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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"file_date": "2019-10-26T21:47:37.516526",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST004695/EBI-a-GCST004695_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/hg38/hg38.fa; 1.1.1",
"reference": "file:/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST004695/EBI-a-GCST004695.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST004695/EBI-a-GCST004695_data.vcf.gz; Date=Sat Oct 26 22:08:29 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST004695/ebi-a-GCST004695.vcf.gz; Date=Sat May 9 15:07:30 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/dev/ebi_gwas_import/processed/EBI-a-GCST004695/EBI-a-GCST004695.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST004695/ldsc.txt \
--snplist /data/ref/snplist.gz \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Sat Oct 26 22:33:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST004695/EBI-a-GCST004695.vcf.gz ...
and extracting SNPs specified in /data/ref/snplist.gz ...
Traceback (most recent call last):
File "./ldsc/ldsc.py", line 647, in <module>
sumstats.estimate_h2(args, log)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
args, log, args.h2)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 246, in _read_ld_sumstats
sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 165, in _read_sumstats
sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna, slh=args.snplist)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/parse.py", line 85, in sumstats
x = read_vcf(fh, alleles, slh)
File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/parse.py", line 161, in read_vcf
with gzip.open(slh) as f:
File "/mnt/storage/home/gh13047/mr-eve/conda/ldsc/lib/python2.7/gzip.py", line 34, in open
return GzipFile(filename, mode, compresslevel)
File "/mnt/storage/home/gh13047/mr-eve/conda/ldsc/lib/python2.7/gzip.py", line 94, in __init__
fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: '/data/ref/snplist.gz'
Analysis finished at Sat Oct 26 22:34:40 2019
Total time elapsed: 1.0m:23.64sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9508,
"inflation_factor": 1.0674,
"mean_EFFECT": 0.0002,
"n": "-Inf",
"n_snps": 12350997,
"n_clumped_hits": 1,
"n_p_sig": 13,
"n_mono": 0,
"n_ns": 1152723,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 409086,
"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": "NA",
"ldsc_nsnp_merge_regression_ld": "NA",
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": "NA",
"ldsc_intercept_se": "NA",
"ldsc_lambda_gc": "NA",
"ldsc_mean_chisq": "NA",
"ldsc_ratio": "NA"
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | TRUE |
| n_p_sig | FALSE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | TRUE |
| ldsc_intercept_beta | TRUE |
| 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 | 3 | 58 | 0 | 12329908 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 84 | 0 | 53978 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 103 | 0 | 30751 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 12330615 | 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 | 8.614830e+00 | 5.745101e+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 | 7.895960e+07 | 5.624860e+07 | 302.0000000 | 3.266944e+07 | 6.964686e+07 | 1.145157e+08 | 2.492383e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.824000e-04 | 5.173510e-02 | -0.7195880 | -1.410280e-02 | 5.660000e-05 | 1.427840e-02 | 8.439520e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.649620e-02 | 3.630420e-02 | 0.0080215 | 1.109320e-02 | 1.897570e-02 | 4.854660e-02 | 5.316400e-01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.898784e-01 | 2.907752e-01 | 0.0000000 | 2.362621e-01 | 4.858889e-01 | 7.416688e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.898784e-01 | 2.907752e-01 | 0.0000000 | 2.362622e-01 | 4.858895e-01 | 7.416684e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.018359e-01 | 2.570614e-01 | 0.0001000 | 1.038560e-02 | 7.460490e-02 | 3.181930e-01 | 9.990000e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 409086 | 0.9668236 | NA | NA | NA | NA | NA | NA | NA | 2.061026e-01 | 2.488387e-01 | 0.0000000 | 8.985600e-03 | 9.804310e-02 | 3.256790e-01 | 1.000000e+00 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 636285 | rs545945172 | T | C | -0.0022148 | 0.0175061 | 0.8993209 | 0.8993258 | 0.0994010 | 0.0956470 | NA |
