Summary
Summary {data-width=650}
Manhattan plot
manhattan_plot
QQ plot
qq_plot
AF plot
af_plot
P-Z plot
pz_plot
beta_std plot
beta_std_plot
Metadata
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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/fb7b45f3-cd8c-4ed3-8783-e6c6338b2ee8/call-vcf/inputs/-261022254/upload.txt.gz --id ieu-b-5070 --json /data/cromwell-executions/qc/fb7b45f3-cd8c-4ed3-8783-e6c6338b2ee8/call-vcf/inputs/-261022254/ieu-b-5070_data.json --ref /data/cromwell-executions/qc/fb7b45f3-cd8c-4ed3-8783-e6c6338b2ee8/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/fb7b45f3-cd8c-4ed3-8783-e6c6338b2ee8/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5070/ieu-b-5070.vcf.gz --alias alias.txt --cohort_cases 22778 --cohort_controls 35362; 1.3.0",
"file_date": "2022-05-10T17:04:21.370285",
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}
LDSC
*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call:
./ldsc.py \
--h2 /data/cromwell-executions/qc/fb7b45f3-cd8c-4ed3-8783-e6c6338b2ee8/call-ldsc/inputs/-261022254/ieu-b-5070.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5070/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Tue May 10 17:17:24 2022
Reading summary statistics from /data/cromwell-executions/qc/fb7b45f3-cd8c-4ed3-8783-e6c6338b2ee8/call-ldsc/inputs/-261022254/ieu-b-5070.vcf.gz ...
Read summary statistics for 10359743 SNPs.
Dropped 388964 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1139031 SNPs remain.
After merging with regression SNP LD, 1139031 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 2017.2698 (34.7539)
Lambda GC: 5315.2449
Mean Chi^2: 2172.8081
Intercept: 12.4291 (0.141)
Ratio: 0.0053 (6.4918e-05)
Analysis finished at Tue May 10 17:18:40 2022
Total time elapsed: 1.0m:15.97sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9227,
"inflation_factor": 1.1412,
"mean_EFFECT": 0.0952,
"n": "-Inf",
"n_snps": 10360199,
"n_clumped_hits": 20,
"n_p_sig": 1727,
"n_mono": 0,
"n_ns": 495239,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 555337,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NaN",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1139031,
"ldsc_nsnp_merge_regression_ld": 1139031,
"ldsc_observed_scale_h2_beta": 2017.2698,
"ldsc_observed_scale_h2_se": 34.7539,
"ldsc_intercept_beta": 12.4291,
"ldsc_intercept_se": 0.141,
"ldsc_lambda_gc": 5315.2449,
"ldsc_mean_chisq": 2172.8081,
"ldsc_ratio": 0.0053
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | TRUE |
| n_p_sig | TRUE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | FALSE |
| ldsc_intercept_beta | TRUE |
| n_clumped_hits | FALSE |
| r2_sum1 | FALSE |
| r2_sum2 | FALSE |
| r2_sum3 | FALSE |
| r2_sum4 | FALSE |
Definitions
General metrics
af_correlation: Correlation coefficient betweenAFandAF_reference.inflation_factor(lambda): Genomic inflation factor.mean_EFFECT: Mean ofEFFECTsize.n: Maximum value of reported sample size across all SNPs, \(n\).n_clumped_hits: Number of clumped hits.n_snps: Number of SNPsn_p_sig: Number of SNPs with pvalue below5e-8.n_mono: Number of monomorphic (MAF == 1orMAF == 0) SNPs.n_ns: Number of SNPs with nonsense values:- alleles other than
A, C, G or T. - P-values
< 0or> 1. - negative or infinite standard errors (
<= 0or= Infinity). - infinite beta estimates or allele frequencies
< 0or> 1.
- alleles other than
n_mac: Number of cases whereMAC(\(2 \times N \times MAF\)) is less than6.is_snpid_unique:trueif the combination ofIDREFALTis unique and therefore no duplication in snpid.n_miss_<*>: Number ofNAobservations for<*>column.
se_n metrics
n_est: Estimated sample size value, \(\widehat{n}\).ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expectratio_se_nto be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.- \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
- \({z}_j = \frac{\beta_j}{{se}_j}\),
- and \(\beta_j\) is the reported effect size.
ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean ofdiffand the mean ofdiff2(expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.- \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
- \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.- \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
- \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
- and \({se}_j\) is the reported standard error.
sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.- \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
- \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>:r2statistics under various assumptions1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).
LDSC metrics
Metrics from LD regression
ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.ldsc_observed_scale_h2_{beta,se}Coefficient value and SE for total observed scale h2.ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.ldsc_lambda_gc: Lambda GC statistics.ldsc_mean_chisq: Mean \(\chi^2\) statistics.ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).
