Journal
BMC Genomics
Publication Date
2015
Volume
16
Issue
415
Document Type
Open Access Publication
DOI
10.1186/s12864-015-1592-3
Rights and Permissions
Nikolskiy et al. BMC Genomics (2015) 16:415 DOI 10.1186/s12864-015-1592-3
Recommended Citation
Nikolskiy, Igor; Conrad, Donald F.; Chun, Sung; Fay, Justin C.; Cheverud, James M.; and Lawson, Heather A., "Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides." BMC Genomics. 16, 415. (2015).
https://digitalcommons.wustl.edu/open_access_pubs/3892
12864_2015_1592_MOESM1_ESM.pdf (77 kB)
LG/J, SM/J and LG/J x SM/J polymorphic SNPs overview
12864_2015_1592_MOESM2_ESM.pdf (103 kB)
LG/J, SM/J and LG/J x SM/J polymorphic indels overview
12864_2015_1592_MOESM3_ESM.gz (18607 kB)
SNPs in LG/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM4_ESM.gz (8214 kB)
Indels in LG/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM5_ESM.gz (19183 kB)
SNPs in SM/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM6_ESM.gz (8219 kB)
Indels in SM/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM7_ESM.txt (1512 kB)
Structural variants found in LG/J and SM/J
12864_2015_1592_MOESM8_ESM.pdf (83 kB)
Distances between the LG/J and SM/J strains and other sequenced strains
12864_2015_1592_MOESM9_ESM.pdf (213 kB)
Phylogenetic tree of 20 sequenced mouse strains
12864_2015_1592_MOESM10_ESM.txt (3270 kB)
Amino acid changing mutations and corresponding deleterious predicted scores using SIFT/polyphen/LRT for both LG/J and SM/J strains
12864_2015_1592_MOESM11_ESM.gz (5550 kB)
VEP output of variants in predicted regulatory features for both LG/J and SM/J
12864_2015_1592_MOESM12_ESM.txt (163 kB)
VEP output of variants in predicted motifs for both LG/J and SM/J
12864_2015_1592_MOESM13_ESM.txt (1639 kB)
Predicted IBD regions in LG/J and SM/J sequenced genomes
12864_2015_1592_MOESM14_ESM.txt (19 kB)
QTL metrics and sequence integration
12864_2015_1592_MOESM15_ESM.pdf (150 kB)
Distribution of the number of variants predicted to have functional consequences in QTL intervals and in 1000 sets of randomly selected non-QTL regions of similar size
LG/J, SM/J and LG/J x SM/J polymorphic SNPs overview
12864_2015_1592_MOESM2_ESM.pdf (103 kB)
LG/J, SM/J and LG/J x SM/J polymorphic indels overview
12864_2015_1592_MOESM3_ESM.gz (18607 kB)
SNPs in LG/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM4_ESM.gz (8214 kB)
Indels in LG/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM5_ESM.gz (19183 kB)
SNPs in SM/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM6_ESM.gz (8219 kB)
Indels in SM/J discovered by integrating output from SamTools pileup and FreeBayes variant discovery tools
12864_2015_1592_MOESM7_ESM.txt (1512 kB)
Structural variants found in LG/J and SM/J
12864_2015_1592_MOESM8_ESM.pdf (83 kB)
Distances between the LG/J and SM/J strains and other sequenced strains
12864_2015_1592_MOESM9_ESM.pdf (213 kB)
Phylogenetic tree of 20 sequenced mouse strains
12864_2015_1592_MOESM10_ESM.txt (3270 kB)
Amino acid changing mutations and corresponding deleterious predicted scores using SIFT/polyphen/LRT for both LG/J and SM/J strains
12864_2015_1592_MOESM11_ESM.gz (5550 kB)
VEP output of variants in predicted regulatory features for both LG/J and SM/J
12864_2015_1592_MOESM12_ESM.txt (163 kB)
VEP output of variants in predicted motifs for both LG/J and SM/J
12864_2015_1592_MOESM13_ESM.txt (1639 kB)
Predicted IBD regions in LG/J and SM/J sequenced genomes
12864_2015_1592_MOESM14_ESM.txt (19 kB)
QTL metrics and sequence integration
12864_2015_1592_MOESM15_ESM.pdf (150 kB)
Distribution of the number of variants predicted to have functional consequences in QTL intervals and in 1000 sets of randomly selected non-QTL regions of similar size