| 1 | 649192 | rs201942322 | A | T | 0.0005529 | 0.0160628 | 0.9725401 | 0.9725391 | 0.1187170 | 0.1369810 | NA |
| 1 | 662622 | rs61769339 | G | A | -0.0022356 | 0.0162097 | 0.8902990 | 0.8903037 | 0.1104060 | 0.1475640 | NA |
| 1 | 692794 | rs530212009 | CA | C | 0.0008428 | 0.0162495 | 0.9586430 | 0.9586371 | 0.1107850 | 0.1894970 | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0002015 | 0.0162274 | 0.9900890 | 0.9900922 | 0.1110020 | 0.1417730 | NA |
| 1 | 693823 | rs61769351 | G | C | 0.0002920 | 0.0162105 | 0.9856320 | 0.9856298 | 0.1112730 | 0.1491610 | NA |
| 1 | 707522 | rs371890604 | G | C | -0.0007415 | 0.0166487 | 0.9644771 | 0.9644779 | 0.0996311 | 0.1293930 | NA |
| 1 | 711310 | rs200531508 | G | A | -0.0273880 | 0.0243888 | 0.2614460 | 0.2614483 | 0.0473102 | 0.0736821 | NA |
| 1 | 727841 | rs116587930 | G | A | -0.0060856 | 0.0207182 | 0.7689622 | 0.7689637 | 0.0570456 | 0.0127796 | NA |
| 1 | 729679 | rs4951859 | C | G | -0.0033949 | 0.0144097 | 0.8137440 | 0.8137439 | 0.8492110 | 0.6399760 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51228888 | rs201882178 | T | G | 0.0144727 | 0.0108295 | 0.1814099 | 0.1814139 | 0.3562200 | 0.2929310 | NA |
| 22 | 51228910 | rs145146472 | G | A | 0.0099101 | 0.0112879 | 0.3799750 | 0.3799762 | 0.3016550 | 0.2276360 | NA |
| 22 | 51229455 | rs534865882 | G | C | 0.0200754 | 0.0221471 | 0.3646918 | 0.3646939 | 0.0538600 | 0.0483227 | NA |
| 22 | 51229656 | rs564838851 | G | A | -0.0011422 | 0.0193412 | 0.9529030 | 0.9529089 | 0.0729923 | 0.0774760 | NA |
| 22 | 51229717 | rs200078515 | A | T | 0.0102401 | 0.0113622 | 0.3674582 | 0.3674593 | 0.2979490 | 0.2294330 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0003590 | 0.0192676 | 0.9851360 | 0.9851350 | 0.0716520 | 0.0730831 | NA |
| 22 | 51231220 | rs368226325 | A | G | 0.0226353 | 0.0221422 | 0.3066528 | 0.3066533 | 0.0538929 | 0.0601038 | NA |
| 22 | 51232581 | rs200771213 | T | C | 0.0092824 | 0.0113661 | 0.4141141 | 0.4141172 | 0.3014930 | 0.2270370 | NA |
| 22 | 51236013 | rs200507571 | A | AT | 0.0132580 | 0.0119087 | 0.2655792 | 0.2655780 | 0.2536450 | 0.1487620 | NA |
| 22 | 51237712 | rs370652263 | G | A | 0.0133237 | 0.0219508 | 0.5438649 | 0.5438641 | 0.0559220 | 0.0690895 | NA |
bcf preview
1 636285 rs545945172 T C . PASS AF=0.099401 ES:SE:LP:AF:ID -0.00221475:0.0175061:0.0460853:0.099401:rs545945172
1 649192 rs201942322 A T . PASS AF=0.118717 ES:SE:LP:AF:ID 0.000552944:0.0160628:0.0120925:0.118717:rs201942322
1 662622 rs61769339 G A . PASS AF=0.110406 ES:SE:LP:AF:ID -0.00223564:0.0162097:0.0504641:0.110406:rs61769339
1 692794 rs530212009 CA C . PASS AF=0.110785 ES:SE:LP:AF:ID 0.000842763:0.0162495:0.0183431:0.110785:rs530212009
1 693731 rs12238997 A G . PASS AF=0.111002 ES:SE:LP:AF:ID -0.00020151:0.0162274:0.00432576:0.111002:rs12238997
1 693823 rs61769351 G C . PASS AF=0.111273 ES:SE:LP:AF:ID 0.000291972:0.0162105:0.00628521:0.111273:rs61769351
1 707522 rs371890604 G C . PASS AF=0.0996311 ES:SE:LP:AF:ID -0.000741451:0.0166487:0.0157081:0.0996311:rs371890604
1 711310 rs200531508 G A . PASS AF=0.0473102 ES:SE:LP:AF:ID -0.027388:0.0243888:0.582618:0.0473102:rs200531508
1 727841 rs116587930 G A . PASS AF=0.0570456 ES:SE:LP:AF:ID -0.00608557:0.0207182:0.114095:0.0570456:rs116587930
1 729679 rs4951859 C G . PASS AF=0.849211 ES:SE:LP:AF:ID -0.00339491:0.0144097:0.0895122:0.849211:rs4951859
1 730087 rs148120343 T C . PASS AF=0.0571586 ES:SE:LP:AF:ID -0.00607242:0.0209301:0.112541:0.0571586:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122336 ES:SE:LP:AF:ID -0.00357003:0.0152424:0.0889421:0.122336:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121387 ES:SE:LP:AF:ID -0.00306034:0.0152591:0.0751839:0.121387:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121219 ES:SE:LP:AF:ID -0.00159336:0.01527:0.0376832:0.121219:rs141242758