Flags
When a metric needs attention, the flag should return TRUE.
af_correlation:abs(af_correlation)< 0.7.inflation_factor:inflation_factor> 1.2.n:n(max reported sample size) < 10000.is_snpid_non_unique: NOTis_snpid_unique.mean_EFFECT_nonfinite:mean(EFFECT)isNA,NaN, orInf.mean_EFFECT_05:abs(mean(EFFECT))> 0.5.mean_EFFECT_01:abs(mean(EFFECT))> 0.1.mean_chisq:ldsc_mean_chisq> 1.3 orldsc_mean_chisq< 0.7.n_p_sig:n_p_sig> 1000.miss_<*>:n_miss_<*>/n_snps> 0.01.ldsc_ratio:ldsc_ratio> 0.5ldsc_intercept_beta:ldsc_intercept_beta> 1.5n_clumped_hits:n_clumped_hits> 1000r2_sum<*>:r2_sum<*>> 0.5
Plots
- Manhattan plot
- Red line: \(-log_{10}^{5 \times 10^{-8}}\)
- Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
- QQ plot
- AF plot
- P-Z plot
- beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)
Diagnostics
Details
Summary stats
| skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 39 | 0.9999962 | 3 | 83 | 0 | 10151725 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 13 | 0 | 12357 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 13 | 0 | 12888 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 10360199 | 0.0000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.072000e+00 | 6.171876e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.838423e+07 | 5.613741e+07 | 78.0000 | 3.220999e+07 | 6.894469e+07 | 1.143693e+08 | 2.492405e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.520060e-02 | 2.624992e+00 | -4344.2100 | -9.951100e-01 | 9.114700e-01 | 1.004110e+00 | 2.199310e+03 | ▁▁▁▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.879360e-02 | 2.195740e-01 | 0.0133 | 1.960000e-02 | 3.080000e-02 | 8.520000e-02 | 9.679000e+01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.778941e-01 | 2.949307e-01 | 0.0000 | 2.163002e-01 | 4.711997e-01 | 7.333005e-01 | 1.000000e+00 | ▇▇▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.434500e-03 | 4.215660e-02 | 0.0000 | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | 9.999992e-01 | ▇▁▁▁▁ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.496680e-01 | 2.816117e-01 | 0.0009 | 2.200000e-02 | 1.210000e-01 | 4.080000e-01 | 9.994000e-01 | ▇▂▂▁▁ |
| numeric | AF_reference | 555337 | 0.9463971 | NA | NA | NA | NA | NA | NA | NA | 2.305124e-01 | 2.487163e-01 | 0.0000 | 2.156550e-02 | 1.377800e-01 | 3.676120e-01 | 1.000000e+00 | ▇▂▂▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 10352 | rs1557426776 | TA | T | 1.06727 | 0.0261 | 0.0126200 | 0 | 0.5920 | NA | NA |
| 1 | 11008 | rs575272151 | C | G | -1.01329 | 0.0576 | 0.8187000 | 0 | 0.0510 | 0.0880591 | NA |
| 1 | 11012 | rs544419019 | C | G | -1.01329 | 0.0576 | 0.8187000 | 0 | 0.0510 | 0.0880591 | NA |
| 1 | 13110 | rs540538026 | G | A | 1.64296 | 0.1998 | 0.0129599 | 0 | 0.0128 | 0.0267572 | NA |
| 1 | 13116 | rs62635286 | T | G | -0.94535 | 0.0716 | 0.4324999 | 0 | 0.0440 | 0.0970447 | NA |
| 1 | 13118 | rs200579949 | A | G | -0.94535 | 0.0716 | 0.4324999 | 0 | 0.0440 | 0.0970447 | NA |
| 1 | 13273 | rs531730856 | G | C | 1.03262 | 0.0526 | 0.5417002 | 0 | 0.0804 | 0.0950479 | NA |
| 1 | 14464 | rs546169444 | A | T | -1.05096 | 0.0724 | 0.4923999 | 0 | 0.0480 | 0.0958466 | NA |
