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/d840c6af-8c99-4ad9-a614-9edf7c76f3e5/call-vcf/inputs/562856128/upload.txt.gz --id ieu-b-13 --json /data/cromwell-executions/qc/d840c6af-8c99-4ad9-a614-9edf7c76f3e5/call-vcf/inputs/562856128/ieu-b-13_data.json --ref /data/cromwell-executions/qc/d840c6af-8c99-4ad9-a614-9edf7c76f3e5/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/d840c6af-8c99-4ad9-a614-9edf7c76f3e5/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-13/ieu-b-13.vcf.gz --rm_chr_prefix --cohort_cases 793 --cohort_controls 29677; 1.2.1",
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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/d840c6af-8c99-4ad9-a614-9edf7c76f3e5/call-ldsc/inputs/562856128/ieu-b-13.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-13/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Fri Jun 26 15:35:13 2020
Reading summary statistics from /data/cromwell-executions/qc/d840c6af-8c99-4ad9-a614-9edf7c76f3e5/call-ldsc/inputs/562856128/ieu-b-13.vcf.gz ...
Read summary statistics for 4979752 SNPs.
Dropped 11863 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 950434 SNPs remain.
After merging with regression SNP LD, 950434 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1 (0.0209)
Lambda GC: 1.1234
Mean Chi^2: 1.1352
Intercept: 1.0671 (0.0094)
Ratio: 0.4967 (0.0695)
Analysis finished at Fri Jun 26 15:35:58 2020
Total time elapsed: 45.58sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9302,
"inflation_factor": 1.0966,
"mean_EFFECT": -0.0002,
"n": "-Inf",
"n_snps": 4979765,
"n_clumped_hits": 1,
"n_p_sig": 36,
"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": 29885,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NA",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 950434,
"ldsc_nsnp_merge_regression_ld": 950434,
"ldsc_observed_scale_h2_beta": 0.1,
"ldsc_observed_scale_h2_se": 0.0209,
"ldsc_intercept_beta": 1.0671,
"ldsc_intercept_se": 0.0094,
"ldsc_lambda_gc": 1.1234,
"ldsc_mean_chisq": 1.1352,
"ldsc_ratio": 0.4963
}
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 | 1 | 0.9999998 | 3 | 35 | 0 | 4979761 | 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 | 4979765 | 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 | 8.644392e+00 | 5.872053e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.978735e+07 | 5.501566e+07 | 3.30120e+04 | 3.476682e+07 | 7.127038e+07 | 1.143898e+08 | 2.492190e+08 | ▇▇▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.697000e-04 | 2.796600e-03 | -2.54956e-02 | -1.694500e-03 | -1.623000e-04 | 1.362400e-03 | 3.033860e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.437600e-03 | 1.164100e-03 | 1.24810e-03 | 1.632800e-03 | 1.966200e-03 | 2.785000e-03 | 7.928700e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.830677e-01 | 2.936216e-01 | 0.00000e+00 | 