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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"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_20002_1165.vcf.gz --id UKB-b:131 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20002_1165.txt.gz --cohort_cases 1006 --cohort_controls 461927 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-13T08:01:28.003266",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-131/ukb-b-131.vcf.gz; Date=Sun May 10 09:34:50 2020"
}
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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-131/UKB-b-131_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-131/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-131/UKB-b-131_data.vcf.gz ...
Read summary statistics for 1354429 SNPs.
Dropped 110 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 350799 SNPs remain.
After merging with regression SNP LD, 350799 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0016 (0.0013)
Lambda GC: 1.0064
Mean Chi^2: 1.0114
Intercept: 1.0287 (0.0116)
Ratio: 2.5251 (1.0203)
Analysis finished at Thu Oct 17 14:42:37 2019
Total time elapsed: 27.58sQC metrics
Metrics
Metrics
{
"af_correlation": 0.5543,
"inflation_factor": 1,
"mean_EFFECT": 8.7933e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 10812,
"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": 350799,
"ldsc_nsnp_merge_regression_ld": 350799,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0287,
"ldsc_intercept_se": 0.0116,
"ldsc_lambda_gc": 1.0064,
"ldsc_mean_chisq": 1.0114,
"ldsc_ratio": 2.5175
}
Flags
| name | value |
|---|---|
| af_correlation | TRUE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | FALSE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | FALSE |
| n_p_sig | FALSE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | TRUE |
| ldsc_intercept_beta | FALSE |
| 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 | 0 | 1.0000000 | 4 | 58 | 0 | 1354321 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 1354429 | 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 | 8.681191e+00 | 5.769216e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.844265e+07 | 5.650137e+07 | 1.23330e+04 | 3.161956e+07 | 6.889402e+07 | 1.143316e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.000000e-07 | 9.950000e-05 | -4.75800e-04 | -6.630000e-05 | 8.000000e-07 | 6.730000e-05 | 5.440000e-04 | ▁▃▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.880000e-05 | 2.500000e-06 | 9.34000e-05 | 9.740000e-05 | 9.840000e-05 | 9.990000e-05 | 1.827000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.993713e-01 | 2.898135e-01 | 1.80000e-06 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.993733e-01 | 2.897835e-01 | 1.80000e-06 | 2.480420e-01 | 4.992188e-01 | 7.513803e-01 | 9.999993e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.851504e-01 | 8.752480e-02 | 3.47913e-01 | 4.080270e-01 | 4.776180e-01 | 5.579900e-01 | 6.520870e-01 | ▇▇▆▆▅ |
| numeric | AF_reference | 10812 | 0.9920173 | NA | NA | NA | NA | NA | NA | NA | 4.627861e-01 | 1.412985e-01 | 1.99700e-04 | 3.578270e-01 | 4.574680e-01 | 5.634980e-01 | 1.000000e+00 | ▁▆▇▃▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | -0.0001943 | 0.0001719 | 0.2599998 | 0.2583162 | 0.623763 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0001750 | 0.0001703 | 0.2999998 | 0.3039649 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0000056 | 0.0001676 | 0.9699999 | 0.9733741 | 0.456851 | 0.420727 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0001283 | 0.0001189 | 0.2800000 | 0.2805222 | 0.515650 | 0.275160 | NA |
| 1 | 840753 | rs4970382 | T | C | 0.0001181 | 0.0000988 | 0.2300001 | 0.2319648 | 0.400106 | 0.468850 | NA |
