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": "2019-10-26T21:44:16.167884",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005903/EBI-a-GCST005903_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-GCST005903/EBI-a-GCST005903.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005903/EBI-a-GCST005903_data.vcf.gz; Date=Sat Oct 26 21:58:00 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST005903/ebi-a-GCST005903.vcf.gz; Date=Sat May 9 17:55:46 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-GCST005903/EBI-a-GCST005903.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-GCST005903/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 22:21:48 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005903/EBI-a-GCST005903.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 22:22:39 2019
Total time elapsed: 51.08sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9407,
"inflation_factor": 1.063,
"mean_EFFECT": 2.6375e-06,
"n": "-Inf",
"n_snps": 7640987,
"n_clumped_hits": 1,
"n_p_sig": 1,
"n_mono": 0,
"n_ns": 0,
"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": 67823,
"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 | 7620546 | 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 | 7625086 | 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 | 8.647951e+00 | 5.756866e+00 | 1.000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.880604e+07 | 5.641491e+07 | 828.000000 | 3.232435e+07 | 6.937042e+07 | 1.146648e+08 | 2.492235e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.600000e-06 | 1.363000e-03 | -0.014850 | -6.647000e-04 | 3.000000e-07 | 6.632000e-04 | 1.357900e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.170100e-03 | 6.662000e-04 | 0.000578 | 6.444000e-04 | 8.794000e-04 | 1.523200e-03 | 9.019100e-03 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.904710e-01 | 2.911157e-01 | 0.000000 | 2.358685e-01 | 4.867882e-01 | 7.427454e-01 | 9.999998e-01 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.904703e-01 | 2.911162e-01 | 0.000000 | 2.358681e-01 | 4.867868e-01 | 7.427417e-01 | 9.999998e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.524547e-01 | 2.608591e-01 | 0.010000 | 4.042760e-02 | 1.463300e-01 | 3.990610e-01 | 9.899980e-01 | ▇▂▂▁▁ |
| numeric | AF_reference | 67823 | 0.9911053 | NA | NA | NA | NA | NA | NA | NA | 2.517517e-01 | 2.524720e-01 | 0.000000 | 4.432910e-02 | 1.615420e-01 | 3.939700e-01 | 1.000000e+00 | ▇▃▂▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 15850 | rs575961614 | G | A | -0.0008724 | 0.0028700 | 0.7611320 | 0.7611359 | 0.0212510 | 0.0005990 | NA |
| 1 | 82103 | rs2020400 | T | C | -0.0038445 | 0.0014332 | 0.0073063 | 0.0073083 | 0.9248990 | NA | NA |
| 1 | 174747 | rs1399732465 | C | T | -0.0002499 | 0.0028791 | 0.9308271 | 0.9308266 | 0.0257265 | NA | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0014572 | 0.0019779 | 0.4612857 | 0.4612799 | 0.0747264 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0009324 | 0.0014281 | 0.5138425 | 0.5138417 | 0.9133710 | NA | NA |
| 1 | 568800 | rs375217967 | G | A | -0.0106020 | 0.0039277 | 0.0069518 | 0.0069488 | 0.0168716 | 0.0778754 | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0004826 | 0.0009646 | 0.6168080 | 0.6168087 | 0.1157600 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0029974 | 0.0014117 | 0.0337287 | 0.0337324 | 0.0670992 | 0.0315495 | NA |
