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": "2019-10-26T21:46:26.399375",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006488/EBI-a-GCST006488_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-GCST006488/EBI-a-GCST006488.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006488/EBI-a-GCST006488_data.vcf.gz; Date=Sat Oct 26 22:07:26 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST006488/ebi-a-GCST006488.vcf.gz; Date=Sat May 9 14:11:08 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-GCST006488/EBI-a-GCST006488.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-GCST006488/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 22:32:13 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006488/EBI-a-GCST006488.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 22:33:42 2019
Total time elapsed: 1.0m:28.63sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9508,
"inflation_factor": 1.0327,
"mean_EFFECT": 0.0001,
"n": "-Inf",
"n_snps": 12334883,
"n_clumped_hits": 1,
"n_p_sig": 3,
"n_mono": 0,
"n_ns": 1152127,
"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": 407227,
"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 | 12313789 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 84 | 0 | 53923 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 103 | 0 | 30755 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 12314500 | 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 | 8.614283e+00 | 5.745058e+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 | 7.896320e+07 | 5.625196e+07 | 302.0000000 | 3.266838e+07 | 6.964509e+07 | 1.145212e+08 | 2.492383e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.332000e-04 | 7.844720e-02 | -0.8850640 | -2.134660e-02 | -6.180000e-05 | 2.114640e-02 | 1.123890e+00 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.566300e-02 | 5.537170e-02 | 0.0121516 | 1.695440e-02 | 2.895710e-02 | 7.392770e-02 | 8.183050e-01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.950645e-01 | 2.898021e-01 | 0.0000000 | 2.433548e-01 | 4.930739e-01 | 7.457375e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.950645e-01 | 2.898021e-01 | 0.0000000 | 2.433543e-01 | 4.930744e-01 | 7.457367e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.021023e-01 | 2.571439e-01 | 0.0001000 | 1.046760e-02 | 7.496170e-02 | 3.187150e-01 | 9.997000e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 407227 | 0.9669311 | NA | NA | NA | NA | NA | NA | NA | 2.063575e-01 | 2.488954e-01 | 0.0000000 | 8.985600e-03 | 9.824280e-02 | 3.260780e-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 | 0.0026586 | 0.0267705 | 0.9208939 | 0.9208921 | 0.0992885 | 0.0956470 | NA |
| 1 | 649192 | rs201942322 | A | T | -0.0016872 | 0.0245566 | 0.9452211 | 0.9452248 | 0.1187560 | 0.1369810 | NA |
| 1 | 662622 | rs61769339 | G | A | -0.0061587 | 0.0248031 | 0.8038900 | 0.8038982 | 0.1104050 | 0.1475640 | NA |
| 1 | 692794 | rs530212009 | CA | C | 0.0087326 | 0.0249898 | 0.7267600 | 0.7267553 | 0.1100400 | 0.1894970 | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0032016 | 0.0248329 | 0.8974110 | 0.8974170 | 0.1110400 | 0.1417730 | NA |
| 1 | 693823 | rs61769351 | G | C | -0.0026634 | 0.0248133 | 0.9145160 | 0.9145215 | 0.1112540 | 0.1491610 | NA |
| 1 | 707522 | rs371890604 | G | C | -0.0065350 | 0.0255666 | 0.7982601 | 0.7982553 | 0.0989854 | 0.1293930 | NA |
| 1 | 711310 | rs200531508 | G | A | -0.0619112 | 0.0375357 | 0.0990672 | 0.0990667 | 0.0468910 | 0.0736821 | NA |
