Method
Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels
-
* Corresponding author: David J Adams da1@sanger.ac.uk
- † Equal contributors
1 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH, UK
2 Mammalian Genetics Unit, MRC-Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 ORD, UK
3 Department of Genetics, Case Western Reserve University, Adelbert Rd, Cleveland, OH 44106-4955. USA
Genome Biology 2009, 10:R112 doi:10.1186/gb-2009-10-10-r112
Published: 13 October 2009Additional files
Additional data file 1:
Effects of applying different p score thresholds on the accuracy and sensitivity of SNP calling from A/J sequence.
Format: XLS Size: 39KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 2:
Effects of applying different p-score thresholds on the accuracy and sensitivity of SNP calling from CAST/Ei sequence.
Format: XLS Size: 40KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 3:
Analysis of the accuracy of indel calling from A/J Illumina and capillary data.
Format: PPT Size: 104KB Download file
This file can be viewed with: Microsoft PowerPoint Viewer
Additional data file 4:
A complete list of deletions in A/J passing quality control filters, predicted by examining aberrantly mapping read pairs to the C57BL/6J genome. The list includes predicted start and end coordinates, the length of the deletion and the number of read pairs that predict the deletion.
Format: XLS Size: 44KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 5:
A complete list of deletions in A/J passing quality control filters, predicted by examining aberrantly mapping read pairs to the C57BL/6J genome. The list includes predicted start and end coordinates, the length of the deletion and the number of read pairs it is predicted by.
Format: XLS Size: 58KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 6:
Variants predicted by HMM structural variants (both amplifications and deletions) predicted by the HMM based on mapping depth and heterozygotes.
Format: XLS Size: 25KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 7:
Single nucleotide differences between C57BL/6J and A/J that affect Ensembl coding exons, marked as either synonymous, non-synonymous or splice site changes. Also indicated are the sequencing depth and phred-like quality score.
Format: XLS Size: 731KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 8:
Single nucleotide differences between C57BL/6J and CAST/Ei that affect Ensembl coding exons, marked as either synonymous, non-synonymous or splice site changes. Also indicated are the sequencing depth and phred-like quality score.
Format: XLS Size: 1.7MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 9:
Genes affected by predicted structural variants (predicted by both read-pair mapping and the HMM) in both strains. The genes, strain, type of variant and exons affected are indicated. Type is either deletion (as predicted from read-pair mapping), copy number loss (CN_Loss) or copy number gain (CB_Gain).
Format: XLS Size: 50KB Download file
This file can be viewed with: Microsoft Excel Viewer