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_20001_1003.vcf.gz --id UKB-b:12339 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20001_1003.txt.gz --cohort_cases 1436 --cohort_controls 461497 --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": "2019-09-13T07:56:42.479074",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-12339/ukb-b-12339.vcf.gz; Date=Sun May 10 03:23:43 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-12339/UKB-b-12339_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12339/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:37 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12339/UKB-b-12339_data.vcf.gz ...
Read summary statistics for 2386530 SNPs.
Dropped 266 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, 605896 SNPs remain.
After merging with regression SNP LD, 605896 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0039 (0.0014)
Lambda GC: 1.0272
Mean Chi^2: 1.0317
Intercept: 0.9896 (0.0117)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:42:09 2019
Total time elapsed: 32.49sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7542,
"inflation_factor": 1.0475,
"mean_EFFECT": 5.8467e-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": 18872,
"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": 605896,
"ldsc_nsnp_merge_regression_ld": 605896,
"ldsc_observed_scale_h2_beta": 0.0039,
"ldsc_observed_scale_h2_se": 0.0014,
"ldsc_intercept_beta": 0.9896,
"ldsc_intercept_se": 0.0117,
"ldsc_lambda_gc": 1.0272,
"ldsc_mean_chisq": 1.0317,
"ldsc_ratio": -0.3281
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| 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 | FALSE |
| 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 | 2386267 | 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 | 2386530 | 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 | 8.650403e+00 | 5.766934e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.860128e+07 | 5.664104e+07 | 5687.0000000 | 3.173272e+07 | 6.903234e+07 | 1.147898e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.000000e-07 | 1.246000e-04 | -0.0006278 | -8.350000e-05 | 1.000000e-07 | 8.390000e-05 | 6.704000e-04 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.223000e-04 | 6.100000e-06 | 0.0001115 | 1.171000e-04 | 1.206000e-04 | 1.264000e-04 | 2.415000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.942809e-01 | 2.900153e-01 | 0.0000001 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.942773e-01 | 2.899900e-01 | 0.0000001 | 2.419277e-01 | 4.927750e-01 | 7.451305e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.572352e-01 | 1.459011e-01 | 0.2437330 | 3.288370e-01 | 4.367015e-01 | 5.748680e-01 | 7.562670e-01 | ▇▆▅▅▃ |
| numeric | AF_reference | 18872 | 0.9920923 | NA | NA | NA | NA | NA | NA | NA | 4.384174e-01 | 1.728171e-01 | 0.0001997 | 3.027160e-01 | 4.243210e-01 | 5.646960e-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 | -0.0002588 | 0.0002053 | 0.2099999 | 0.2074566 | 0.623763 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0002904 | 0.0002034 | 0.1499999 | 0.1532863 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0000454 | 0.0002002 | 0.8200001 | 0.8208105 | 0.456851 | 0.4207270 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0000073 | 0.0001420 | 0.9599999 | 0.9592587 | 0.515650 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | 0.0000430 | 0.0001665 | 0.8000000 | 0.7961641 | 0.706753 | 0.6176120 | NA |
| 1 | 776546 | rs12124819 | A | G | -0.0000882 | 0.0001518 | 0.5600000 | 0.5612547 | 0.265390 | 0.0756789 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0001231 | 0.0001947 | 0.5300002 | 0.5270825 | 0.340397 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | 0.0000100 | 0.0001302 | 0.9400001 | 0.9386570 | 0.697259 | 0.6912940 | NA |
| 1 | 831489 | rs4970385 | C | T | -0.0000314 | 0.0001279 | 0.8100000 | 0.8058976 | 0.705403 | 0.6491610 | NA |
| 1 | 831909 | rs9697642 | C | T | -0.0000254 | 0.0001279 | 0.8400000 | 0.8425772 | 0.705448 | 0.6485620 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | 0.0001261 | 0.0001336 | 0.3500000 | 0.3454948 | 0.713658 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0001061 | 0.0001329 | 0.4199997 | 0.4248029 | 0.695471 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | 0.0001039 | 0.0001340 | 0.4400003 | 0.4382323 | 0.715505 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0000093 | 0.0001243 | 0.9400001 | 0.9406769 | 0.381826 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0000692 | 0.0001211 | 0.5700002 | 0.5679872 | 0.451063 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0000700 | 0.0001251 | 0.5800000 | 0.5758880 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | 0.0000691 | 0.0001416 | 0.6300007 | 0.6254846 | 0.254557 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0000838 | 0.0001404 | 0.5500004 | 0.5503150 | 0.271547 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0000055 | 0.0001334 | 0.9699999 | 0.9672156 | 0.331455 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0000107 | 0.0001365 | 0.9400001 | 0.9376890 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID -0.000258755:0.000205265:0.677781:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.000290392:0.000203353:0.823909:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID -4.53524e-05:0.000200229:0.0861861:0.456851:rs6702460
