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": "2019-10-26T09:28:11.534002",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005898/EBI-a-GCST005898_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-GCST005898/EBI-a-GCST005898.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005898/EBI-a-GCST005898_data.vcf.gz; Date=Sat Oct 26 09:42:42 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST005898/ebi-a-GCST005898.vcf.gz; Date=Sun May 10 07:17:45 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-GCST005898/EBI-a-GCST005898.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-GCST005898/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 10:06:33 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005898/EBI-a-GCST005898.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 10:06:35 2019
Total time elapsed: 2.64sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9232,
"inflation_factor": 0.9609,
"mean_EFFECT": 0.0214,
"n": "-Inf",
"n_snps": 417240,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 31121,
"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": 45133,
"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 | 5 | 12 | 0 | 411883 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 42 | 0 | 2749 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 37 | 0 | 1764 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 411887 | 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 | 2.300000e+01 | 0.000000e+00 | 2.300000e+01 | 2.300000e+01 | 2.300000e+01 | 2.300000e+01 | 2.300000e+01 | ▁▁▇▁▁ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.750939e+07 | 4.628064e+07 | 2.699555e+06 | 3.289829e+07 | 8.290992e+07 | 1.190964e+08 | 1.549302e+08 | ▇▅▆▆▆ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.137210e-02 | 7.158957e-01 | -2.229160e+01 | -4.360000e-02 | 7.000000e-03 | 7.730000e-02 | 2.164130e+01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.074655e+00 | 8.597421e+00 | 2.530000e-02 | 3.350000e-02 | 8.700000e-02 | 3.355000e-01 | 9.329390e+02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.062534e-01 | 2.924913e-01 | 5.200000e-06 | 2.530003e-01 | 5.085001e-01 | 7.620001e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.062517e-01 | 2.924922e-01 | 5.300000e-06 | 2.529645e-01 | 5.084684e-01 | 7.621322e-01 | 9.999888e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.675331e-01 | 2.462307e-01 | 1.000000e-03 | 5.200000e-03 | 3.370000e-02 | 2.415000e-01 | 9.990000e-01 | ▇▁▁▁▁ |
| numeric | AF_reference | 45133 | 0.8904238 | NA | NA | NA | NA | NA | NA | NA | 1.874645e-01 | 2.403106e-01 | 0.000000e+00 | 5.033100e-03 | 7.496690e-02 | 2.974830e-01 | 1.000000e+00 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 2699555 | rs311165 | C | A | 0.0461 | 0.0374 | 0.2176001 | 0.2177175 | 0.4517 | 0.5533770 | NA |
| 23 | 2699645 | rs28579419 | G | T | 0.0703 | 0.0437 | 0.1073999 | 0.1076829 | 0.1406 | 0.0405298 | NA |
| 23 | 2699676 | rs60075487 | G | A | 0.0760 | 0.0530 | 0.1515999 | 0.1515830 | 0.1624 | 0.2717880 | NA |
| 23 | 2699898 | rs60233760 | C | CT | 0.0876 | 0.0526 | 0.0958297 | 0.0958331 | 0.1590 | 0.2678150 | NA |
| 23 | 2699968 | rs2306737 | A | G | -0.0754 | 0.0316 | 0.0168799 | 0.0170292 | 0.5477 | 0.5274170 | NA |