| 1 | 727841 | rs116587930 | G | A | 0.0259669 | 0.0316565 | 0.4120624 | 0.4120618 | 0.0570574 | 0.0127796 | NA |
| 1 | 729679 | rs4951859 | C | G | -0.0090671 | 0.0221096 | 0.6817388 | 0.6817338 | 0.8498070 | 0.6399760 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51228888 | rs201882178 | T | G | 0.0210959 | 0.0165433 | 0.2022418 | 0.2022409 | 0.3579800 | 0.2929310 | NA |
| 22 | 51228910 | rs145146472 | G | A | 0.0143712 | 0.0172212 | 0.4039969 | 0.4039957 | 0.3031780 | 0.2276360 | NA |
| 22 | 51229455 | rs534865882 | G | C | 0.0269719 | 0.0337720 | 0.4244935 | 0.4244952 | 0.0540839 | 0.0483227 | NA |
| 22 | 51229656 | rs564838851 | G | A | -0.0297192 | 0.0295401 | 0.3143822 | 0.3143853 | 0.0730354 | 0.0774760 | NA |
| 22 | 51229717 | rs200078515 | A | T | 0.0144199 | 0.0173388 | 0.4056038 | 0.4056037 | 0.2994930 | 0.2294330 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0279206 | 0.0294347 | 0.3428412 | 0.3428441 | 0.0717178 | 0.0730831 | NA |
| 22 | 51231220 | rs368226325 | A | G | 0.0370823 | 0.0337693 | 0.2721579 | 0.2721578 | 0.0540943 | 0.0601038 | NA |
| 22 | 51232581 | rs200771213 | T | C | 0.0107233 | 0.0173420 | 0.5363534 | 0.5363494 | 0.3029190 | 0.2270370 | NA |
| 22 | 51236013 | rs200507571 | A | AT | 0.0361637 | 0.0183200 | 0.0483816 | 0.0483816 | 0.2526090 | 0.1487620 | NA |
| 22 | 51237712 | rs370652263 | G | A | 0.0253221 | 0.0334989 | 0.4497032 | 0.4497041 | 0.0560945 | 0.0690895 | NA |
bcf preview
1 636285 rs545945172 T C . PASS AF=0.0992885 ES:SE:LP:AF:ID 0.00265858:0.0267705:0.0357904:0.0992885:rs545945172
1 649192 rs201942322 A T . PASS AF=0.118756 ES:SE:LP:AF:ID -0.00168715:0.0245566:0.0244666:0.118756:rs201942322
1 662622 rs61769339 G A . PASS AF=0.110405 ES:SE:LP:AF:ID -0.00615874:0.0248031:0.0948034:0.110405:rs61769339
1 692794 rs530212009 CA C . PASS AF=0.11004 ES:SE:LP:AF:ID 0.00873256:0.0249898:0.138609:0.11004:rs530212009
1 693731 rs12238997 A G . PASS AF=0.11104 ES:SE:LP:AF:ID -0.00320158:0.0248329:0.0470086:0.11104:rs12238997
1 693823 rs61769351 G C . PASS AF=0.111254 ES:SE:LP:AF:ID -0.00266339:0.0248133:0.0388087:0.111254:rs61769351
1 707522 rs371890604 G C . PASS AF=0.0989854 ES:SE:LP:AF:ID -0.00653497:0.0255666:0.0978556:0.0989854:rs371890604
1 711310 rs200531508 G A . PASS AF=0.046891 ES:SE:LP:AF:ID -0.0619112:0.0375357:1.00407:0.046891:rs200531508
1 727841 rs116587930 G A . PASS AF=0.0570574 ES:SE:LP:AF:ID 0.0259669:0.0316565:0.385037:0.0570574:rs116587930
1 729679 rs4951859 C G . PASS AF=0.849807 ES:SE:LP:AF:ID -0.00906711:0.0221096:0.166382:0.849807:rs4951859
1 730087 rs148120343 T C . PASS AF=0.057135 ES:SE:LP:AF:ID 0.0291491:0.0320143:0.440624:0.057135:rs148120343
1 731718 rs58276399 T C . PASS AF=0.1219 ES:SE:LP:AF:ID -0.00203978:0.0233833:0.0312916:0.1219:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121029 ES:SE:LP:AF:ID -0.00437206:0.023403:0.0696603:0.121029:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120888 ES:SE:LP:AF:ID -0.00237546:0.0234258:0.0365772:0.120888:rs141242758
1 735985 rs12405651 G A . PASS AF=0.0313526 ES:SE:LP:AF:ID 0.0439665:0.0462715:0.465952:0.0313526:rs12405651
1 736289 rs79010578 T A . PASS AF=0.126902 ES:SE:LP:AF:ID 0.00623551:0.0235923:0.101525:0.126902:rs79010578
1 736736 rs10454457 A G . PASS AF=0.0317702 ES:SE:LP:AF:ID 0.0696489:0.0455644:0.898363:0.0317702:rs10454457
1 740285 rs193160839 G A . PASS AF=0.0259252 ES:SE:LP:AF:ID 0.0640398:0.051203:0.675629:0.0259252:rs193160839