1 735985 rs12405651 G A . PASS AF=0.0316763 ES:SE:LP:AF:ID 0.0122813:0.0300372:0.165813:0.0316763:rs12405651
1 736289 rs79010578 T A . PASS AF=0.12776 ES:SE:LP:AF:ID -0.000454262:0.0153586:0.0103705:0.12776:rs79010578
1 736736 rs10454457 A G . PASS AF=0.0318368 ES:SE:LP:AF:ID 0.0264094:0.0297754:0.425851:0.0318368:rs10454457
1 740285 rs193160839 G A . PASS AF=0.0259861 ES:SE:LP:AF:ID 0.0176279:0.0333405:0.224029:0.0259861:rs193160839
1 740578 rs7521650 G C . PASS AF=0.00122482 ES:SE:LP:AF:ID -0.0539653:0.14494:0.148956:0.00122482:rs7521650
1 745642 rs200097270 AC A . PASS AF=0.0301812 ES:SE:LP:AF:ID 0.0130176:0.0304654:0.174466:0.0301812:rs200097270
1 746211 rs201075335 A AG . PASS AF=0.0349713 ES:SE:LP:AF:ID 0.00885983:0.0276662:0.125643:0.0349713:rs201075335
1 746727 rs144595511 G A . PASS AF=0.0302968 ES:SE:LP:AF:ID 0.0124919:0.030348:0.167098:0.0302968:rs144595511
1 747040 rs531539579 G T . PASS AF=0.00102556 ES:SE:LP:AF:ID -0.218849:0.158439:0.776782:0.00102556:rs531539579
1 747753 rs200313238 TGC T . PASS AF=0.0300183 ES:SE:LP:AF:ID 0.014339:0.0305206:0.194847:0.0300183:rs200313238
1 749963 rs529266287 T TAA . PASS AF=0.866409 ES:SE:LP:AF:ID 0.00236495:0.014312:0.0611052:0.866409:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00153428 ES:SE:LP:AF:ID -0.193641:0.128345:0.881534:0.00153428:rs190826124
1 751343 rs28544273 T A . PASS AF=0.126315 ES:SE:LP:AF:ID -0.00354715:0.0142552:0.095019:0.126315:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.144794 ES:SE:LP:AF:ID -0.0133557:0.0140608:0.465734:0.144794:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12645 ES:SE:LP:AF:ID -0.00361786:0.0142355:0.0972429:0.12645:rs28527770
1 752307 rs201062411 AT A . PASS AF=0.0317886 ES:SE:LP:AF:ID 0.00844519:0.0278557:0.118185:0.0317886:rs201062411
1 752478 rs146277091 G A . PASS AF=0.0323063 ES:SE:LP:AF:ID 0.00912638:0.0275706:0.130398:0.0323063:rs146277091
1 752566 rs3094315 G A . PASS AF=0.84233 ES:SE:LP:AF:ID 0.00344282:0.0132231:0.0998602:0.84233:rs3094315
1 752593 rs372531941 T G . PASS AF=0.0299152 ES:SE:LP:AF:ID 0.00531348:0.0293797:0.0672828:0.0299152:rs372531941
1 752617 rs149886465 C A . PASS AF=0.0313675 ES:SE:LP:AF:ID 0.0134154:0.0281597:0.198057:0.0313675:rs149886465
1 752721 rs3131972 A G . PASS AF=0.840491 ES:SE:LP:AF:ID 0.00191043:0.0131088:0.0534844:0.840491:rs3131972
1 752894 rs3131971 T C . PASS AF=0.84097 ES:SE:LP:AF:ID 0.00140809:0.013136:0.0387517:0.84097:rs3131971
1 753405 rs3115860 C A . PASS AF=0.871913 ES:SE:LP:AF:ID 0.00488459:0.0141597:0.136605:0.871913:rs3115860
1 753425 rs3131970 T C . PASS AF=0.871906 ES:SE:LP:AF:ID 0.00482871:0.0141596:0.134844:0.871906:rs3131970
1 753474 rs2073814 C G . PASS AF=0.839141 ES:SE:LP:AF:ID 0.00394291:0.0131687:0.116554:0.839141:rs2073814
1 753541 rs2073813 G A . PASS AF=0.126845 ES:SE:LP:AF:ID -0.00347314:0.0141837:0.0933639:0.126845:rs2073813
1 754063 rs12184312 G T . PASS AF=0.0317288 ES:SE:LP:AF:ID 0.012797:0.0281516:0.187478:0.0317288:rs12184312
1 754105 rs12184325 C T . PASS AF=0.0359804 ES:SE:LP:AF:ID 0.00954918:0.0256945:0.148644:0.0359804:rs12184325
1 754121 rs12184335 T G . PASS AF=0.0292921 ES:SE:LP:AF:ID 0.00057366:0.0295347:0.00678251:0.0292921:rs12184335
1 754163 rs12184336 T C . PASS AF=0.0252888 ES:SE:LP:AF:ID 0.0136852:0.0337127:0.164443:0.0252888:rs12184336
1 754182 rs3131969 A G . PASS AF=0.87098 ES:SE:LP:AF:ID 0.00302061:0.0140721:0.080902:0.87098:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870968 ES:SE:LP:AF:ID 0.00311341:0.0140719:0.0836003:0.870968:rs3131968
1 754211 rs12184313 G A . PASS AF=0.0277097 ES:SE:LP:AF:ID 0.00560525:0.0313519:0.0664586:0.0277097:rs12184313
1 754334 rs3131967 T C . PASS AF=0.871303 ES:SE:LP:AF:ID 0.00357357:0.0140858:0.0970577:0.871303:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00520083 ES:SE:LP:AF:ID -0.00419048:0.071277:0.0208533:0.00520083:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00515344 ES:SE:LP:AF:ID 0.000954571:0.071285:0.00466497:0.00515344:rs142682604