Genotypes of 36 wild caught mice, 62 wild derived laboratory strains and 100 classical strains

Description

We selected 198 samples for genotyping with the Mouse Diversity array including 36 wild caught mice, 62 wild-derived laboratory strains and 100 classical strains. Wild caught mice, including representatives from M. m. domesticus, M. m. musculus and M. m. castaneus, were used as references to infer the phylogenetic origin of laboratory strains (http://msub.csbio.unc.edu/). Our laboratory samples include strains derived from different stocks and by different laboratories as well as 13 sets of classical substrains that are thought to be closely related to each other. We used 549,599 SNPs that passed quality control filtering and performed additional steps to improve the quality of the genotype calls. Our genotype data include SNPs, deletions larger than 100kb, and VINOs (Variable INtensity Oligonucleotides). The latter represent previously unknown genetic variants that substantially alter the performance of SNP detection probes. There are six possible calls: homozygous for either allele (A or B), heterozygous (H), VINO (V), deletion (D) and no call (N). There are 117,203 probes with VINOs in at least one of the 198 strains. In analyses based on SNPs, we treated VINOs as no calls. In analyses based on VINOs we treated data as binary for presence and absence of VINOs.

Reference

Subspecific origin and haplotype diversity in the laboratory mouse
Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Yu AH, Nachman MW, Pialek J, Tucker P, Boursot P, McMillan L, Churchill GA, de Villena FP.
Nat Genet. 2011 May 29;43(7):648-55. PMCID: PMC3125408 [ Full Text ] [ News Article ]

Adaptive evolution and effective population size in wild house mice
Phifer-Rixey M, Bonhomme F, Boursot P, Churchill GA, Piálek J, Tucker P, Nachman M.
Mol Biol Evol. 2012 Oct;29(10):2949-55. PMCID: PMC3457769 [Available on 2013/10/1]

Datasets

Mastersheet - New_master_file_project7.xlsx

Strains

Classical (100)
129P1/ReJ
129P3/J
129S1/SvlmJ
129S6
129T2/SvEmsJ
129X1/SvJ
A/J
A/WySnJ
AEJ/GnLeJ
AEJ/GnRk a[e]/a[e]
AKR/J
ALR/LtJ
ALS/LtJ
BALB/cByJ
BALB/cJ
BDP/J
BPH/2J
BPL/1J
BPN/3J
BTBR T<+>tf/J
BUB/BnJ
BXSB/MpJ
C3H/HeJ
C3HeB/FeJ
C57BL/10J
C57BL/10ScNJ
C57BL/10ScSnJ
C57BL/6CR
C57BL/6J
C57BL/6NCI
C57BL/6Tc
C57BLKS/J
C57BR/cdJ
C57L/J
C58/J
CBA/CaJ
CBA/J
CE/J
CHMU/LeJ
DBA/1J
DBA/1LacJ
DBA/2DeJ
DBA/2J
DBA/HaSmnJ
DDK/Pas
DDY/JclSidSeyFrkJ
DLS/LeJ
EL/SuzSeyFrkJ
FVB/NJ
HPG/BmJ
I/LnJ
IBWSP2
IBWSR2
ICOLD2
IHOT1
IHOT2
ILS
ISS
JE/LeJ
KK/HlJ
LG/J
LP/J
LT/SvEiJ
MRL/MpJ
NOD/ShiLtJ
NON/ShiLtJ
NONcNZO10/LtJ
NONcNZO5/LtJ
NOR/LtJ
NU/J
NZB/BlNJ
NZL/LtJ
NZM2410/J
NZO/HlLtJ
NZW/LacJ
P/J
PL/J
PN/nBSwUmabJ
RF/J
RHJ/LeJ
RIIIS/J
RSV/LeJ
SB/LeJ
SEA/GnJ
SEC/1GnLeJ
SEC/1ReJ
SH1/LeJ
SI/Col Tyrp1 Dnahc11/J
SJL/Bm
SJL/J
SM/J
SSL/LeJ
ST/bJ
STX/Le
SWR/J
TALLYHO/JngJ
TKDU/DnJ
TSJ/LeJ
YBR/EiJ
ZRDCT Rax<+>ChUmdJ
Wild Derived (62)
22MO
BIK/g
BULS
BUSNA
BZO
CALB/RkJ
CASA/RkJ
CAST/EiJ
CIM
CKN
CKS
CZECHI/EiJ
CZECHII/EiJ
DCA
DCP
DDO
DEB
DGA
DIK
DJO
DKN
DMZ
DOT
IS/CamRkJ
JF1/Ms
LEWES/EiJ
MBK
MBS
MCZ
MDG
MDGI
MDH
MGA
MH
MOLD/RkJ
MOLF/EiJ
MOLG/DnJ
MOR/RkJ
MPB
MSM/Ms
PERA/EiJ
PERC/EiJ
POHN/Deh
PWD/PhJ
PWK/PhJ
RBA/DnJ
RBB/DnJ
RBF/DnJ
SF/CamEiJ
SKIVE/EiJ
SOD1/EiJ
STLT
STRA
STRB
STUF
STUP
STUS
TIRANO/EiJ
WLA
WMP
WSB/EiJ
ZALENDE/EiJ
Wild (36)
BAG102
BAG3
BAG56
BAG68
BAG74
BAG94
BAG99
IN13
IN17
IN25
IN34
IN38
IN40
IN47
IN54
IN59
IN60
KCT222
MWN1026
MWN1030
MWN1106
MWN1194
MWN1198
MWN1214
MWN1279
MWN1287
RDS10105
RDS12763
RDS13554
Yu2095m
Yu2097m
Yu2099f
Yu2113m
Yu2115m
Yu2116m
Yu2120f

Chromosomes

All
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chrX
chrY
chrM

Format

nucleotide (A-C-G-T)        allele call (A-B)