| 23 | 2700027 | rs2306736 | T | C | -0.0724 | 0.0320 | 0.0236903 | 0.0236665 | 0.5526 | 0.4903310 | NA |
| 23 | 2700089 | rs41297271 | A | G | 0.4281 | 0.1538 | 0.0053699 | 0.0053778 | 0.0092 | 0.0039735 | NA |
| 23 | 2700157 | rs5939319 | G | A | 0.0699 | 0.0428 | 0.1022000 | 0.1024317 | 0.1418 | 0.0415894 | NA |
| 23 | 2700202 | rs5939320 | A | G | 0.0701 | 0.0339 | 0.0388302 | 0.0386544 | 0.3114 | 0.3533770 | NA |
| 23 | 2700302 | rs72619369 | T | A | 0.0443 | 0.0423 | 0.2946002 | 0.2949698 | 0.1723 | 0.3369540 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154921127 | rs58486544 | T | C | -0.7992 | 0.4667 | 0.0868500 | 0.0868139 | 0.0449 | 0.1451660 | NA |
| 23 | 154923225 | rs148193288 | T | G | 0.2462 | 0.2265 | 0.2771003 | 0.2770475 | 0.0055 | 0.0021192 | NA |
| 23 | 154923311 | rs141127553 | C | T | -0.9034 | 0.4951 | 0.0680393 | 0.0680490 | 0.0425 | 0.0309934 | NA |
| 23 | 154925045 | rs509981 | C | T | -0.0575 | 0.0298 | 0.0533003 | 0.0536651 | 0.2438 | 0.3634440 | NA |
| 23 | 154925895 | rs538470 | C | T | -0.0628 | 0.0306 | 0.0401597 | 0.0401417 | 0.2359 | 0.3634440 | NA |
| 23 | 154927197 | rs200614200 | TAC | T | -0.0584 | 0.0302 | 0.0528299 | 0.0531408 | 0.2403 | NA | NA |
| 23 | 154927199 | rs645904 | C | T | -0.0585 | 0.0298 | 0.0499804 | 0.0496360 | 0.2429 | 0.3674170 | NA |
| 23 | 154927581 | rs644138 | G | A | -0.0694 | 0.0294 | 0.0180198 | 0.0182481 | 0.2977 | 0.4635760 | NA |
| 23 | 154929412 | rs557132 | C | T | -0.0619 | 0.0297 | 0.0374697 | 0.0371442 | 0.2425 | 0.3568210 | NA |
| 23 | 154930230 | rs781880 | A | G | -0.0600 | 0.0302 | 0.0466498 | 0.0469496 | 0.2410 | 0.3618540 | NA |
bcf preview
X 2699555 rs311165 C A . PASS AF=0.4517 ES:SE:LP:AF:ID 0.0461:0.0374:0.662341:0.4517:rs311165
X 2699645 rs28579419 G T . PASS AF=0.1406 ES:SE:LP:AF:ID 0.0703:0.0437:0.968996:0.1406:rs28579419
X 2699676 rs60075487 G A . PASS AF=0.1624 ES:SE:LP:AF:ID 0.076:0.053:0.819301:0.1624:rs60075487
X 2699898 rs60233760 C CT . PASS AF=0.159 ES:SE:LP:AF:ID 0.0876:0.0526:1.0185:0.159:rs60233760
X 2699968 rs2306737 A G . PASS AF=0.5477 ES:SE:LP:AF:ID -0.0754:0.0316:1.77263:0.5477:rs2306737
X 2700027 rs2306736 T C . PASS AF=0.5526 ES:SE:LP:AF:ID -0.0724:0.032:1.62543:0.5526:rs2306736
X 2700089 rs41297271 A G . PASS AF=0.0092 ES:SE:LP:AF:ID 0.4281:0.1538:2.27003:0.0092:rs41297271
X 2700157 rs5939319 G A . PASS AF=0.1418 ES:SE:LP:AF:ID 0.0699:0.0428:0.990549:0.1418:rs5939319
X 2700202 rs5939320 A G . PASS AF=0.3114 ES:SE:LP:AF:ID 0.0701:0.0339:1.41083:0.3114:rs5939320
X 2700302 rs72619369 T A . PASS AF=0.1723 ES:SE:LP:AF:ID 0.0443:0.0423:0.530767:0.1723:rs72619369
X 2700613 rs4892819 A G . PASS AF=0.5369 ES:SE:LP:AF:ID -0.0375:0.0372:0.503347:0.5369:rs4892819
X 2700633 rs148775111 G T . PASS AF=0.0089 ES:SE:LP:AF:ID -0.0101:0.1876:0.0189519:0.0089:rs148775111
X 2701185 rs1970797 C T . PASS AF=0.8748 ES:SE:LP:AF:ID -0.0173:0.0475:0.144784:0.8748:rs1970797
X 2702339 rs111595179 T C . PASS AF=0.079 ES:SE:LP:AF:ID 0.1069:0.145:0.336205:0.079:rs111595179
X 2702568 rs5982854 G A . PASS AF=0.047 ES:SE:LP:AF:ID -0.0941:0.0787:0.633951:0.047:rs5982854
X 2702698 rs73433431 C T . PASS AF=0.0776 ES:SE:LP:AF:ID 0.0891:0.1456:0.267044:0.0776:rs73433431
X 2702946 rs5982856 G T . PASS AF=0.0472 ES:SE:LP:AF:ID -0.0875:0.0783:0.577903:0.0472:rs5982856
