Specifications

Specifications

BeadChip Content Markers per Sample
Total Fixed Markers 4,301,331
Custom Markers up to 500,000
Feature Description
Number of Samples per BeadChip 4
DNA Requirement 400 ng
Assay Infinium LCG Quad
Instrument Support HiScanSQ or iScan
Sample Throughput* > 460 samples / week
Scan Time / Sample 15 minutes (HiScan)
25 minutes (iScan)

% Variation Captured
(r2 > 0.8)

1 kGP
MAF >5%

1 kGP
MAF >1%

CEU

0.87 0.83

CHB + JPT

0.85 0.76

YRI

0.71 0.58
Data Performance Value/Product Specification
Call Rate 99.9% / > 99% avg
Reproducibility 99.99% / > 99.9%
Log R Dev 0.12 / < 0.30**
Spacing Mean / Median / 90th%
Spacing (kb) 0.68 / 0.36 / 1.57
Marker Categories Number of Markers
Number of SNPs with 10kb of RefSeq genes 2,311,849
Nonsynonymous SNPs
(NCBI annotated)
84,004
MHC / ADME 43,904 / 43,615
Sex Chromosomes
(X / Y / PAR Loci)
113,213 / 2,498 / 511
Mitochondrial 267
Indels / multi-base substitutions 4,722

* Estimate assumes one iScan system, one AutoLoader2, one Tecan Robot, and a five-day work week.

Compared against the June 2011 1kGP data release.

§ Values derived from 454 reference samples.

** Value expected for typical projects using standard Illumina protocols.

Provided by the 1kGP structural variation group.