| 1 | 14599 | rs531646671 | T | A | 0.94885 | 0.0439 | 0.2317000 | 0 | 0.0986 | 0.1475640 | NA |
| 1 | 14604 | rs541940975 | A | G | -1.05390 | 0.0439 | 0.2317998 | 0 | 0.0990 | 0.1475640 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154924557 | rs141848012 | T | A | 1.05180 | 0.0587 | 0.3892002 | 0.0000000 | 0.0402 | 0.0296689 | NA |
| 23 | 154925045 | rs509981 | C | T | 0.98629 | 0.0189 | 0.4645998 | 0.0000000 | 0.2510 | 0.3634440 | NA |
| 23 | 154925406 | rs183894977 | T | C | -1.11997 | 0.1650 | 0.4923999 | 0.0000000 | 0.0200 | 0.0052980 | NA |
| 23 | 154925895 | rs538470 | C | T | 0.98620 | 0.0192 | 0.4693005 | 0.0000000 | 0.2510 | 0.3634440 | NA |
| 23 | 154927185 | rs185685661 | T | C | -1.05201 | 0.0326 | 0.1198999 | 0.0000000 | 0.1200 | 0.1796030 | NA |
| 23 | 154927199 | rs645904 | C | T | 0.98639 | 0.0189 | 0.4687001 | 0.0000000 | 0.2520 | 0.3674170 | NA |
| 23 | 154927581 | rs644138 | G | A | 0.98157 | 0.0184 | 0.3124000 | 0.0000000 | 0.2670 | 0.4635760 | NA |
| 23 | 154928151 | rs144607509 | C | T | 0.97941 | 0.5333 | 0.9689001 | 0.0662825 | 0.0113 | 0.0084768 | NA |
| 23 | 154929412 | rs557132 | C | T | 0.98531 | 0.0197 | 0.4523004 | 0.0000000 | 0.2600 | 0.3568210 | NA |
| 23 | 154930230 | rs781880 | A | G | -1.01654 | 0.0186 | 0.3774001 | 0.0000000 | 0.2590 | 0.3618540 | NA |
bcf preview
1 10352 rs1557426776 TA T . PASS AF=0.592 ES:SE:LP:AF:ID 1.06727:0.0261:1.89894:0.592:rs1557426776
1 11008 rs575272151 C G . PASS AF=0.051 ES:SE:LP:AF:ID -1.01329:0.0576:0.0868752:0.051:rs575272151
1 11012 rs544419019 C G . PASS AF=0.051 ES:SE:LP:AF:ID -1.01329:0.0576:0.0868752:0.051:rs544419019
1 13110 rs540538026 G A . PASS AF=0.0128 ES:SE:LP:AF:ID 1.64296:0.1998:1.8874:0.0128:rs540538026
1 13116 rs62635286 T G . PASS AF=0.044 ES:SE:LP:AF:ID -0.94535:0.0716:0.364014:0.044:rs62635286
1 13118 rs62028691 A G . PASS AF=0.044 ES:SE:LP:AF:ID -0.94535:0.0716:0.364014:0.044:rs62028691
1 13273 rs531730856 G C . PASS AF=0.0804 ES:SE:LP:AF:ID 1.03262:0.0526:0.266241:0.0804:rs531730856
1 14464 rs546169444 A T . PASS AF=0.048 ES:SE:LP:AF:ID -1.05096:0.0724:0.307682:0.048:rs546169444
1 14599 rs707680 T A . PASS AF=0.0986 ES:SE:LP:AF:ID 0.94885:0.0439:0.635074:0.0986:rs707680
1 14604 rs1418508701 A G . PASS AF=0.099 ES:SE:LP:AF:ID -1.0539:0.0439:0.634887:0.099:rs1418508701
1 14930 rs6682385 A G . PASS AF=0.434 ES:SE:LP:AF:ID -0.97453:0.0264:0.483597:0.434:rs6682385
1 14933 rs199856693 G A . PASS AF=0.03 ES:SE:LP:AF:ID 0.91001:0.0825:0.596879:0.03:rs199856693
1 15211 rs3982632 T G . PASS AF=0.519 ES:SE:LP:AF:ID -1.0202:0.0261:0.353106:0.519:rs3982632
1 15274 rs1328799397 A G . PASS AF=0.459 ES:SE:LP:AF:ID -0.95047:0.0267:1.24336:0.459:rs1328799397
1 15274 rs1328799397 A T . PASS AF=0.541 ES:SE:LP:AF:ID -1.05043:0.0267:1.18456:0.541:rs1328799397
1 15644 rs564003018 G A . PASS AF=0.0157 ES:SE:LP:AF:ID 0.97863:0.1011:0.0805035:0.0157:rs564003018
1 15774 rs374029747 G A . PASS AF=0.0248 ES:SE:LP:AF:ID 1.05908:0.0801:0.324588:0.0248:rs374029747
1 15777 rs2691317 A G . PASS AF=0.05 ES:SE:LP:AF:ID -0.999:0.0637:0.0054629:0.05:rs2691317
