The effect of PCR primer site heterozygosity on resequencing projects Quinlan AR, Marth GT. Primer-site SNPs mask mutations in resequencing projects. Nature Methods

Our study quantifies the negative effects of heterozygosity within PCR primer binding sites on the discovery of mutations in resequencing projects. We find that increasing amplicon coverage reduces the impact of this phenomenon and significantly increases the likelihood that SNPs are found in the resequencing project.
This site houses the ENCODE sequence data that was used in the study. Below are ten files associated with each of the ten resequenced ENCODE regions. When each file is extracted (use tar -zxvf ), one will find a main directory for each amplicon in the resequenced region. Under each amplicon directory is are the following directories, following Phred/Phrap convention: trace_dir, chromat_dir, phd_dir, poly_dir, edit_dir. Within the edit_dir, one will find the assembly file (CLUSTER.polybayes.alignment.ace) and an output file from Polyphred (polyphred.out). The latter file contains all of the discovered SNPs in the assembled traces from the given amplicon, as well as the genotypes for each trace at each SNP position.
For further information on these data, please visit the Hapmap website.


ENCODE Regions, Sequence Traces and SNP Files used in this Study
Region
name
Chromosome
band
Genomic interval
(NCBI)
Amplicons,
Traces
& SNPs File

File Size
(Gb)
ENr112 2p16.3 Chr2:51633239..52133238 ENr112.tar.gz 8.1 Gb
ENr131 2q37.1 Chr2:234778639..235278638 ENr131.tar.gz 6.7 Gb
ENr113 4q26 Chr4:118705475..119205474 ENr113.tar.gz 12.1 Gb
ENm010 7p15.2 Chr7:26699793..27199792 ENm010.tar.gz 5.5 Gb
ENm013 7q21.13 Chr7:89395718..89895717 ENm013.tar.gz 9.7 Gb
ENm014 7q31.33 Chr7:126135436..126632577 ENm014.tar.gz 10.1 Gb
ENr321 8q24.11 Chr8:118769628..119269627 ENr321.tar.gz 10.6 Gb
ENr232 9q34.11 Chr9:127061347..127561346 ENr232.tar.gz 8.0 Gb
ENr123 12q12 Chr12:38626477..39126476 ENr123.tar.gz 8.2 Gb
ENr213 18q12.1 Chr18:23717221..24217220 ENr213.tar.gz 13.1 Gb