2.200002e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▆▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.830696e-01 | 2.935949e-01 | 0.00000e+00 | 2.241804e-01 | 4.770561e-01 | 7.377522e-01 | 9.999996e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.073463e-01 | 2.581766e-01 | 1.00004e-02 | 8.982740e-02 | 2.267680e-01 | 4.773370e-01 | 9.899970e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 29885 | 0.9939987 | NA | NA | NA | NA | NA | NA | NA | 3.086322e-01 | 2.467945e-01 | 1.99700e-04 | 1.046330e-01 | 2.382190e-01 | 4.694490e-01 | 1.000000e+00 | ▇▅▃▂▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1029805 | rs6689308 | A | G | -0.0002761 | 0.0020872 | 0.8900000 | 0.8947730 | 0.1637450 | 0.3156950 | NA |
| 1 | 1030565 | rs6687776 | C | T | 0.0019525 | 0.0021001 | 0.3500000 | 0.3525245 | 0.1639200 | 0.3067090 | NA |
| 1 | 1030633 | rs6678318 | G | A | 0.0019580 | 0.0021001 | 0.3500000 | 0.3511744 | 0.1639270 | 0.3065100 | NA |
| 1 | 1031973 | rs9651270 | C | T | 0.0001754 | 0.0021186 | 0.9299999 | 0.9340006 | 0.1603530 | 0.3107030 | NA |
| 1 | 1033596 | rs6604964 | T | C | 0.0002016 | 0.0021203 | 0.9199999 | 0.9242563 | 0.1602200 | 0.3117010 | NA |
| 1 | 1033670 | rs6604966 | T | C | 0.0002176 | 0.0021210 | 0.9199999 | 0.9182859 | 0.1601740 | 0.3158950 | NA |
| 1 | 1033680 | rs6604967 | T | A | 0.0002142 | 0.0021210 | 0.9199999 | 0.9195594 | 0.1601600 | 0.3117010 | NA |
| 1 | 1033994 | rs6698368 | C | T | 0.0001947 | 0.0021205 | 0.9299999 | 0.9268292 | 0.1602230 | 0.3115020 | NA |
| 1 | 1034200 | rs77977351 | T | C | 0.0001904 | 0.0021206 | 0.9299999 | 0.9284452 | 0.1602280 | 0.3115020 | NA |
| 1 | 1036601 | rs72910156 | C | T | 0.0019948 | 0.0051187 | 0.6999999 | 0.6967490 | 0.0236596 | 0.0399361 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 139314056 | rs5955415 | C | G | 0.0004511 | 0.0021835 | 0.8400000 | 0.8363403 | 0.096641 | 0.125033 | NA |
| 23 | 139314798 | rs62609008 | C | A | 0.0004898 | 0.0021927 | 0.8200001 | 0.8232340 | 0.095730 | 0.106755 | NA |
| 23 | 139315107 | rs62609010 | T | A | 0.0004446 | 0.0021914 | 0.8400000 | 0.8392386 | 0.095819 | 0.107020 | NA |
| 23 | 139316769 | rs73230748 | T | C | 0.0004673 | 0.0021873 | 0.8300000 | 0.8308150 | 0.096218 | 0.121060 | NA |
| 23 | 139317055 | rs62609011 | C | A | 0.0004592 | 0.0021870 | 0.8300000 | 0.8337079 | 0.096261 | 0.116026 | NA |
| 23 | 139317165 | rs28877369 | C | G | 0.0004882 | 0.0021878 | 0.8200001 | 0.8234152 | 0.096185 | 0.116291 | NA |
| 23 | 139317337 | rs55757628 | A | G | 0.0004428 | 0.0021908 | 0.8400000 | 0.8398213 | 0.095890 | 0.107285 | NA |
| 23 | 139319949 | rs140616281 | A | G | 0.0004841 | 0.0021926 | 0.8300000 | 0.8252665 | 0.095817 | 0.116291 | NA |
| 23 | 139320136 | rs76621315 | C | G | 0.0004583 | 0.0021860 | 0.8300000 | 0.8339257 | 0.096383 | 0.114437 | NA |