| 1 | 843405 | rs11516185 | A | G | 0.0001502 | 0.0001226 | 0.2200002 | 0.2206898 | 0.362599 | 0.375399 | NA |
| 1 | 850218 | rs6664536 | T | A | 0.0000143 | 0.0000985 | 0.8800001 | 0.8847759 | 0.590333 | 0.345248 | NA |
| 1 | 850371 | rs6679046 | G | T | -0.0000036 | 0.0000990 | 0.9699999 | 0.9710288 | 0.603726 | 0.508786 | NA |
| 1 | 850780 | rs6657440 | C | T | -0.0000050 | 0.0000990 | 0.9599999 | 0.9595964 | 0.603944 | 0.560304 | NA |
| 1 | 852037 | rs4970463 | G | A | 0.0000168 | 0.0000986 | 0.8600001 | 0.8645724 | 0.589688 | 0.345048 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51158017 | rs6010065 | G | C | -0.0001215 | 0.0000971 | 0.2099999 | 0.2107169 | 0.461423 | 0.547524 | NA |
| 22 | 51158499 | rs8136930 | T | G | -0.0001171 | 0.0000972 | 0.2300001 | 0.2282395 | 0.461648 | 0.544728 | NA |
| 22 | 51161019 | rs5770994 | C | T | 0.0000879 | 0.0000969 | 0.3599996 | 0.3642917 | 0.482193 | 0.425719 | NA |
| 22 | 51163039 | rs715584 | G | T | -0.0000995 | 0.0000984 | 0.3100002 | 0.3120088 | 0.426984 | 0.473642 | NA |
| 22 | 51164109 | rs5770995 | G | C | -0.0001029 | 0.0000978 | 0.2900000 | 0.2927688 | 0.452716 | 0.510982 | NA |
| 22 | 51164115 | rs5770996 | C | T | -0.0001212 | 0.0000977 | 0.2200002 | 0.2150092 | 0.456928 | 0.514776 | NA |
| 22 | 51174048 | rs9628245 | G | C | 0.0000847 | 0.0001104 | 0.4400003 | 0.4432812 | 0.380130 | 0.433107 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0000290 | 0.0001041 | 0.7800007 | 0.7804480 | 0.381826 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0000255 | 0.0001014 | 0.8000000 | 0.8012626 | 0.451063 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0000139 | 0.0001047 | 0.8900000 | 0.8945112 | 0.386333 | 0.422923 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID -0.000194275:0.000171867:0.585027:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.000175028:0.000170266:0.522879:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID -5.59562e-06:0.00016765:0.0132283:0.456851:rs6702460
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID 0.000128289:0.00011888:0.552842:0.51565:rs12029736
1 840753 rs4970382 T C . PASS AF=0.400106 ES:SE:LP:AF:ID 0.000118068:9.87758e-05:0.638272:0.400106:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362599 ES:SE:LP:AF:ID 0.000150171:0.000122619:0.657577:0.362599:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590333 ES:SE:LP:AF:ID 1.42724e-05:9.84863e-05:0.0555173:0.590333:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603726 ES:SE:LP:AF:ID -3.5969e-06:9.90392e-05:0.0132283:0.603726:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603944 ES:SE:LP:AF:ID -5.01661e-06:9.9025e-05:0.0177288:0.603944:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589688 ES:SE:LP:AF:ID 1.68248e-05:9.86464e-05:0.0655015:0.589688:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589667 ES:SE:LP:AF:ID 1.62542e-05:9.86021e-05:0.0604807:0.589667:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607674 ES:SE:LP:AF:ID -1.43352e-05:9.92466e-05:0.05061:0.607674:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607833 ES:SE:LP:AF:ID -1.49702e-05:9.92601e-05:0.0555173:0.607833:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610318 ES:SE:LP:AF:ID -3.16917e-06:9.93575e-05:0.0132283:0.610318:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603286 ES:SE:LP:AF:ID -5.29223e-06:9.90634e-05:0.0177288:0.603286:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610338 ES:SE:LP:AF:ID -3.45394e-06:9.93594e-05:0.0132283:0.610338:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389935 ES:SE:LP:AF:ID 9.71436e-06:9.93783e-05:0.0362122:0.389935:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389918 ES:SE:LP:AF:ID 9.6288e-06:9.93833e-05:0.0362122:0.389918:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350351 ES:SE:LP:AF:ID -6.43049e-06:0.000102095:0.0222764:0.350351:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610554 ES:SE:LP:AF:ID 3.2474e-05:9.99176e-05:0.124939:0.610554:rs2880024
