain RGD ID	631848
Secondary Analysis:	GATK

SHR/OlaIpcvPrin (KNAW)

Sample ID:	755
Strain RGD ID	9586450
Secondary Analysis:	GATK

SHRSP/Gcrc (KNAW)

Sample ID:	756
Strain RGD ID	734759
Secondary Analysis:	GATK

SR/JrHsd (KNAW)

Sample ID:	726
Strain RGD ID	1582184
Secondary Analysis:	GATK

SR/JrHsd (MCW)

Sample ID:	718
Strain RGD ID	1582184
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14
Breeder:	Harlan Laboratories

SS/Jr (KNAW)

Sample ID:	727
Strain RGD ID	10041
Secondary Analysis:	GATK

SS/JrHsdMcwi (KNAW)

Sample ID:	728
Strain RGD ID	61499
Secondary Analysis:	GATK

SS/JrHsdMcwi (MCW)

Sample ID:	719
Strain RGD ID	61499
Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.5.9-r16 and GATK v1.3-14
Grant Information:	R01 HL089930

WAG/Rij (KNAW)

Sample ID:	729
Strain RGD ID	737924
Secondary Analysis:	GATK

WKY/Gcrc (KNAW)

Sample ID:	758
Strain RGD ID	734760
Secondary Analysis:	GATK

WKY/N (KNAW)

Sample ID:	759
Strain RGD ID	70454
Secondary Analysis:	GATK

WKY/NCrl (KNAW)

Sample ID:	760
Strain RGD ID	1358112
Secondary Analysis:	GATK

WKY/NHsd (KNAW)

Sample ID:	761
Strain RGD ID	61105
Secondary Analysis:	GATK

WN/N (KNAW)

Sample ID:	720
Strain RGD ID	10045
Secondary Analysis:	GATK

ZF (KyushuU)

Sample ID:	783
Strain RGD ID	12859278
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

ZFDM (KyushuU)

Sample ID:	784
Strain RGD ID	12859279
Sequenced By:	Kyushu University (Dr. Mikita Suyama) Kyoto University (Dr. Takashi Kuramoto)
Platform:	Illumina NextSeq 500
Secondary Analysis:	BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2)
Breeder:	NBRP-Rat/Kyoto University
Grant Information:	supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development

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