Table 3.
Sequence composition of quartiles of the genome, defined according to the extent of linkage disequilibrium
|
Genome covered by HapMap
|
Genome quantiles, defined using LD
|
||||||
|---|---|---|---|---|---|---|---|
| Mean | (±S.E.) | (Low LD) Q1 | Q2 | Q3 | (High LD) Q4 | Trend | |
| Basic sequence features | |||||||
| GC bases | 4080.3 | (±2.3) | 4349.6 | 4102.3 | 3964.8 | 3904.6 | Decreases with LD |
| Bases in CpG islands | 72.0 | (±0.7) | 93.8 | 72.8 | 63.4 | 57.9 | Decreases with LD |
| Polymorphism (π) | 10.1 | (±0.02) | 11.9 | 10.6 | 9.6 | 8.3 | Decreases with LD |
| Genes and related features | |||||||
| Known genes (per 1000 kb) | 6.4 | (±0.4) | 6.6 | 6.1 | 6.2 | 6.7 | U shaped |
| Genic bases (exon, intron, UTR) | 3854.7 | (±16.9) | 3764.8 | 3456.9 | 3603.1 | 4594.0 | U shaped |
| Coding bases | 116.2 | (±0.8) | 112.4 | 104.1 | 112.0 | 136.2 | U shaped |
| Exonic bases | 222.1 | (±1.5) | 225.8 | 204.2 | 214.6 | 243.9 | U shaped |
| Intronic bases | 3678.0 | (±16.6) | 3584.5 | 3293.5 | 3432.5 | 4401.5 | U shaped |
| UTR (3′ and 5′) | 105.9 | (±0.8) | 113.4 | 100.1 | 102.6 | 107.7 | U shaped |
| Other features | |||||||
| Bases in transcription factor binding sites | 101.7 | (±0.3) | 110.1 | 107.1 | 98.7 | 90.8 | Decreases with LD |
| Bases in transcribed fragmentsa | 251.3 | (±2.4) | 290.9 | 258.0 | 232.9 | 223.3 | Decreases with LD |
| Predictions of conserved elements (phastCons) | 485.0 | (±1.5) | 520.5 | 499.1 | 465.9 | 454.5 | Decreases with LD |
| Conserved noncoding sequence | 139.1 | (±0.6) | 164.6 | 154.3 | 132.1 | 105.7 | Decreases with LD |
| Identical base in alignment with M. musculus | 2531.5 | (±4.7) | 2768.9 | 2678.6 | 2466.2 | 2212.2 | Decreases with LD |
| Identical base in alignment with R. norvegicus | 2454.0 | (±4.8) | 2679.8 | 2600.5 | 2395.5 | 2140.4 | Decreases with LD |
| Repeat content | |||||||
| Total bases in repeats | 4787.2 | (±5.0) | 4421.4 | 4642.0 | 4858.8 | 5226.7 | Increases with LD |
| Bases in LINE repeats | 2090.7 | (±4.6) | 1649.7 | 1988.4 | 2235.9 | 2488.9 | Increases with LD |
| Bases in SINE repeats | 1359.7 | (±3.9) | 1474.0 | 1307.8 | 1261.6 | 1395.3 | U shaped |
| Bases in LTR repeats | 851.2 | (±2.4) | 808.3 | 872.1 | 895.0 | 829.2 | ∩ shaped |
| Bases in DNA repeats | 302.6 | (±0.7) | 306.9 | 305.2 | 301.0 | 297.3 | Decreases with LD |
| Bases in simple repeats | 89.0 | (±0.3) | 109.3 | 91.2 | 82.1 | 73.4 | Decreases with LD |
| Bases in low complexity repeats | 57.6 | (±0.1) | 56.1 | 56.8 | 58.9 | 58.5 | Increases with LD |
| Bases in satellite repeats | 20.8 | (±1.3) | 5.4 | 6.9 | 8.4 | 62.5 | Increases with LD |
| Bases in other repeats | 14.0 | (±0.2) | 10.4 | 12.0 | 14.3 | 19.4 | Increases with LD |
a
Only applies to chromosomes 6, 7, 13, 14, 18, 19, 20, 21, 22, and X.
Average base counts (per 10,000 bases) and standard errors are presented for each feature.