Supplemental data 1 for Gymrek et al: A framework to interpret short tandem repeat variation in humans
# Description of data file
Column names are given in the comment line. Below is a brief description of each column:
1. chrom: chromosome name
2. start: start coordinate of the STR (according to lobSTR's hg19 reference)
3. end: end coordinate of the STR (according to lobSTR's hg19 reference)
4. est_logmu_ml: Estimated log10 mutation rate
5. est_beta_eff_ml: Estimated effective length constraint (beta/strsd**2)
6. est_beta_ml: Estimated length constraint
7. est_pgeom_ml: Estimated step size parameter
8. stderr_ml: Standard error on the mutation rate estimate. Negative standard errors are undefined.
9. up: Estimated probability for stutter to increase the unit length
10. down: Estimated probability for stutter to decrease the unit length
11. p: Estimated stutter step size parameter
12. period: length of the repeat unit
13. motif: motif of the repeat unit
14. uninterrupted_length: Longest interrupted perfect repeat track
15. pred_mu_1: Mu predicted by the neutral mutation model
16. pred_mu_se_1: standard error of pred_mu_1
17. zscore_1: Zscore calculated from pred_mu_1, pred_mu_se_1, est_logmu_ml, and stderr_ml
18. pred_mu_2: columns 18-20 are same as columns 15-17, but the model is trained without filtering loci with high or undefined standard errors
19. pred_mu_se_2
20. zscore_2
21. filter1: True if the locus has characteristics that were filtered before training Model 1 (columns 15-17, used in the main text).
# Notes on predicted mutation rates:
Loci with NaN for fields 14-21 were not included in the constraint analysis. The main text reports constraint scores calculated using Model 1. The differences between Model 1 and Model 2 are as follows:
Model 1: Loci with high, zero, or undefined standard errors were excluded from training (see column "filter1").
Model 2: Training did not exclude loci based on standard errors.