| 23 | 139325995 | rs62609013 | G | A | 0.0006239 | 0.0021876 | 0.7800007 | 0.7755102 | 0.096224 | 0.101987 | NA |
bcf preview
1 1029805 rs891281851 A G . PASS AF=0.163745 ES:SE:LP:AF:ID -0.000276064:0.00208717:0.05061:0.163745:rs891281851
1 1030565 rs6687776 C T . PASS AF=0.16392 ES:SE:LP:AF:ID 0.00195248:0.00210011:0.455932:0.16392:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.163927 ES:SE:LP:AF:ID 0.00195798:0.00210013:0.455932:0.163927:rs6678318
1 1031973 rs9651270 C T . PASS AF=0.160353 ES:SE:LP:AF:ID 0.00017545:0.00211864:0.0315171:0.160353:rs9651270
1 1033596 rs6604964 T C . PASS AF=0.16022 ES:SE:LP:AF:ID 0.000201582:0.00212027:0.0362122:0.16022:rs6604964
1 1033670 rs1370950991 T C . PASS AF=0.160174 ES:SE:LP:AF:ID 0.000217604:0.00212104:0.0362122:0.160174:rs1370950991
1 1033680 rs1370950991 T A . PASS AF=0.16016 ES:SE:LP:AF:ID 0.000214197:0.002121:0.0362122:0.16016:rs1370950991
1 1033994 rs6698368 C T . PASS AF=0.160223 ES:SE:LP:AF:ID 0.000194736:0.0021205:0.0315171:0.160223:rs6698368
1 1034200 rs77977351 T C . PASS AF=0.160228 ES:SE:LP:AF:ID 0.000190435:0.00212063:0.0315171:0.160228:rs77977351
1 1036601 rs72910156 C T . PASS AF=0.0236596 ES:SE:LP:AF:ID 0.00199483:0.00511872:0.154902:0.0236596:rs72910156
1 1036860 rs11579922 A C . PASS AF=0.127096 ES:SE:LP:AF:ID 0.00113951:0.00232002:0.207608:0.127096:rs11579922
1 1036959 rs1162868282 T C . PASS AF=0.113129 ES:SE:LP:AF:ID -0.00031334:0.00241821:0.0457575:0.113129:rs1162868282
1 1037303 rs11260592 T C . PASS AF=0.140276 ES:SE:LP:AF:ID 0.000555086:0.00220113:0.09691:0.140276:rs11260592
1 1037313 rs11260593 A G . PASS AF=0.140356 ES:SE:LP:AF:ID 0.00057446:0.00220117:0.102373:0.140356:rs11260593
1 1037367 rs11260594 G A . PASS AF=0.140275 ES:SE:LP:AF:ID 0.000555403:0.00220138:0.09691:0.140275:rs11260594
1 1038088 rs66622470 G C . PASS AF=0.140345 ES:SE:LP:AF:ID 0.000517725:0.00220005:0.091515:0.140345:rs66622470
1 1039098 rs11260595 C A . PASS AF=0.0239936 ES:SE:LP:AF:ID 0.00204845:0.00507491:0.161151:0.0239936:rs11260595
1 1039268 rs9329410 T C . PASS AF=0.140509 ES:SE:LP:AF:ID 0.000490203:0.00219794:0.0861861:0.140509:rs9329410
1 1039817 rs1205065516 A G . PASS AF=0.140411 ES:SE:LP:AF:ID 0.000477474:0.0021992:0.0809219:0.140411:rs1205065516
1 1040026 rs6671356 T C . PASS AF=0.140809 ES:SE:LP:AF:ID 0.000527144:0.00219476:0.091515:0.140809:rs6671356
1 1040472 rs6664124 C T . PASS AF=0.140711 ES:SE:LP:AF:ID 0.000514504:0.00219601:0.091515:0.140711:rs6664124
1 1040794 rs6687681 G A . PASS AF=0.140688 ES:SE:LP:AF:ID 0.000515373:0.00219621:0.091515:0.140688:rs6687681
1 1040824 rs6656379 T C . PASS AF=0.140832 ES:SE:LP:AF:ID 0.000485709:0.00219517:0.0861861:0.140832:rs6656379
1 1040985 rs6697379 C G . PASS AF=0.140663 ES:SE:LP:AF:ID 0.000511094:0.00219627:0.0861861:0.140663:rs6697379
