The summary statistics of FinMetSeq SV paper
wgs_stats/${trait}.wgs.mac10.txt.gz
| Colunms | contents |
|---|---|
| TRAIT | quantitative trait tested |
| PIPELINE | pipeline used to detect the SV |
| ID | the ID of SV |
| CHR | chromosome |
| POS | starting point of the SV, in GRCh38 reference |
| P | p value in discovery phase with WGS data only |
| BETA | beta in discovery phase with WGS data only |
| SEBETA | standard deviation of the beta in discovery phase with WGS data only |
| R2 | R2 in discovery phase with WGS data only |
| AC | the alternative allele count from WGS data, noted for GenomeSTRiP and CNVnator those are #. alternative copy number carriers |
| AF | allele frequency |
| N | sample size, (sample availability varied by trait) |
The full name of the trait abbreviations can be found from Locke et al. 2020 (PMID:31367044) and Davis et al. 2017 (PMID:29084231)
replication_summary_stats.txt
| Colunms | contents |
|---|---|
| ID | SV ID from original pipeline (CNV_chr_$pos_$end are GenomeSTRiP CNVs, chr_$pos_$end are CNVnator CNVs, and number IDs belong to LUMPY) |
| TRAIT | the traits tested for association with (combined means male and female data combined) |
| CHR | chromosome |
| POS | starting point of the SV, in GRCh38 reference |
| P_WGS | p value in discovery phase with WGS data only |
| BETA_WGS | beta in discovery phase with WGS data only |
| AC_WGS | the alternative allele count from WGS data, noted for GenomeSTRiP and CNVnator those are #. alternative copy number carriers |
| N_WGS | sample size of WGS association tests (sample availability varied by trait) |
| P_WES_FE | WES replication meta p value under fixed effects model |
| BETA_WES_FE | WES replication meta beta under fixed effects model |
| TOP_EXON | Top exon signal (in hg19 reference) |
| N_IMP | sample size of imputed SVs' association test (replication phase) |
| GENOCNT_IMP | count for HOMREF/HET/HOMALT in imputated SV |
| MAF_IMP | minor allele frequency for imputed SV |
| P_IMP | replication p value using imputed genotype |
| BETA_IMP | replication beta using imputed genottype |
| TYPE | SV type |
| DR2_IMP | BEAGLE score for imputation quality, an estimated correlation between imputed genotype and real genotype |
| AF_IMP_CALLSET | allele frequency in the imputed callset |
| maxR2 | the max genotype correlation with flanking SNPs within 1MB region (calculated by WGS data only) |
| EXON_R2_BATCH1 | the genotype correlation between WGS detected SV and the exon XHMM-processed read-depth data in batch1 |
| EXON_R2_BATCH2 | the genotype correlation between WGS detected SV and the exon XHMM-processed read-depth data in batch2 |
| exon_r2_ave | average of the previous two columns |
| imp_r2_higher | whether the imputation correlation (DR2) is higher than exon_r2_ave |
| combined_p | combined p values from discovery (P_WGS) and replication (P_IMP or P_WES_FE) using fisher's method |