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Variant Visualizer
Step 1: Select strains to compare Rnor_5.0 assembly
ACI/EurMcwi (KNAW) see strain report
 
Secondary Analysis: GATK
ACI/EurMcwi (MCW) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
BBDP/WorN (KNAW) see strain report
 
Secondary Analysis: GATK
BDIX.Cg-Tal/NemOda (KyushuU) see strain report
 
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) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
BN-Lx/CubPrin (KNAW) see strain report
 
Secondary Analysis: GATK
BN/SsN (KNAW) see strain report
 
Secondary Analysis: GATK
BN/SsNSlc (KyushuU) see strain report
 
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) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
COP/CrCrl (MCW & UW) see strain report
 
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) see strain report
 
Secondary Analysis: GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)
DA/BklArbNsi (KNAW) see strain report
 
Secondary Analysis: GATK
DOB/Oda (KyushuU) see strain report
 
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/DuCrlCrlj (KyushuU) see strain report
 
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) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
F344/NHsd (KNAW) see strain report
 
Secondary Analysis: GATK
F344/NRrrc (Illumina) (KNAW) see strain report
 
Platform: Illumina
Secondary Analysis: GATK
F344/NRrrc (SOLiD) (KNAW) see strain report
 
Platform: SOLID
Secondary Analysis: GATK
F344/NSlc (KyushuU) see strain report
 
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) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
FHH/EurMcwi (MCW) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
FHL/EurMcwi (MCW) see strain report
 
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) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
HTX/Kyo (KyushuU) see strain report
 
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) see strain report
 
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) see strain report
 
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) see strain report
 
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) see strain report
 
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) see strain report
 
Secondary Analysis: GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)
LE/Stm (Illumina) (KNAW) see strain report
 
Secondary Analysis: GATK
LE/Stm (KyushuU) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
LEC/Tj (KyushuU) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
LEW/NCrl (KNAW) see strain report
 
Secondary Analysis: GATK
LH/MavRrrc (KNAW) see strain report
 
Secondary Analysis: GATK
LL/MavRrrc (KNAW) see strain report
 
Secondary Analysis: GATK
LN/MavRrrc (KNAW) see strain report
 
Secondary Analysis: GATK
M520/N (KNAW) see strain report
 
Secondary Analysis: GATK
MHS/Gib (KNAW) see strain report
 
Secondary Analysis: GATK
MNS/Gib (KNAW) see strain report
 
Secondary Analysis: GATK
MR/N (KNAW) see strain report
 
Secondary Analysis: GATK
NIG-III/Hok (KyushuU) see strain report
 
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) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
SBH/Ygl (MCW) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
SBN/Ygl (MCW) see strain report
 
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) see strain report
 
Secondary Analysis: GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6)
SHR/NCrlPrin (KNAW) see strain report
 
Secondary Analysis: GATK
SHR/NHsd (KNAW) see strain report
 
Secondary Analysis: GATK
SHR/OlaIpcv (KNAW) see strain report
 
Secondary Analysis: GATK
SHR/OlaIpcvPrin (KNAW) see strain report
 
Secondary Analysis: GATK
SHRSP/Gcrc (KNAW) see strain report
 
Secondary Analysis: GATK
SR/JrHsd (KNAW) see strain report
 
Secondary Analysis: GATK
SR/JrHsd (MCW) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
SS/JrHsdMcwi (KNAW) see strain report
 
Secondary Analysis: GATK
SS/JrHsdMcwi (MCW) see strain report
 
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) see strain report
 
Secondary Analysis: GATK
WKY/Gcrc (KNAW) see strain report
 
Secondary Analysis: GATK
WKY/N (KNAW) see strain report
 
Secondary Analysis: GATK
WKY/NCrl (KNAW) see strain report
 
Secondary Analysis: GATK
WKY/NHsd (KNAW) see strain report
 
Secondary Analysis: GATK
WN/N (KNAW) see strain report
 
Secondary Analysis: GATK
ZF (KyushuU) see strain report
 
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) see strain report
 
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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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.