Frequently Asked Questions
- Q1. What are the aims of the project?
- Q2. What technology did Perlegen use to resequence the 15 inbred mouse strains?
- Q3. What base-calling and SNP-detection analysis methods did Perlegen use?
- Q4. How do I access the base calls generated by the project?
- Q5. What is the reliability of base calls generated during the project?
- Q6. How do the trace files generated for the Perlegen's resequencing data compare with dideoxy sequencing data trace files?
- Q7. How does Perlegen's approach compare with whole-genome shotgun sequencing for producing 1.5X draft sequence?
- Q8. What is the reliability of SNP calls generated during the project?
- Q9. How can I determine the number of SNPs/trace files generated by the project?
- Q10. How can I access the SNP and genotype data?
- Q11. How do I download data? What do I do with them?
- Q12. Why are there 'N's in the genotyping data?
- Q13. Is there genotype information for the C57BL6/J reference strain?
- Q14. How can I find the flanking sequence for each SNP?
- Q15. What is the history of the Perlegen's data releases?
- Q16. How can I search using the Reference Cluster ID (rs#) of a SNP?
- Q17. Do "unmapped" SNPs or SNPs on "ChrUn" appear in the browser?
- Q18. Which mouse strains were used for resequencing?
- Q19. Were male or female mice used for resequencing?
- Q20. How can I access the sequences of the PCR primer pairs used to amplify the mouse genomic DNA for genotyping?
- Q21. What PCR conditions were used to amplify the mouse genomic DNA for genotyping, and what proportion of primer pairs amplified successfully using these conditions?
- Q22. Why does the trace file for my SNP appear to be unavailable?
- Q23. Why are there cases where there is more than one local_identifier/ss_id corresponding a single location?
- Q24. Which mouse strains were used for imputing genotypes?
- Q25. How were genotypes for the 8.27 million SNPs imputed for the 40 additional mouse strains?
- Q26. How was the phylogenetic information displayed on the haplotype block track of the genome browser generated?
If you have further questions about the Mouse Resequencing Project at Perlegen, please contact us.