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_20004_1558.vcf.gz --id UKB-b:13003 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20004_1558.txt.gz --cohort_cases 1581 --cohort_controls 461352 --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": "2019-09-13T13:29:51.583514",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-13003/ukb-b-13003.vcf.gz; Date=Sun May 10 04:30:31 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-13003/UKB-b-13003_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13003/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-13003/UKB-b-13003_data.vcf.gz ...
Read summary statistics for 2632981 SNPs.
Dropped 315 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, 663416 SNPs remain.
After merging with regression SNP LD, 663416 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0012 (0.0011)
Lambda GC: 1.0058
Mean Chi^2: 1.0074
Intercept: 1.0206 (0.0099)
Ratio: 2.7675 (1.3331)
Analysis finished at Thu Oct 17 14:42:48 2019
Total time elapsed: 38.46sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7833,
"inflation_factor": 1,
"mean_EFFECT": -3.6293e-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": 20861,
"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": 663416,
"ldsc_nsnp_merge_regression_ld": 663416,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0206,
"ldsc_intercept_se": 0.0099,
"ldsc_lambda_gc": 1.0058,
"ldsc_mean_chisq": 1.0074,
"ldsc_ratio": 2.7838
}
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 | 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 | 1.000000 | 4 | 58 | 0 | 2632669 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 2632981 | 0.000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 8.662119e+00 | 5.768767e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.854344e+07 | 5.663204e+07 | 5687.0000000 | 3.170924e+07 | 6.891217e+07 | 1.147155e+08 | 2.492013e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | -4.000000e-07 | 1.309000e-04 | -0.0007128 | -8.800000e-05 | -1.000000e-06 | 8.730000e-05 | 6.371000e-04 | ▁▁▇▂▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 1.298000e-04 | 7.700000e-06 | 0.0001170 | 1.231000e-04 | 1.275000e-04 | 1.352000e-04 | 2.631000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.989164e-01 | 2.900068e-01 | 0.0000002 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.989170e-01 | 2.899819e-01 | 0.0000002 | 2.473524e-01 | 4.979989e-01 | 7.506224e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.483911e-01 | 1.580908e-01 | 0.2213790 | 3.093000e-01 | 4.238620e-01 | 5.744440e-01 | 7.786210e-01 | ▇▆▅▃▃ |
| numeric | AF_reference | 20861 | 0.992077 | NA | NA | NA | NA | NA | NA | NA | 4.305375e-01 | 1.805633e-01 | 0.0001997 | 2.873400e-01 | 4.131390e-01 | 5.628990e-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 | 0.0000188 | 0.0002154 | 0.9299999 | 0.9305373 | 0.623763 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0001526 | 0.0002133 | 0.4700002 | 0.4743657 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0000091 | 0.0002101 | 0.9699999 | 0.9654726 | 0.456851 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0002702 | 0.0002399 | 0.2599998 | 0.2600836 | 0.240960 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0001403 | 0.0001490 | 0.3500000 | 0.3461187 | 0.515650 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | 0.0000496 | 0.0001746 | 0.7800007 | 0.7762502 | 0.706753 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | 0.0000120 | 0.0001425 | 0.9299999 | 0.9328162 | 0.761304 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0005051 | 0.0001592 | 0.0015000 | 0.0015107 | 0.265390 | 0.0756789 | NA |
| 1 | 808631 | rs11240779 | G | A | -0.0000682 | 0.0001447 | 0.6400000 | 0.6374280 | 0.772626 | 0.4534740 | NA |
| 1 | 808928 | rs11240780 | C | T | -0.0000727 | 0.0001450 | 0.6200004 | 0.6158175 | 0.772854 | 0.4522760 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | 0.0001199 | 0.0001402 | 0.3900004 | 0.3925338 | 0.713658 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0001912 | 0.0001395 | 0.1700000 | 0.1703894 | 0.695471 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | 0.0001335 | 0.0001406 | 0.3400001 | 0.3426238 | 0.715505 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0002172 | 0.0001304 | 0.0959997 | 0.0957425 | 0.381826 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0002464 | 0.0001271 | 0.0530005 | 0.0525463 | 0.451063 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0001453 | 0.0001312 | 0.2700001 | 0.2683066 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0001350 | 0.0001485 | 0.3599996 | 0.3635138 | 0.254557 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0001082 | 0.0001473 | 0.4600002 | 0.4625860 | 0.271547 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0001320 | 0.0001399 | 0.3500000 | 0.3453753 | 0.331455 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0001529 | 0.0001433 | 0.2900000 | 0.2856982 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID 1.87719e-05:0.000215351:0.0315171:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -0.000152625:0.000213344:0.327902:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID -9.09322e-06:0.000210067:0.0132283:0.456851:rs6702460
1 534192 rs6680723 C T . PASS AF=0.24096 ES:SE:LP:AF:ID 0.000270229:0.000239949:0.585027:0.24096:rs6680723
