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_20087_161.vcf.gz --id UKB-b:20057 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20087_161.txt.gz --cohort_cases 1367 --cohort_controls 63582 --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": "2019-09-13T13:37:24.691676",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-20057/ukb-b-20057.vcf.gz; Date=Sun May 10 02:05:09 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-20057/UKB-b-20057_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20057/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:04 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20057/UKB-b-20057_data.vcf.gz ...
Read summary statistics for 2256438 SNPs.
Dropped 245 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, 574736 SNPs remain.
After merging with regression SNP LD, 574736 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0066 (0.0096)
Lambda GC: 1.021
Mean Chi^2: 1.0135
Intercept: 1.0036 (0.0106)
Ratio: 0.2675 (0.7863)
Analysis finished at Thu Oct 17 14:42:43 2019
Total time elapsed: 38.74sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7368,
"inflation_factor": 1.0475,
"mean_EFFECT": 5.634e-06,
"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": 17849,
"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": 574736,
"ldsc_nsnp_merge_regression_ld": 574736,
"ldsc_observed_scale_h2_beta": 0.0066,
"ldsc_observed_scale_h2_se": 0.0096,
"ldsc_intercept_beta": 1.0036,
"ldsc_intercept_se": 0.0106,
"ldsc_lambda_gc": 1.021,
"ldsc_mean_chisq": 1.0135,
"ldsc_ratio": 0.2667
}
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 | 2256195 | 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 | 2256438 | 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 | 8.651070e+00 | 5.767843e+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 | 7.863329e+07 | 5.665330e+07 | 5687.0000000 | 3.174414e+07 | 6.910419e+07 | 1.147457e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.600000e-06 | 8.469000e-04 | -0.0048199 | -5.668000e-04 | 8.000000e-06 | 5.789000e-04 | 5.665100e-03 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.377000e-04 | 3.810000e-05 | 0.0007690 | 8.061000e-04 | 8.272000e-04 | 8.632000e-04 | 1.640200e-03 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.956149e-01 | 2.894250e-01 | 0.0000054 | 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 | 4.956125e-01 | 2.893963e-01 | 0.0000054 | 2.434642e-01 | 4.937891e-01 | 7.464360e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.613952e-01 | 1.390974e-01 | 0.2560360 | 3.391392e-01 | 4.427730e-01 | 5.742298e-01 | 7.439640e-01 | ▇▆▅▅▃ |
| numeric | AF_reference | 17849 | 0.9920897 | NA | NA | NA | NA | NA | NA | NA | 4.420940e-01 | 1.687078e-01 | 0.0001997 | 3.105030e-01 | 4.297120e-01 | 5.650960e-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 | 0.0012143 | 0.0014174 | 0.3900004 | 0.3915988 | 0.623812 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0008129 | 0.0014132 | 0.5700002 | 0.5651625 | 0.399144 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0012261 | 0.0013900 | 0.3800004 | 0.3777404 | 0.455916 | 0.4207270 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0009457 | 0.0009799 | 0.3300000 | 0.3344684 | 0.513304 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0015145 | 0.0011480 | 0.1900002 | 0.1870621 | 0.705804 | 0.6176120 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0030768 | 0.0010514 | 0.0034000 | 0.0034282 | 0.263729 | 0.0756789 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0005023 | 0.0013418 | 0.7099994 | 0.7081368 | 0.340108 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | -0.0007456 | 0.0008977 | 0.4100001 | 0.4062234 | 0.696612 | 0.6912940 | NA |