1 740578 rs7521650 G C . PASS AF=0.00119743 ES:SE:LP:AF:ID -0.0903846:0.224851:0.1626:0.00119743:rs7521650
1 745642 rs200097270 AC A . PASS AF=0.0298549 ES:SE:LP:AF:ID 0.0481331:0.0470187:0.514314:0.0298549:rs200097270
1 746211 rs201075335 A AG . PASS AF=0.0350586 ES:SE:LP:AF:ID 0.0565138:0.0422851:0.741391:0.0350586:rs201075335
1 746727 rs144595511 G A . PASS AF=0.0299841 ES:SE:LP:AF:ID 0.0472249:0.0468057:0.504464:0.0299841:rs144595511
1 747040 rs531539579 G T . PASS AF=0.00107045 ES:SE:LP:AF:ID -0.148386:0.235384:0.277011:0.00107045:rs531539579
1 747753 rs200313238 TGC T . PASS AF=0.0296914 ES:SE:LP:AF:ID 0.0481425:0.0470947:0.51334:0.0296914:rs200313238
1 749963 rs529266287 T TAA . PASS AF=0.867032 ES:SE:LP:AF:ID 6.48378e-05:0.0219578:0.00102441:0.867032:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00144191 ES:SE:LP:AF:ID -0.073336:0.207557:0.140356:0.00144191:rs190826124
1 751343 rs28544273 T A . PASS AF=0.125682 ES:SE:LP:AF:ID -0.00506922:0.0218846:0.0878726:0.125682:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.144444 ES:SE:LP:AF:ID -0.0139109:0.0215755:0.284757:0.144444:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12583 ES:SE:LP:AF:ID -0.00558393:0.0218504:0.097836:0.12583:rs28527770
1 752307 rs201062411 AT A . PASS AF=0.0319162 ES:SE:LP:AF:ID 0.0551262:0.0424897:0.711096:0.0319162:rs201062411
1 752478 rs146277091 G A . PASS AF=0.0324255 ES:SE:LP:AF:ID 0.0569802:0.0420401:0.756223:0.0324255:rs146277091
1 752566 rs3094315 G A . PASS AF=0.842711 ES:SE:LP:AF:ID -0.00285879:0.0202599:0.0516917:0.842711:rs3094315
1 752593 rs372531941 T G . PASS AF=0.0299511 ES:SE:LP:AF:ID 0.0572848:0.044879:0.69507:0.0299511:rs372531941
1 752617 rs149886465 C A . PASS AF=0.0313863 ES:SE:LP:AF:ID 0.0633655:0.0430377:0.850987:0.0313863:rs149886465
1 752721 rs3131972 A G . PASS AF=0.84089 ES:SE:LP:AF:ID -0.00526887:0.0200818:0.100707:0.84089:rs3131972
1 752894 rs3131971 T C . PASS AF=0.841383 ES:SE:LP:AF:ID -0.00554569:0.0201257:0.106299:0.841383:rs3131971
1 753405 rs3115860 C A . PASS AF=0.872511 ES:SE:LP:AF:ID 0.00754661:0.0217219:0.137703:0.872511:rs3115860
1 753425 rs3131970 T C . PASS AF=0.872505 ES:SE:LP:AF:ID 0.0074653:0.0217217:0.13603:0.872505:rs3131970
1 753474 rs2073814 C G . PASS AF=0.839557 ES:SE:LP:AF:ID -0.00204267:0.020175:0.0365163:0.839557:rs2073814
1 753541 rs2073813 G A . PASS AF=0.126248 ES:SE:LP:AF:ID -0.00534907:0.0217632:0.0937469:0.126248:rs2073813
1 754063 rs12184312 G T . PASS AF=0.0319213 ES:SE:LP:AF:ID 0.054793:0.0428949:0.695794:0.0319213:rs12184312
1 754105 rs12184325 C T . PASS AF=0.036205 ES:SE:LP:AF:ID 0.0549387:0.0391404:0.794717:0.036205:rs12184325
1 754121 rs12184335 T G . PASS AF=0.0293682 ES:SE:LP:AF:ID 0.0422172:0.0451115:0.456733:0.0293682:rs12184335
1 754163 rs12184336 T C . PASS AF=0.0254757 ES:SE:LP:AF:ID 0.0704632:0.051287:0.770902:0.0254757:rs12184336
1 754182 rs3131969 A G . PASS AF=0.871596 ES:SE:LP:AF:ID 0.0048104:0.0215896:0.0842399:0.871596:rs3131969
1 754192 rs3131968 A G . PASS AF=0.871577 ES:SE:LP:AF:ID 0.00498927:0.0215889:0.0876536:0.871577:rs3131968
1 754211 rs12184313 G A . PASS AF=0.0278996 ES:SE:LP:AF:ID 0.0527513:0.0477031:0.570566:0.0278996:rs12184313
1 754334 rs3131967 T C . PASS AF=0.871918 ES:SE:LP:AF:ID 0.0055349:0.0216085:0.0980847:0.871918:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00531385 ES:SE:LP:AF:ID -0.0788406:0.107062:0.335839:0.00531385:rs150578204
1 754458 rs142682604 G T . PASS AF=0.0052567 ES:SE:LP:AF:ID -0.0742218:0.107237:0.310821:0.0052567:rs142682604