1 1041700 rs6604968 A G . PASS AF=0.140802 ES:SE:LP:AF:ID 0.000486372:0.00219552:0.0861861:0.140802:rs6604968
1 1041786 rs6604969 T C . PASS AF=0.140813 ES:SE:LP:AF:ID 0.000469544:0.00219529:0.0809219:0.140813:rs6604969
1 1042483 rs12733365 C T . PASS AF=0.140691 ES:SE:LP:AF:ID 0.0005558:0.00219598:0.09691:0.140691:rs12733365
1 1042527 rs1486993720 G C . PASS AF=0.112983 ES:SE:LP:AF:ID 0.000180128:0.00242195:0.0268721:0.112983:rs1486993720
1 1042673 rs897825316 C T . PASS AF=0.141838 ES:SE:LP:AF:ID 0.000803035:0.0022024:0.142668:0.141838:rs897825316
1 1042927 rs4970354 G T . PASS AF=0.140671 ES:SE:LP:AF:ID 0.000517212:0.00219581:0.091515:0.140671:rs4970354
1 1043053 rs4970355 A G . PASS AF=0.140599 ES:SE:LP:AF:ID 0.000541264:0.00219628:0.091515:0.140599:rs4970355
1 1045473 rs11586034 G A . PASS AF=0.112154 ES:SE:LP:AF:ID -3.06475e-05:0.0024311:0.00436481:0.112154:rs11586034
1 1046073 rs11590188 C A . PASS AF=0.138956 ES:SE:LP:AF:ID -0.000104305:0.00220954:0.0177288:0.138956:rs11590188
1 1046164 rs386627439 C T . PASS AF=0.140648 ES:SE:LP:AF:ID 0.00052048:0.00219601:0.091515:0.140648:rs386627439
1 1046717 rs34820586 G C . PASS AF=0.113041 ES:SE:LP:AF:ID 0.000131023:0.00242136:0.0177288:0.113041:rs34820586
1 1046861 rs12723165 G A . PASS AF=0.113032 ES:SE:LP:AF:ID 0.000132165:0.00242133:0.0177288:0.113032:rs12723165
1 1047374 rs12743678 T A . PASS AF=0.140259 ES:SE:LP:AF:ID 0.000508593:0.00219855:0.0861861:0.140259:rs12743678
1 1048501 rs7518814 G A . PASS AF=0.138961 ES:SE:LP:AF:ID -0.000113566:0.00220955:0.0177288:0.138961:rs7518814
1 1048955 rs4970405 A G . PASS AF=0.104843 ES:SE:LP:AF:ID 0.000145248:0.00250113:0.0222764:0.104843:rs4970405
1 1048989 rs4970406 A G . PASS AF=0.113774 ES:SE:LP:AF:ID 0.000258244:0.00241804:0.0409586:0.113774:rs4970406
1 1049083 rs4970407 C A . PASS AF=0.112936 ES:SE:LP:AF:ID -9.3446e-05:0.00242331:0.0132283:0.112936:rs4970407
1 1049950 rs12726255 A G . PASS AF=0.138987 ES:SE:LP:AF:ID -0.000303235:0.00221346:0.05061:0.138987:rs12726255
1 1052946 rs12755848 G T . PASS AF=0.111942 ES:SE:LP:AF:ID 8.51253e-05:0.00243859:0.0132283:0.111942:rs12755848
1 1053452 rs4970409 G A . PASS AF=0.111945 ES:SE:LP:AF:ID 8.39459e-05:0.0024384:0.0132283:0.111945:rs4970409
1 1053670 rs4970410 G A . PASS AF=0.137847 ES:SE:LP:AF:ID -0.000365274:0.00222509:0.0604807:0.137847:rs4970410
1 1053724 rs4970411 A G . PASS AF=0.137468 ES:SE:LP:AF:ID -0.000229367:0.00222852:0.0362122:0.137468:rs4970411
1 1054552 rs12567697 G A . PASS AF=0.110961 ES:SE:LP:AF:ID 0.000179506:0.00244924:0.0268721:0.110961:rs12567697
1 1054893 rs4970412 T C . PASS AF=0.137635 ES:SE:LP:AF:ID -0.000483916:0.00222708:0.0809219:0.137635:rs4970412
1 1055653 rs34808604 C G . PASS AF=0.111102 ES:SE:LP:AF:ID 0.000149253:0.00244726:0.0222764:0.111102:rs34808604
1 1055797 rs76744376 A G . PASS AF=0.111602 ES:SE:LP:AF:ID 0.000290676:0.00244376:0.0409586:0.111602:rs76744376