| 1 | 717587 | rs144155419 | G | A | -0.0017362 | 0.0025679 | 0.4989649 | 0.4989666 | 0.0158778 | 0.0045926 | NA |
| 1 | 722670 | rs116030099 | T | C | -0.0007920 | 0.0011745 | 0.5001151 | 0.5001289 | 0.1015830 | 0.0413339 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51218377 | rs2519461 | G | C | 0.0002687 | 0.0011148 | 0.8095525 | 0.8095598 | 0.0736137 | 0.0826677 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0009554 | 0.0008605 | 0.2669070 | 0.2669014 | 0.1377200 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0002300 | 0.0011163 | 0.8367737 | 0.8367684 | 0.0738368 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | -0.0008092 | 0.0014992 | 0.5893591 | 0.5893571 | 0.0418842 | 0.0473243 | NA |
| 22 | 51220517 | rs9616980 | C | G | 0.0033668 | 0.0033587 | 0.3161331 | 0.3161448 | 0.0101005 | 0.0027955 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0009026 | 0.0014975 | 0.5466634 | 0.5466653 | 0.0496775 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0001888 | 0.0011170 | 0.8657769 | 0.8657847 | 0.0733326 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0012224 | 0.0013185 | 0.3538832 | 0.3538673 | 0.0543840 | 0.0880591 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0002009 | 0.0011210 | 0.8577742 | 0.8577829 | 0.0731347 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0004756 | 0.0026521 | 0.8576715 | 0.8576700 | 0.0199164 | NA | NA |
bcf preview
1 15850 rs575961614 G A . PASS AF=0.021251 ES:SE:LP:AF:ID -0.00087245:0.00287:0.11854:0.021251:rs575961614
1 82103 rs2020400 T C . PASS AF=0.924899 ES:SE:LP:AF:ID -0.0038445:0.0014332:2.1363:0.924899:rs2020400
1 174747 rs1399732465 C T . PASS AF=0.0257265 ES:SE:LP:AF:ID -0.00024992:0.0028791:0.031131:0.0257265:rs1399732465
1 234313 rs8179466 C T . PASS AF=0.0747264 ES:SE:LP:AF:ID -0.0014572:0.0019779:0.33603:0.0747264:rs8179466
1 546697 rs12025928 A G . PASS AF=0.913371 ES:SE:LP:AF:ID -0.00093236:0.0014281:0.28917:0.913371:rs12025928
1 568800 rs375217967 G A . PASS AF=0.0168716 ES:SE:LP:AF:ID -0.010602:0.0039277:2.1579:0.0168716:rs375217967
1 693731 rs12238997 A G . PASS AF=0.11576 ES:SE:LP:AF:ID -0.00048265:0.00096457:0.20985:0.11576:rs12238997
1 705882 rs72631875 G A . PASS AF=0.0670992 ES:SE:LP:AF:ID 0.0029974:0.0014117:1.472:0.0670992:rs72631875
1 717587 rs144155419 G A . PASS AF=0.0158778 ES:SE:LP:AF:ID -0.0017362:0.0025679:0.30193:0.0158778:rs144155419
1 722670 rs116030099 T C . PASS AF=0.101583 ES:SE:LP:AF:ID -0.00079195:0.0011745:0.30093:0.101583:rs116030099
1 724849 rs12126395 C A . PASS AF=0.0318946 ES:SE:LP:AF:ID 2.377e-05:0.0027913:0.0029608:0.0318946:rs12126395
1 730087 rs148120343 T C . PASS AF=0.0562198 ES:SE:LP:AF:ID 0.0017517:0.0013466:0.71374:0.0562198:rs148120343
1 731453 rs186002080 G A . PASS AF=0.0157877 ES:SE:LP:AF:ID 0.0049503:0.003048:0.9815:0.0157877:rs186002080
1 732989 rs369030935 C T . PASS AF=0.0262225 ES:SE:LP:AF:ID -0.0018152:0.0022222:0.383:0.0262225:rs369030935
1 734349 rs141242758 T C . PASS AF=0.120831 ES:SE:LP:AF:ID -0.00015661:0.00091604:0.06336:0.120831:rs141242758
1 736689 rs181876450 T C . PASS AF=0.0110481 ES:SE:LP:AF:ID -0.0033173:0.0032796:0.50617:0.0110481:rs181876450
1 753405 rs3115860 C A . PASS AF=0.871214 ES:SE:LP:AF:ID 0.0001301:0.0008697:0.054981:0.871214:rs3115860
1 753541 rs2073813 G A . PASS AF=0.128332 ES:SE:LP:AF:ID -9.7679e-05:0.00087141:0.040601:0.128332:rs2073813