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID 7.25294e-06:0.000141981:0.0177288:0.51565:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID 4.29988e-05:0.000166459:0.09691:0.706753:rs3115847
1 776546 rs12124819 A G . PASS AF=0.26539 ES:SE:LP:AF:ID -8.81682e-05:0.000151758:0.251812:0.26539:rs12124819
1 814495 rs74461805 C A . PASS AF=0.340397 ES:SE:LP:AF:ID -0.000123131:0.000194684:0.275724:0.340397:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697259 ES:SE:LP:AF:ID 1.00237e-05:0.000130249:0.0268721:0.697259:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705403 ES:SE:LP:AF:ID -3.14261e-05:0.000127893:0.091515:0.705403:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705448 ES:SE:LP:AF:ID -2.53983e-05:0.000127888:0.0757207:0.705448:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705634 ES:SE:LP:AF:ID -2.75288e-05:0.000127894:0.0809219:0.705634:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705662 ES:SE:LP:AF:ID -2.80054e-05:0.000127908:0.0809219:0.705662:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730134 ES:SE:LP:AF:ID -1.15048e-05:0.000131393:0.0315171:0.730134:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294371 ES:SE:LP:AF:ID 2.76095e-05:0.000127902:0.0809219:0.294371:rs28765502
1 836896 rs28705752 T C . PASS AF=0.269503 ES:SE:LP:AF:ID 0.000129668:0.000130379:0.49485:0.269503:rs28705752
1 838555 rs4970383 C A . PASS AF=0.246197 ES:SE:LP:AF:ID 0.00011072:0.000134189:0.387216:0.246197:rs4970383
1 839103 rs28562941 A G . PASS AF=0.27001 ES:SE:LP:AF:ID 0.000124919:0.000130471:0.468521:0.27001:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400106 ES:SE:LP:AF:ID 4.19906e-05:0.000117971:0.142668:0.400106:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362599 ES:SE:LP:AF:ID -0.000169371:0.000146448:0.60206:0.362599:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590333 ES:SE:LP:AF:ID -5.39584e-06:0.000117625:0.0177288:0.590333:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603726 ES:SE:LP:AF:ID -2.87553e-06:0.000118285:0.00877392:0.603726:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603944 ES:SE:LP:AF:ID -6.55427e-06:0.000118268:0.0177288:0.603944:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589688 ES:SE:LP:AF:ID -4.4641e-06:0.000117816:0.0132283:0.589688:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589667 ES:SE:LP:AF:ID 5.81913e-07:0.000117763:-0:0.589667:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607674 ES:SE:LP:AF:ID 1.21251e-05:0.000118533:0.0362122:0.607674:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607833 ES:SE:LP:AF:ID 2.08452e-05:0.000118549:0.0655015:0.607833:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610318 ES:SE:LP:AF:ID 1.84797e-05:0.000118665:0.0555173:0.610318:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603286 ES:SE:LP:AF:ID -2.74196e-06:0.000118314:0.00877392:0.603286:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610338 ES:SE:LP:AF:ID 1.80496e-05:0.000118668:0.0555173:0.610338:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389935 ES:SE:LP:AF:ID -1.80696e-05:0.00011869:0.0555173:0.389935:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389918 ES:SE:LP:AF:ID -1.85279e-05:0.000118696:0.0555173:0.389918:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350351 ES:SE:LP:AF:ID -6.28064e-05:0.000121935:0.21467:0.350351:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610554 ES:SE:LP:AF:ID 2.30222e-05:0.000119334:0.0705811:0.610554:rs2880024
1 868418 rs28546443 C T . PASS AF=0.297865 ES:SE:LP:AF:ID -9.69151e-06:0.000131115:0.0268721:0.297865:rs28546443
1 870645 rs28576697 T C . PASS AF=0.291287 ES:SE:LP:AF:ID 0.000103695:0.00013007:0.366532:0.291287:rs28576697
1 871334 rs4072383 G T . PASS AF=0.720619 ES:SE:LP:AF:ID -6.32133e-05:0.000129265:0.207608:0.720619:rs4072383
1 872352 rs1806780 G C . PASS AF=0.267526 ES:SE:LP:AF:ID 6.27394e-05:0.000131017:0.200659:0.267526:rs1806780
1 873558 rs1110052 G T . PASS AF=0.715253 ES:SE:LP:AF:ID -3.97056e-05:0.000128237:0.119186:0.715253:rs1110052
1 875770 rs4970379 A G . PASS AF=0.600084 ES:SE:LP:AF:ID -1.58887e-05:0.000120326:0.05061:0.600084:rs4970379
1 881627 rs2272757 G A . PASS AF=0.65239 ES:SE:LP:AF:ID -9.67137e-05:0.00012155:0.366532:0.65239:rs2272757
1 882033 rs2272756 G A . PASS AF=0.243921 ES:SE:LP:AF:ID 0.000122033:0.000135375:0.431798:0.243921:rs2272756
1 890104 rs28631199 G A . PASS AF=0.246773 ES:SE:LP:AF:ID 7.23107e-05:0.000134843:0.229148:0.246773:rs28631199
1 891059 rs13303065 C T . PASS AF=0.652428 ES:SE:LP:AF:ID -9.74066e-05:0.000121531:0.376751:0.652428:rs13303065
1 891945 rs13303106 A G . PASS AF=0.65249 ES:SE:LP:AF:ID -0.000100377:0.000121673:0.387216:0.65249:rs13303106
1 900505 rs28705211 G C . PASS AF=0.271766 ES:SE:LP:AF:ID 0.000126593:0.000131537:0.468521:0.271766:rs28705211
1 903245 rs28690976 A G . PASS AF=0.566937 ES:SE:LP:AF:ID -0.000100548:0.000120848:0.387216:0.566937:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386683 ES:SE:LP:AF:ID 2.56252e-05:0.000120519:0.0809219:0.386683:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571412 ES:SE:LP:AF:ID 0.000119252:0.000116719:0.508638:0.571412:rs3829740
1 910394 rs28477686 C T . PASS AF=0.324456 ES:SE:LP:AF:ID 1.00612e-05:0.000126511:0.0268721:0.324456:rs28477686
1 912049 rs7367995 T C . PASS AF=0.58525 ES:SE:LP:AF:ID -2.20302e-05:0.000117902:0.0705811:0.58525:rs7367995