X 2703354 rs5982584 G C . PASS AF=0.0471 ES:SE:LP:AF:ID -0.0853:0.0783:0.559563:0.0471:rs5982584
X 2703391 rs1486175 T C . PASS AF=0.7105 ES:SE:LP:AF:ID 0.0067:0.0294:0.0866631:0.7105:rs1486175
X 2703476 rs143272590 T C . PASS AF=0.0079 ES:SE:LP:AF:ID 0.5892:0.4709:0.676129:0.0079:rs143272590
X 2703500 rs11413215 A AT . PASS AF=0.7011 ES:SE:LP:AF:ID 0.0014:0.0297:0.0170055:0.7011:rs11413215
X 2703544 rs6420589 A G . PASS AF=0.8216 ES:SE:LP:AF:ID -0.008:0.0383:0.0783135:0.8216:rs6420589
X 2703633 rs1419931 A G . PASS AF=0.71 ES:SE:LP:AF:ID 0.009:0.0291:0.121076:0.71:rs1419931
X 2704335 rs6641645 G C . PASS AF=0.7072 ES:SE:LP:AF:ID 0.0075:0.0293:0.0983782:0.7072:rs6641645
X 2704469 rs5939322 T C . PASS AF=0.7134 ES:SE:LP:AF:ID 0.0063:0.0296:0.0806604:0.7134:rs5939322
X 2704556 rs6641647 A G . PASS AF=0.7117 ES:SE:LP:AF:ID 0.007:0.0296:0.090444:0.7117:rs6641647
X 2704609 rs5939323 T C . PASS AF=0.7136 ES:SE:LP:AF:ID 0.0063:0.0296:0.0805558:0.7136:rs5939323
X 2704808 rs6642018 T C . PASS AF=0.7135 ES:SE:LP:AF:ID 0.0073:0.0296:0.0932879:0.7135:rs6642018
X 2704989 rs6642019 T C . PASS AF=0.7111 ES:SE:LP:AF:ID 0.0047:0.0296:0.0582402:0.7111:rs6642019
X 2705011 rs113922957 C T . PASS AF=0.0769 ES:SE:LP:AF:ID 0.1064:0.1473:0.327717:0.0769:rs113922957
X 2705265 rs112589751 C T . PASS AF=0.0768 ES:SE:LP:AF:ID 0.1064:0.1474:0.327533:0.0768:rs112589751
X 2705462 rs5982858 G A . PASS AF=0.0475 ES:SE:LP:AF:ID -0.0817:0.0774:0.535958:0.0475:rs5982858
X 2705464 rs59808240 T A . PASS AF=0.6636 ES:SE:LP:AF:ID 0.014:0.029:0.201695:0.6636:rs59808240
X 2706143 rs34253565 AAG A . PASS AF=0.047 ES:SE:LP:AF:ID -0.0663:0.077:0.409827:0.047:rs113045181
X 2706153 rs200182301 GAC G . PASS AF=0.0491 ES:SE:LP:AF:ID -0.0665:0.0804:0.389021:0.0491:rs200182301
X 2706340 rs5982859 G A . PASS AF=0.0469 ES:SE:LP:AF:ID -0.0672:0.0769:0.417482:0.0469:rs5982859
X 2706487 rs5982860 G T . PASS AF=0.047 ES:SE:LP:AF:ID -0.0655:0.0762:0.408824:0.047:rs5982860
X 2706896 rs58649691 T TA . PASS AF=0.7777 ES:SE:LP:AF:ID -0.0093:0.0638:0.0537934:0.7777:rs58649691
X 2707060 rs5939117 A G . PASS AF=0.7203 ES:SE:LP:AF:ID -0.0219:0.0607:0.143815:0.7203:rs5939117
X 2707142 rs5939324 T C . PASS AF=0.7575 ES:SE:LP:AF:ID 0.0767:0.0916:0.395018:0.7575:rs5939324
X 2707978 rs311166 T C . PASS AF=0.8733 ES:SE:LP:AF:ID -0.1413:0.1062:0.736838:0.8733:rs311166
X 2708651 rs56231504 G A . PASS AF=0.147 ES:SE:LP:AF:ID -0.1847:0.1048:1.10763:0.147:rs56231504
X 2709004 rs200860951 GTAAA G . PASS AF=0.5309 ES:SE:LP:AF:ID -0.0408:0.0799:0.214955:0.5309:rs200860951
X 2709047 rs180838415 C T . PASS AF=0.0022 ES:SE:LP:AF:ID -0.8339:0.9127:0.442613:0.0022:rs180838415
X 2709093 rs200724145 TTTC T . PASS AF=0.0544 ES:SE:LP:AF:ID -0.1578:0.1754:0.433798:0.0544:rs200724145
X 2710506 rs311167 G C . PASS AF=0.6678 ES:SE:LP:AF:ID -0.0055:0.051:0.0390538:0.6678:rs311167
X 2710840 rs311168 C T . PASS AF=0.6633 ES:SE:LP:AF:ID -0.0135:0.0506:0.102703:0.6633:rs311168
X 2710995 rs311169 C T . PASS AF=0.6676 ES:SE:LP:AF:ID -0.0091:0.0508:0.0669178:0.6676:rs311169
X 2711429 rs311170 G A . PASS AF=0.6663 ES:SE:LP:AF:ID -0.007:0.0507:0.0507076:0.6663:rs311170
X 2711722 rs4892892 C T . PASS AF=0.6637 ES:SE:LP:AF:ID 0.0024:0.0508:0.0163286:0.6637:rs4892892