| 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 |
1 kGP† |
1 kGP† |
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.