Table 3 Univariate logistic predictors of whether or not a TR is polymorphic in the Whole Genome Shotgun datasets.
From: Marked variation in predicted and observed variability of tandem repeat loci across the human genome
Predictor1 | Variable class | Mean among variants | Mean among invariants | % increase among variants | Logistic Pseudo R 2 |
|---|---|---|---|---|---|
unit_length | Repeat | 3.115 | 5.828 | -46.6 | 0.19 |
score | Repeat | 84.569 | 61.891 | 36.6 | 0.14 |
copy_number | Repeat | 20.440 | 11.724 | 74.3 | 0.08 |
%match | Repeat | 94.261 | 89.711 | 5.1 | 0.05 |
AC | Repeat | 2.252 | 1.396 | 61.3 | 0.04 |
%indels | Repeat | 2.083 | 4.619 | -54.9 | 0.04 |
CA | Repeat | 2.280 | 1.757 | 29.8 | 0.03 |
SNP_allele_freq | Repeat flank | 0.166 | 0.167 | -0.6 | 0.02 |
AA | Repeat | 1.025 | 1.183 | -13.4 | 0.01 |
blocklength | Repeat | 57.130 | 48.430 | 18.0 | 0.01 |
G+C_repeat | Repeat | 32.098 | 28.592 | 12.3 | < 0.01 |
entropy | Repeat | 1.050 | 1.100 | -4.5 | < 0.01 |
CC | Repeat | 1.052 | 1.150 | -8.5 | < 0.01 |
CpG_flank500 | Repeat flank | 4.695 | 5.496 | -14.6 | < 0.01 |
G+C_flank500 | Repeat flank | 41.427 | 42.363 | -2.2 | < 0.01 |
tm_flank500 | Repeat flank | 53.014 | 53.418 | -0.8 | < 0.01 |
G+C_flank20 | Repeat flank | 38.653 | 39.873 | -3.1 | < 0.01 |
tm_flank20 | Repeat flank | 51.606 | 52.134 | -1.0 | < 0.01 |
C | Repeat | 15.695 | 13.831 | 13.5 | < 0.01 |
G | Repeat | 15.559 | 13.717 | 13.4 | < 0.01 |
GC | Repeat | 1.010 | 1.088 | -7.2 | < 0.01 |
TA | Repeat | 0.921 | 0.877 | 5.0 | < 0.01 |
A | Repeat | 33.180 | 35.523 | -6.6 | < 0.01 |
CpG flank 20 | Repeat flank | 0.190 | 0.226 | -15.9 | < 0.01 |
tm_repeat | Repeat | 48.744 | 47.967 | 1.6 | < 0.01 |
num_SNPs | Repeat flank | 2.380 | 2.220 | 7.2 | < 0.01 |
RNA_free_energy | Repeat | -3.978 | -3.157 | 26.0 | < 0.01 |
nearest_promoter | Distant repeat flank | 475996.5 | 439298.5 | 8.3 | < 0.01 |
CG | Repeat | 0.930 | 0.973 | -4.4 | < 0.01 |
AT | Repeat | 0.991 | 0.963 | 2.9 | < 0.01 |
AG | Repeat | 1.313 | 1.354 | -3.0 | < 0.01 |
T | Repeat | 34.591 | 35.767 | -3.3 | < 0.01 |
pop_size | 6.317 | 5.642 | 12.0 | < 0.01 | |
nearest_gene | Distant repeat flank | 143738.9 | 133874.5 | 7.4 | < 0.01 |
nearest_CDS | Distant repeat flank | 151516.1 | 141369.5 | 7.2 | < 0.01 |
GA | Repeat | 1.346 | 1.382 | -2.7 | < 0.01 |
nearest_regulatory | Distant repeat flank | -3642189 | -3363138 | 8.3 | < 0.01 |
nearest_MCS | Distant repeat flank | 66672.9 | 72695.2 | -8.3 | < 0.01 |