1 875770 rs4970379 A G . PASS AF=0.600084 ES:SE:LP:AF:ID 0.000105169:0.000100748:0.522879:0.600084:rs4970379
1 903245 rs28690976 A G . PASS AF=0.566937 ES:SE:LP:AF:ID 0.00014045:0.000101185:0.769551:0.566937:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386683 ES:SE:LP:AF:ID -1.16367e-05:0.00010091:0.0409586:0.386683:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571412 ES:SE:LP:AF:ID -0.000171528:9.77277e-05:1.10237:0.571412:rs3829740
1 912049 rs7367995 T C . PASS AF=0.58525 ES:SE:LP:AF:ID 7.91325e-05:9.87186e-05:0.376751:0.58525:rs7367995
1 913889 rs2340596 G A . PASS AF=0.599213 ES:SE:LP:AF:ID 7.30316e-05:9.88793e-05:0.337242:0.599213:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602521 ES:SE:LP:AF:ID 5.66639e-05:9.9179e-05:0.244125:0.602521:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600078 ES:SE:LP:AF:ID 7.43474e-05:9.89884e-05:0.346787:0.600078:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584292 ES:SE:LP:AF:ID 7.41771e-05:9.84332e-05:0.346787:0.584292:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589106 ES:SE:LP:AF:ID 6.87966e-05:9.85835e-05:0.309804:0.589106:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584205 ES:SE:LP:AF:ID 7.66725e-05:9.8387e-05:0.356547:0.584205:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589331 ES:SE:LP:AF:ID 6.77661e-05:9.85078e-05:0.309804:0.589331:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583932 ES:SE:LP:AF:ID 0.000164228:0.000101874:0.958607:0.583932:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567888 ES:SE:LP:AF:ID 0.000128544:9.83053e-05:0.721246:0.567888:rs13303278
1 924528 rs34712273 C A . PASS AF=0.578492 ES:SE:LP:AF:ID 9.4452e-05:9.85876e-05:0.468521:0.578492:rs34712273
1 930533 rs3128110 C G . PASS AF=0.386078 ES:SE:LP:AF:ID -0.000104223:9.98472e-05:0.522879:0.386078:rs3128110
1 930567 rs3121574 A G . PASS AF=0.38612 ES:SE:LP:AF:ID -0.000104569:9.98497e-05:0.537602:0.38612:rs3121574
1 930751 rs3128111 C G . PASS AF=0.385075 ES:SE:LP:AF:ID -0.000109323:9.99103e-05:0.568636:0.385075:rs3128111
1 931166 rs2710880 A G . PASS AF=0.386762 ES:SE:LP:AF:ID -0.000104405:9.9866e-05:0.522879:0.386762:rs2710880
1 931362 rs2799060 G A . PASS AF=0.385568 ES:SE:LP:AF:ID -0.000111474:9.99146e-05:0.585027:0.385568:rs2799060
1 933790 rs9442392 G A . PASS AF=0.578607 ES:SE:LP:AF:ID 0.000114325:9.85543e-05:0.60206:0.578607:rs9442392
1 936111 rs1936360 C T . PASS AF=0.573546 ES:SE:LP:AF:ID 0.000115407:9.85306e-05:0.619789:0.573546:rs1936360
1 940005 rs2799056 A G . PASS AF=0.399259 ES:SE:LP:AF:ID -0.000152766:9.95012e-05:0.920819:0.399259:rs2799056
1 940096 rs4503294 C T . PASS AF=0.565311 ES:SE:LP:AF:ID 0.000152612:9.82487e-05:0.920819:0.565311:rs4503294
1 941284 rs3128116 C T . PASS AF=0.397393 ES:SE:LP:AF:ID -0.000149309:9.95227e-05:0.886057:0.397393:rs3128116
1 941334 rs57683598 G A . PASS AF=0.397396 ES:SE:LP:AF:ID -0.000149429:9.95289e-05:0.886057:0.397396:rs57683598
1 941539 rs9778087 C T . PASS AF=0.399588 ES:SE:LP:AF:ID -0.000146304:9.95324e-05:0.853872:0.399588:rs9778087
1 943687 rs2465140 G C . PASS AF=0.395208 ES:SE:LP:AF:ID -0.000114715:9.95739e-05:0.60206:0.395208:rs2465140
1 943968 rs13303313 C T . PASS AF=0.569677 ES:SE:LP:AF:ID 0.000118882:9.8299e-05:0.638272:0.569677:rs13303313
1 944564 rs3128117 T C . PASS AF=0.396438 ES:SE:LP:AF:ID -0.000113825:9.94244e-05:0.60206:0.396438:rs3128117