1 15820 rs1316988498 G T . PASS AF=0.542 ES:SE:LP:AF:ID 0.98876:0.0285:0.160145:0.542:rs1316988498
1 15903 rs557514207 GC G . PASS AF=0.184 ES:SE:LP:AF:ID 0.99661:0.0331:0.0370154:0.184:rs557514207
1 16141 rs529651976 C T . PASS AF=0.0132 ES:SE:LP:AF:ID 0.84688:0.3631:0.188961:0.0132:rs529651976
1 30923 rs1165072081 G T . PASS AF=0.979 ES:SE:LP:AF:ID 0.93193:0.1161:0.264641:0.979:rs1165072081
1 47159 rs540662756 T C . PASS AF=0.012 ES:SE:LP:AF:ID -1.05401:0.1725:0.118958:0.012:rs540662756
1 48180 rs529040510 G A . PASS AF=0.0139 ES:SE:LP:AF:ID 0.86286:0.3867:0.153106:0.0139:rs529040510
1 49298 rs10399793 T C . PASS AF=0.9319 ES:SE:LP:AF:ID -1.02778:0.0588:0.193006:0.9319:rs10399793
1 49554 rs539322794 A G . PASS AF=0.044 ES:SE:LP:AF:ID -0.99183:0.0736:0.0403386:0.044:rs539322794
1 51479 rs116400033 T A . PASS AF=0.0579 ES:SE:LP:AF:ID 0.95935:0.0641:0.286174:0.0579:rs116400033
1 52238 rs2691277 T G . PASS AF=0.9847 ES:SE:LP:AF:ID -1.42861:0.7441:0.199489:0.9847:rs2691277
1 54353 rs140052487 C A . PASS AF=0.0164 ES:SE:LP:AF:ID 0.96609:0.1067:0.12697:0.0164:rs140052487
1 54490 rs141149254 G A . PASS AF=0.0447 ES:SE:LP:AF:ID 0.90828:0.0728:0.729787:0.0447:rs141149254
1 54493 rs553010142 C T . PASS AF=0.0195 ES:SE:LP:AF:ID 1.09977:0.2729:0.138167:0.0195:rs553010142
1 54712 rs573184866 T C . PASS AF=0.013 ES:SE:LP:AF:ID -0.82663:0.3406:0.239427:0.013:rs573184866
1 54712 rs573184866 T TTTTC . PASS AF=0.672 ES:SE:LP:AF:ID 1.04133:0.0244:1.01341:0.672:rs573184866
1 54716 rs1166278911 C T . PASS AF=0.184 ES:SE:LP:AF:ID 0.98748:0.037:0.1346:0.184:rs1166278911
1 55164 rs3091274 C A . PASS AF=0.986 ES:SE:LP:AF:ID 0.73067:0.8067:0.15658:0.986:rs3091274
1 55326 rs3107975 T C . PASS AF=0.078 ES:SE:LP:AF:ID -0.99561:0.0517:0.0304909:0.078:rs3107975
1 55545 rs28396308 C T . PASS AF=0.194 ES:SE:LP:AF:ID 0.98886:0.0361:0.121306:0.194:rs28396308
1 57098 rs576772016 G A . PASS AF=0.0109 ES:SE:LP:AF:ID 1.19387:0.3289:0.229148:0.0109:rs576772016
1 57183 rs368339209 A G . PASS AF=0.013 ES:SE:LP:AF:ID -0.77375:0.1497:1.06233:0.013:rs368339209
1 57292 rs201418760 C T . PASS AF=0.076 ES:SE:LP:AF:ID 1.01157:0.0526:0.082547:0.076:rs201418760
1 58814 rs114420996 G A . PASS AF=0.0387 ES:SE:LP:AF:ID 1.00793:0.0767:0.0370154:0.0387:rs114420996
1 59040 rs62637815 T C . PASS AF=0.053 ES:SE:LP:AF:ID -0.90901:0.2247:0.173213:0.053:rs62637815
1 59040 rs62637815 T C . PASS AF=0.04 ES:SE:LP:AF:ID -0.9981:0.0766:0.0086853:0.04:rs62637815
1 60351 rs62637817 A G . PASS AF=0.046 ES:SE:LP:AF:ID -0.90946:0.2227:0.17386:0.046:rs62637817
1 60351 rs62637817 A G . PASS AF=0.037 ES:SE:LP:AF:ID -0.9984:0.0802:0.00696077:0.037:rs62637817
1 62509 rs534313866 T C . PASS AF=0.014 ES:SE:LP:AF:ID -0.73801:0.2901:0.530178:0.014:rs534313866
1 62777 rs3844233 A T . PASS AF=0.114 ES:SE:LP:AF:ID -1.02163:0.0435:0.205651:0.114:rs3844233
1 63093 rs200092917 G A . PASS AF=0.0298 ES:SE:LP:AF:ID 0.97453:0.0882:0.113566:0.0298:rs200092917
1 63268 rs28664618 T C . PASS AF=0.293 ES:SE:LP:AF:ID -1.02603:0.0314:0.383945:0.293:rs28664618
1 63671 rs80011619 G A . PASS AF=0.0621 ES:SE:LP:AF:ID 1.03087:0.0608:0.209715:0.0621:rs80011619