1 754182 rs3131969 A G . PASS AF=0.870815 ES:SE:LP:AF:ID 0.0001618:0.00086818:0.06948:0.870815:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870915 ES:SE:LP:AF:ID 0.00016945:0.00086853:0.072983:0.870915:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870814 ES:SE:LP:AF:ID 0.00016048:0.0008682:0.068873:0.870814:rs3131967
1 755240 rs181660517 T G . PASS AF=0.0141299 ES:SE:LP:AF:ID -0.004239:0.0027824:0.89404:0.0141299:rs181660517
1 755890 rs3115858 A T . PASS AF=0.870871 ES:SE:LP:AF:ID 0.00013575:0.00086713:0.057694:0.870871:rs3115858
1 756604 rs3131962 A G . PASS AF=0.870441 ES:SE:LP:AF:ID 0.00010468:0.0008651:0.043982:0.870441:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869704 ES:SE:LP:AF:ID 0.0001457:0.00086335:0.062491:0.869704:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870579 ES:SE:LP:AF:ID 8.8529e-05:0.00086576:0.036896:0.870579:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870584 ES:SE:LP:AF:ID 8.9289e-05:0.00086583:0.037222:0.870584:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870593 ES:SE:LP:AF:ID 9.4151e-05:0.00086585:0.039334:0.870593:rs3131956
1 758626 rs3131954 C T . PASS AF=0.871051 ES:SE:LP:AF:ID 0.00010933:0.0008681:0.045866:0.871051:rs3131954
1 761732 rs2286139 C T . PASS AF=0.864333 ES:SE:LP:AF:ID -0.00018029:0.00086278:0.078585:0.864333:rs2286139
1 766007 rs61768174 A C . PASS AF=0.105001 ES:SE:LP:AF:ID 0.00024261:0.00096399:0.09621:0.105001:rs61768174
1 768253 rs2977608 A C . PASS AF=0.764108 ES:SE:LP:AF:ID 0.0010085:0.00068452:0.85184:0.764108:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105493 ES:SE:LP:AF:ID -0.0019113:0.00094592:1.3633:0.105493:rs12562034
1 769223 rs60320384 C G . PASS AF=0.128367 ES:SE:LP:AF:ID 2.8788e-05:0.00087081:0.011607:0.128367:rs60320384
1 769885 rs200025137 G A . PASS AF=0.0142669 ES:SE:LP:AF:ID -0.0023445:0.0043687:0.22805:0.0142669:rs200025137
1 770085 rs150344285 G C . PASS AF=0.0106405 ES:SE:LP:AF:ID -0.0010485:0.0040634:0.098875:0.0106405:rs150344285
1 771823 rs2977605 T C . PASS AF=0.870415 ES:SE:LP:AF:ID -5.3417e-05:0.0008665:0.021891:0.870415:rs2977605
1 771967 rs59066358 G A . PASS AF=0.128427 ES:SE:LP:AF:ID 5.5037e-05:0.00087024:0.022472:0.128427:rs59066358
1 772755 rs2905039 A C . PASS AF=0.870432 ES:SE:LP:AF:ID -8.2278e-05:0.00086655:0.034161:0.870432:rs2905039
1 772927 rs116390263 C T . PASS AF=0.0165685 ES:SE:LP:AF:ID 0.011348:0.0038888:2.4533:0.0165685:rs116390263
1 773124 rs142049927 T C . PASS AF=0.0127878 ES:SE:LP:AF:ID 0.013111:0.0044027:2.5372:0.0127878:rs142049927
1 773136 rs146709693 G T . PASS AF=0.0129655 ES:SE:LP:AF:ID 0.01276:0.0043724:2.4535:0.0129655:rs146709693
1 774760 rs187867912 C T . PASS AF=0.0133112 ES:SE:LP:AF:ID -0.0027877:0.0031569:0.42342:0.0133112:rs187867912
1 775125 rs147281566 C T . PASS AF=0.0125003 ES:SE:LP:AF:ID 0.011757:0.0042661:2.2325:0.0125003:rs147281566
1 777122 rs2980319 A T . PASS AF=0.871451 ES:SE:LP:AF:ID -0.00011555:0.00086807:0.048611:0.871451:rs2980319
1 777232 rs112618790 C T . PASS AF=0.0953182 ES:SE:LP:AF:ID -0.0019065:0.0010019:1.2436:0.0953182:rs112618790
1 778745 rs1055606 A G . PASS AF=0.12741 ES:SE:LP:AF:ID 6.8709e-05:0.00087131:0.028193:0.12741:rs1055606
1 779322 rs4040617 A G . PASS AF=0.127643 ES:SE:LP:AF:ID 7.5796e-05:0.00086998:0.031249:0.127643:rs4040617
1 780785 rs2977612 T A . PASS AF=0.870505 ES:SE:LP:AF:ID -6.0469e-05:0.00086604:0.024874:0.870505:rs2977612
1 781845 rs61768199 A G . PASS AF=0.102012 ES:SE:LP:AF:ID 0.00026702:0.00097651:0.1054:0.102012:rs61768199