Perlegen
Long Range
PCR Amplicon Data
Long Range
PCR Protocols
The PCR protocols are documented in the supplemental
materials for Hinds et al., Science 307: 1072–1079 (2005), available at http://www.sciencemag.org/cgi/data/307/5712/1072/DC1/1.
This file contains the nucleotide
sequences for long range PCR primer pairs utilized in the Phase II HapMap
genotyping project. The file is tab
separated text with three columns.
|
Column
|
Description
|
|
PRIMER_PAIR_ID
|
A unique identifier for this primer pair
|
|
PRIMER_1
|
Primer sequence 1
|
|
PRIMER_2
|
Primer sequence 2
|
This file contains filtered BLAST
hits for NCBI Build 35. One row in this
file corresponds to one BLAST hit for both forward and reverse primers. A given primer pair may have multiple BLAST
hits, or no hits at all. Hits have been
filtered to have amplicon lengths less than 24 kb. The file is tab separated text with eight
columns.
|
Column
|
Description
|
|
PRIMER_PAIR_ID
|
A unique identifier for this primer pair
|
|
CHR
|
The chromosome name for this hit
|
|
ACCESSION
|
An NCBI accession number for this hit
|
|
FWD_END
|
The first sequence position within the amplicon
|
|
REV_END
|
The last sequence position within the amplicon
|
|
FWD_HIT
|
Identifies the primer on the forward genomic strand
|
|
REV_HIT
|
Identifies the primer on the reverse genomic strand
|
|
UNIQ_HIT
|
= 1 if this is the only hit for this primer pair
|
|
PERFECT_MATCH
|
= 1 if both primers have perfect full-length matches
|
The forward and reverse amplicon
end positions exclude the primer sequences themselves so these represent the
boundaries of the interval of target DNA that will be amplified. Thus a 20 bp forward primer would map to
sequence positions FWD_END–20 to
FWD_END–1, and a 20 bp reverse
primer would map to (reverse complemented) positions REV_END+1 to REV_END+20. The FWD_HIT
and REV_HIT values indicate which of the two primers in the PP_SEQUENCE table are the “forward”
and “reverse” primers in this case, based on the orientation of the NCBI
reference sequence.