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID -0.000140339:0.000148957:0.455932:0.51565:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID 4.96337e-05:0.000174638:0.107905:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761304 ES:SE:LP:AF:ID 1.20161e-05:0.000142536:0.0315171:0.761304:rs2977608
1 776546 rs12124819 A G . PASS AF=0.26539 ES:SE:LP:AF:ID 0.000505129:0.000159215:2.82391:0.26539:rs12124819
1 808631 rs11240779 G A . PASS AF=0.772626 ES:SE:LP:AF:ID -6.8202e-05:0.000144711:0.19382:0.772626:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772854 ES:SE:LP:AF:ID -7.27365e-05:0.000144955:0.207608:0.772854:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340397 ES:SE:LP:AF:ID 0.000159585:0.000204249:0.366532:0.340397:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697259 ES:SE:LP:AF:ID 0.000194119:0.000136649:0.79588:0.697259:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705403 ES:SE:LP:AF:ID 0.000149277:0.000134177:0.568636:0.705403:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705448 ES:SE:LP:AF:ID 0.000152263:0.000134172:0.585027:0.705448:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705634 ES:SE:LP:AF:ID 0.000150368:0.000134178:0.585027:0.705634:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705662 ES:SE:LP:AF:ID 0.000150093:0.000134192:0.585027:0.705662:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730134 ES:SE:LP:AF:ID 0.00012364:0.000137849:0.431798:0.730134:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294371 ES:SE:LP:AF:ID -0.000150718:0.000134186:0.585027:0.294371:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236696 ES:SE:LP:AF:ID -0.000185654:0.000142863:0.721246:0.236696:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236684 ES:SE:LP:AF:ID -0.000185329:0.000142864:0.721246:0.236684:rs28752186
1 833641 rs28594623 T C . PASS AF=0.239743 ES:SE:LP:AF:ID -0.000210299:0.000142406:0.853872:0.239743:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236686 ES:SE:LP:AF:ID -0.000186022:0.000142863:0.721246:0.236686:rs28484835
1 834832 rs4411087 G C . PASS AF=0.237171 ES:SE:LP:AF:ID -0.000183799:0.000142753:0.69897:0.237171:rs4411087
1 835499 rs4422948 A G . PASS AF=0.241155 ES:SE:LP:AF:ID -0.000173235:0.000141757:0.657577:0.241155:rs4422948
1 836896 rs28705752 T C . PASS AF=0.269503 ES:SE:LP:AF:ID -0.000186593:0.000136785:0.769551:0.269503:rs28705752
1 838555 rs4970383 C A . PASS AF=0.246197 ES:SE:LP:AF:ID -0.000161539:0.000140783:0.60206:0.246197:rs4970383
1 839103 rs28562941 A G . PASS AF=0.27001 ES:SE:LP:AF:ID -0.000198626:0.000136881:0.823909:0.27001:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400106 ES:SE:LP:AF:ID -0.000135226:0.000123767:0.568636:0.400106:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237094 ES:SE:LP:AF:ID -0.000163824:0.000143761:0.60206:0.237094:rs1574243
1 842362 rs28540380 C T . PASS AF=0.235321 ES:SE:LP:AF:ID -0.000208476:0.000145911:0.823909:0.235321:rs28540380
1 843405 rs11516185 A G . PASS AF=0.362599 ES:SE:LP:AF:ID 8.70865e-05:0.000153643:0.244125:0.362599:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590333 ES:SE:LP:AF:ID 1.33285e-05:0.000123404:0.0409586:0.590333:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603726 ES:SE:LP:AF:ID 2.00899e-05:0.000124097:0.0604807:0.603726:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603944 ES:SE:LP:AF:ID 2.3566e-05:0.000124079:0.0705811:0.603944:rs6657440
1 851204 rs28552953 G C . PASS AF=0.224621 ES:SE:LP:AF:ID 2.61878e-05:0.0001468:0.0655015:0.224621:rs28552953
1 852037 rs4970463 G A . PASS AF=0.589688 ES:SE:LP:AF:ID 1.34816e-05:0.000123605:0.0409586:0.589688:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589667 ES:SE:LP:AF:ID 1.70965e-05:0.000123549:0.05061:0.589667:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607674 ES:SE:LP:AF:ID 2.01e-05:0.000124357:0.0604807:0.607674:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607833 ES:SE:LP:AF:ID 1.80895e-05:0.000124374:0.0555173:0.607833:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610318 ES:SE:LP:AF:ID 4.63644e-05:0.000124496:0.148742:0.610318:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603286 ES:SE:LP:AF:ID 1.03803e-05:0.000124127:0.0315171:0.603286:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610338 ES:SE:LP:AF:ID 4.64918e-05:0.000124498:0.148742:0.610338:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389935 ES:SE:LP:AF:ID -3.59622e-05:0.000124522:0.113509:0.389935:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389918 ES:SE:LP:AF:ID -3.61335e-05:0.000124528:0.113509:0.389918:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350351 ES:SE:LP:AF:ID -1.07853e-05:0.000127926:0.0315171:0.350351:rs4040605
1 858801 rs7418179 A G . PASS AF=0.765845 ES:SE:LP:AF:ID -5.89444e-05:0.000143603:0.167491:0.765845:rs7418179
1 860416 rs61464428 G A . PASS AF=0.766637 ES:SE:LP:AF:ID -8.38563e-05:0.000143674:0.251812:0.766637:rs61464428
1 860688 rs60837925 G A . PASS AF=0.766103 ES:SE:LP:AF:ID -8.49049e-05:0.000143576:0.259637:0.766103:rs60837925
1 861630 rs2879816 G A . PASS AF=0.766255 ES:SE:LP:AF:ID -9.35533e-05:0.00014361:0.29243:0.766255:rs2879816
1 862866 rs3892970 C T . PASS AF=0.763121 ES:SE:LP:AF:ID -6.4699e-05:0.000143479:0.187087:0.763121:rs3892970