|
|
ACI/EurMcwi (MCW)
|
|
| 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 |
| Description: |
Medical College of Wisconsin (Dr. Howard Jacob) |
|
|
ACI/N (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
BBDP/WorN (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
BDIX.Cg-Tal/NemOda (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
BDIX/NemOda (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
BN-Lx/Cub (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
|
|
BN/SsN (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
BN/SsNSlc (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
BUF/MNa (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
BUF/N (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
COP/CrCrl (MCW & UW)
|
|
| 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 |
| Description: |
Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull) |
|
|
Crl:SD (UDEL)
|
|
| Secondary Analysis: |
GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6) |
| Description: |
Provided by Barthold at al |
|
|
|
|
DOB/Oda (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
F344/DuCrlCrlj (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
F344/Jcl (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
F344/NCrl (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
F344/NHsd (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
F344/NRrrc (KNAW)
|
|
| Platform: |
Illumina |
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
F344/NRrrc (KNAW)
|
|
| Platform: |
SOLID |
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
F344/NSlc (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
F344/Stm (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
|
|
FHH/EurMcwi (MCW)
|
|
| 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 |
| Description: |
Provided by the Medical College of Wisconsin (Dr. Howard Jacob) |
|
|
|
|
FHL/EurMcwi (MCW)
|
|
| 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 |
| Description: |
Provided by the Medical College of Wisconsin (Dr. Howard Jacob) |
|
|
GH/OmrMcwi (MCW)
|
|
| 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 |
| Description: |
Provided by the Medical College of Wisconsin (Dr. Howard Jacob) |
|
|
GK/Ox (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
HTX/Kyo (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
HWY/Slc (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
IS-Tlk/Kyo (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
IS/Kyo (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
KFRS3B/Kyo (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
LE/OrlBarth (UDEL)
|
|
| Secondary Analysis: |
GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6) |
| Description: |
Provided by Barthold at al |
|
|
|
|
LE/Stm (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
|
|
LEC/Tj (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
LEW/Crl (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
LEW/NCrl (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
|
|
|
|
|
|
M520/N (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
MHS/Gib (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
MNS/Gib (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
MR/N (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
NIG-III/Hok (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
RCS/Kyo (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
SBH/Ygl (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
SBH/Ygl (MCW)
|
|
| 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 |
| Description: |
SBH/Ygl sequenced by MCW |
|
|
SBN/Ygl (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
SBN/Ygl (MCW)
|
|
| 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 |
| Description: |
SBN/Ygl sequenced by MCW |
|
|
SDLEF7/Barth (UDEL)
|
|
| Secondary Analysis: |
GATK (HaplotypeCaller v.3.1-1, VariantAnnotator v.3.1-1, SnpEff v.3.6) |
| Description: |
Provided by Barthold at al |
|
|
|
|
SHR/NHsd (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
|
|
|
|
|
|
SR/JrHsd (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
SR/JrHsd (MCW)
|
|
| 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 |
| Description: |
Provided by the Medical College of Wisconsin (Dr. Howard Jacob) |
|
|
SS/Jr (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
|
|
SS/JrHsdMcwi (MCW)
|
|
| 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 |
| Description: |
Provided by the Medical College of Wisconsin (Dr. Howard Jacob) |
|
|
WAG/Rij (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
WKY/Gcrc (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
WKY/N (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
WKY/NCrl (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
WKY/NHsd (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
WN/N (KNAW)
|
|
| Secondary Analysis: |
GATK |
| Description: |
Provided by Hermsen at al |
|
|
ZF (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
ZFDM (KyushuU)
|
|
| 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 |
| Description: |
Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) |
| Publications: |
Yoshihara M, etal., Genom Data. 2016 Nov 14;10:155-157. eCollection 2016 Dec. |
|
|
Gene-Chemical Interaction Annotations