| 1 | 831489 | rs4970385 | C | T | -0.0007475 | 0.0008815 | 0.4000000 | 0.3964050 | 0.705031 | 0.6491610 | NA |
| 1 | 831909 | rs9697642 | C | T | -0.0007414 | 0.0008815 | 0.4000000 | 0.4002722 | 0.705083 | 0.6485620 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51174662 | rs1858748 | T | C | -0.0011505 | 0.0009448 | 0.2200002 | 0.2232974 | 0.736049 | 0.732827 | NA |
| 22 | 51180501 | rs5770999 | T | C | -0.0008741 | 0.0009182 | 0.3400001 | 0.3411146 | 0.712571 | 0.636981 | NA |
| 22 | 51181919 | rs9616825 | G | C | -0.0015800 | 0.0009144 | 0.0840001 | 0.0839984 | 0.695031 | 0.619409 | NA |
| 22 | 51182485 | rs6009961 | A | G | -0.0007693 | 0.0009212 | 0.4000000 | 0.4036361 | 0.714237 | 0.638379 | NA |
| 22 | 51186143 | rs2879914 | T | C | -0.0008171 | 0.0008579 | 0.3400001 | 0.3408915 | 0.380077 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0005284 | 0.0008357 | 0.5300002 | 0.5271550 | 0.449547 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0017689 | 0.0008612 | 0.0400000 | 0.0399652 | 0.386693 | 0.422923 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0001202 | 0.0009688 | 0.9000000 | 0.9012510 | 0.271468 | 0.167133 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0019625 | 0.0009209 | 0.0329997 | 0.0330920 | 0.331351 | 0.372404 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0026780 | 0.0009409 | 0.0044000 | 0.0044222 | 0.298393 | 0.205072 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623812 ES:SE:LP:AF:ID 0.0012143:0.00141738:0.408935:0.623812:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399144 ES:SE:LP:AF:ID 0.000812888:0.00141325:0.244125:0.399144:rs2462492
1 91536 rs6702460 G T . PASS AF=0.455916 ES:SE:LP:AF:ID 0.0012261:0.00139003:0.420216:0.455916:rs6702460
1 706368 rs12029736 A G . PASS AF=0.513304 ES:SE:LP:AF:ID -0.000945724:0.00097987:0.481486:0.513304:rs12029736
1 763394 rs3115847 G A . PASS AF=0.705804 ES:SE:LP:AF:ID -0.00151454:0.00114797:0.721246:0.705804:rs3115847
1 776546 rs12124819 A G . PASS AF=0.263729 ES:SE:LP:AF:ID 0.00307679:0.00105136:2.46852:0.263729:rs12124819
1 814495 rs74461805 C A . PASS AF=0.340108 ES:SE:LP:AF:ID -0.000502327:0.00134183:0.148742:0.340108:rs74461805
1 830181 rs28444699 A G . PASS AF=0.696612 ES:SE:LP:AF:ID -0.000745606:0.000897717:0.387216:0.696612:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705031 ES:SE:LP:AF:ID -0.000747526:0.000881455:0.39794:0.705031:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705083 ES:SE:LP:AF:ID -0.000741422:0.000881454:0.39794:0.705083:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705261 ES:SE:LP:AF:ID -0.000757783:0.000881413:0.408935:0.705261:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705286 ES:SE:LP:AF:ID -0.000759039:0.000881536:0.408935:0.705286:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730154 ES:SE:LP:AF:ID -0.00131981:0.000905854:0.823909:0.730154:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294729 ES:SE:LP:AF:ID 0.00075712:0.000881508:0.408935:0.294729:rs28765502
1 836896 rs28705752 T C . PASS AF=0.269687 ES:SE:LP:AF:ID 0.000856311:0.000899409:0.468521:0.269687:rs28705752
1 839103 rs28562941 A G . PASS AF=0.270067 ES:SE:LP:AF:ID 0.000879126:0.000900146:0.481486:0.270067:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400406 ES:SE:LP:AF:ID 0.000300792:0.00081372:0.148742:0.400406:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362367 ES:SE:LP:AF:ID -0.000125542:0.00101241:0.0457575:0.362367:rs11516185
