TYPE: CONT
HANDLE: ENSEMBL
NAME: Paul Flicek
FAX: +44 (0)1223 494468
TEL: +44 (0)1223 492581
EMAIL: flicek@ebi.ac.uk
LAB: Ensembl
INST: European Bioinformatics Institute
ADDR: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
||
TYPE: PUB
HANDLE: ENSEMBL
TITLE:
TranscriptSNPView--A genome-wide catalog of mouse coding variation
AUTHORS:
Cunningham,F.;Rios,D.;Griffiths,M.;Smith,J.;Ning,Z;Cox,T.;Flicek,P.;Marin-Garcin,P.;Herrero,J.;Rogers,J.;van der Weyden,L.;Bradley,A.;Adams,D.J.
JOURNAL:Nature Genetics
YEAR: 2006
STATUS: 3
||
TYPE: PUB
HANDLE: ENSEMBL
PMID: 11591649
TITLE:
SSAHA:  A Fast Search Method for Large DNA Databases
AUTHORS:
Ning,Z.;Cox,A.J.;Mullikin,J.C.
JOURNAL:Genome Research
VOLUME:13
PAGES:81-90
YEAR: 2001
STATUS: 4
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TYPE:METHOD
HANDLE:ENSEMBL
ID:MOUSE_STRAIN-READS_SNPS_200606
METHOD_CLASS: Computation
SEC_BOTH_STRANDS: NA
TEMPLATE_TYPE: NA
MULT_PCR_AMPLIFICATION: NA
MULT_CLONES_TESTED: NA
METHOD:
Using ssaha2SNP, mouse sequencing reads from several sources were aligned to the contigs associated with build NCBI35 of the mouse genome.  The read set includes whole genome sequencing reads from the DBA/2J, 129S1/ImJ, 129X1/SvJ, A/J strains of Mus musculus, BAC-end sequence reads from the NOD strain of Mus musculus, and additional sequencing reads from the MSM/Ms strain of Mus musculus molossinus.  The reads for NOD were generated at the Wellcome Trust Sanger Institute, the MSM-Ms reads were generated by Riken.  Reads for the other strains were generated by Celera.  
The settings for ssaha2SNP used a Neighborhood Quality Standard (NQS) of Phred score Q >= 23 for the alternate base, Q >= 15 for the flanking 5 bases on each side of the alternate base, and that 9 of the 10 flanking bases be matched.  Other settings included requirements that matching identity of the read to ref >= 92% if alignment score < 600.
We have also included genotypes for those strains that have same as reference assembly (SARA) SNP alleles for those locations of the genome shown to be variant in at least one of the strains we used, but observed to be the same as the reference assembly for the given strain.  For SARA SNPs we required the alignments pass all of the same quality filters needed to call the alternate base and that the SARA allele meet the same NQS.
All SNPs were mapped back to the NCBI35 build of the Mus musculus genome assembly.  Full data and visualisation are available at http://www.ensembl.org