1 850218 rs6664536 T A . PASS AF=0.589315 ES:SE:LP:AF:ID -0.000129167:0.000809308:0.0604807:0.589315:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603035 ES:SE:LP:AF:ID -2.71949e-05:0.000813179:0.0132283:0.603035:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603381 ES:SE:LP:AF:ID -3.15929e-05:0.000813194:0.0132283:0.603381:rs6657440
1 852037 rs4970463 G A . PASS AF=0.588673 ES:SE:LP:AF:ID -0.000186553:0.000810463:0.0861861:0.588673:rs4970463
1 852063 rs28436996 G A . PASS AF=0.588649 ES:SE:LP:AF:ID -0.000182383:0.000810098:0.0861861:0.588649:rs28436996
1 852875 rs13303369 C T . PASS AF=0.606715 ES:SE:LP:AF:ID 2.16177e-05:0.000814532:0.00877392:0.606715:rs13303369
1 853954 rs1806509 C A . PASS AF=0.60688 ES:SE:LP:AF:ID 4.43498e-05:0.000814617:0.0177288:0.60688:rs1806509
1 854777 rs13303019 A G . PASS AF=0.609504 ES:SE:LP:AF:ID -2.6128e-05:0.000815431:0.0132283:0.609504:rs13303019
1 854978 rs13303057 A C . PASS AF=0.602505 ES:SE:LP:AF:ID 3.58069e-08:0.000813321:-0:0.602505:rs13303057
1 855075 rs6673914 C G . PASS AF=0.609473 ES:SE:LP:AF:ID -2.48664e-05:0.000815323:0.00877392:0.609473:rs6673914
1 856099 rs28534711 T G . PASS AF=0.390835 ES:SE:LP:AF:ID 3.54174e-05:0.000815654:0.0132283:0.390835:rs28534711
1 856108 rs28742275 A G . PASS AF=0.390777 ES:SE:LP:AF:ID 4.01367e-05:0.000815739:0.0177288:0.390777:rs28742275
1 856476 rs4040605 A G . PASS AF=0.352504 ES:SE:LP:AF:ID -0.000147214:0.000837332:0.0655015:0.352504:rs4040605
1 866893 rs2880024 T C . PASS AF=0.608083 ES:SE:LP:AF:ID -0.000316121:0.000822869:0.154902:0.608083:rs2880024
1 868418 rs28546443 C T . PASS AF=0.301063 ES:SE:LP:AF:ID 0.000523866:0.000901238:0.251812:0.301063:rs28546443
1 870645 rs28576697 T C . PASS AF=0.293389 ES:SE:LP:AF:ID 0.000905753:0.000891387:0.508638:0.293389:rs28576697
1 871334 rs4072383 G T . PASS AF=0.717959 ES:SE:LP:AF:ID -0.000997105:0.00088676:0.585027:0.717959:rs4072383
1 872352 rs1806780 G C . PASS AF=0.269716 ES:SE:LP:AF:ID 0.000886176:0.000897769:0.49485:0.269716:rs1806780
1 873558 rs1110052 G T . PASS AF=0.71249 ES:SE:LP:AF:ID -0.000898234:0.000880122:0.508638:0.71249:rs1110052
1 875770 rs4970379 A G . PASS AF=0.598464 ES:SE:LP:AF:ID 0.000168822:0.000829022:0.0757207:0.598464:rs4970379
1 881627 rs2272757 G A . PASS AF=0.65048 ES:SE:LP:AF:ID -5.47287e-05:0.000837464:0.0222764:0.65048:rs2272757
1 891059 rs13303065 C T . PASS AF=0.650626 ES:SE:LP:AF:ID -0.000133764:0.000837382:0.0604807:0.650626:rs13303065
1 891945 rs13303106 A G . PASS AF=0.650689 ES:SE:LP:AF:ID -0.000115179:0.00083834:0.05061:0.650689:rs13303106
1 900505 rs28705211 G C . PASS AF=0.273272 ES:SE:LP:AF:ID 0.000922465:0.000903755:0.508638:0.273272:rs28705211
1 903245 rs28690976 A G . PASS AF=0.565133 ES:SE:LP:AF:ID 0.00112971:0.000832462:0.769551:0.565133:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386217 ES:SE:LP:AF:ID 0.000892494:0.000830722:0.552842:0.386217:rs3892467
1 909238 rs3829740 G C . PASS AF=0.572164 ES:SE:LP:AF:ID 0.000758729:0.000803679:0.455932:0.572164:rs3829740
1 910394 rs28477686 C T . PASS AF=0.322663 ES:SE:LP:AF:ID -0.000283867:0.000872954:0.124939:0.322663:rs28477686
1 912049 rs7367995 T C . PASS AF=0.585242 ES:SE:LP:AF:ID 0.00118453:0.000811471:0.853872:0.585242:rs7367995
1 913889 rs2340596 G A . PASS AF=0.600025 ES:SE:LP:AF:ID 0.000947338:0.000813084:0.619789:0.600025:rs2340596
1 914333 rs13302979 C G . PASS AF=0.60338 ES:SE:LP:AF:ID 0.00133535:0.000815842:1:0.60338:rs13302979
1 914852 rs13303368 G C . PASS AF=0.60101 ES:SE:LP:AF:ID 0.00102019:0.000814341:0.677781:0.60101:rs13303368