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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20547_3/ukb-d-20547_3_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:17:22.147877",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-20547_3/ukb-d-20547_3.vcf.gz; Date=Sat May 9 16:11:30 2020"
}
*********************************************************************
* 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/ukb-d-import/processed/ukb-d-20547_3/ukb-d-20547_3.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/ukb-d-import/processed/ukb-d-20547_3/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 16:41:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20547_3/ukb-d-20547_3.vcf.gz ...
Read summary statistics for 13120562 SNPs.
Dropped 12049 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1283412 SNPs remain.
After merging with regression SNP LD, 1283412 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0273 (0.0043)
Lambda GC: 1.0561
Mean Chi^2: 1.0639
Intercept: 1.0006 (0.0067)
Ratio: 0.0093 (0.1041)
Analysis finished at Mon Nov 25 16:43:23 2019
Total time elapsed: 2.0m:13.11s
{
"af_correlation": 0.9513,
"inflation_factor": 1.0317,
"mean_EFFECT": 3.4407e-06,
"n": 117763,
"n_snps": 13120562,
"n_clumped_hits": 2,
"n_p_sig": 2,
"n_mono": 0,
"n_ns": 1234243,
"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": 455502,
"n_est": 118144.3151,
"ratio_se_n": 1.0016,
"mean_diff": 7.9579e-06,
"ratio_diff": 5.3056,
"sd_y_est1": 0.2663,
"sd_y_est2": 0.2668,
"r2_sum1": 0,
"r2_sum2": 0.0005,
"r2_sum3": 0.0005,
"r2_sum4": 0.0005,
"ldsc_nsnp_merge_refpanel_ld": 1283412,
"ldsc_nsnp_merge_regression_ld": 1283412,
"ldsc_observed_scale_h2_beta": 0.0273,
"ldsc_observed_scale_h2_se": 0.0043,
"ldsc_intercept_beta": 1.0006,
"ldsc_intercept_se": 0.0067,
"ldsc_lambda_gc": 1.0561,
"ldsc_mean_chisq": 1.0639,
"ldsc_ratio": 0.0094
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
is_snpid_non_unique | TRUE |
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 |
General metrics
af_correlation
: Correlation coefficient between AF
and AF_reference
.inflation_factor
(lambda
): Genomic inflation factor.mean_EFFECT
: Mean of EFFECT
size.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 below 5e-8
.n_mono
: Number of monomorphic (MAF == 1
or MAF == 0
) SNPs.n_ns
: Number of SNPs with nonsense values:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 0
or > 1
.n_mac
: Number of cases where MAC
(\(2 \times N \times MAF\)) is less than 6
.is_snpid_unique
: true
if the combination of ID
REF
ALT
is unique and therefore no duplication in snpid.n_miss_<*>
: Number of NA
observations 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 expect ratio_se_n
to 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.
ratio_diff
: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff
and the mean of diff2
(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.
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.
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.
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>
: r2
statistics under various assumptions
1
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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
: NOT is_snpid_unique
.mean_EFFECT_nonfinite
: mean(EFFECT)
is NA
, NaN
, or Inf
.mean_EFFECT_05
: abs(mean(EFFECT))
> 0.5.mean_EFFECT_01
: abs(mean(EFFECT))
> 0.1.mean_chisq
: ldsc_mean_chisq
> 1.3 or ldsc_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<*>
> 0.5Plots
skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 0 | 1.0000000 | 3 | 94 | 0 | 13109167 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 56089 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33046 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.057007e+00 | 6.185520e+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 | 7.898350e+07 | 5.593092e+07 | 3.02000e+02 | 3.285474e+07 | 7.006771e+07 | 1.148138e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.400000e-06 | 5.718900e-03 | -6.39199e-02 | -1.670100e-03 | -1.260000e-05 | 1.637200e-03 | 7.651540e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.180700e-03 | 3.876100e-03 | 9.08900e-04 | 1.297300e-03 | 2.282700e-03 | 5.947800e-03 | 2.063570e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.943194e-01 | 2.901937e-01 | 0.00000e+00 | 2.413821e-01 | 4.932874e-01 | 7.455538e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.943181e-01 | 2.901945e-01 | 0.00000e+00 | 2.413798e-01 | 4.932865e-01 | 7.455528e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.972116e-01 | 2.559322e-01 | 1.35880e-03 | 9.181800e-03 | 6.825370e-02 | 3.080480e-01 | 9.986410e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 455502 | 0.9652833 | NA | NA | NA | NA | NA | 2.012122e-01 | 2.481677e-01 | 0.00000e+00 | 6.789100e-03 | 9.105430e-02 | 3.172920e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.177630e+05 | 0.000000e+00 | 1.17763e+05 | 1.177630e+05 | 1.177630e+05 | 1.177630e+05 | 1.177630e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0007269 | 0.0019118 | 0.7037980 | 0.7037970 | 0.1116950 | 0.1894970 | 117763 |
1 | 693731 | rs12238997 | A | G | 0.0024869 | 0.0018105 | 0.1695641 | 0.1695604 | 0.1167150 | 0.1417730 | 117763 |
1 | 707522 | rs371890604 | G | C | 0.0012077 | 0.0020313 | 0.5521423 | 0.5521414 | 0.0983485 | 0.1293930 | 117763 |
1 | 717587 | rs144155419 | G | A | 0.0114555 | 0.0048677 | 0.0186054 | 0.0186043 | 0.0157583 | 0.0045926 | 117763 |
1 | 723329 | rs189787166 | A | T | -0.0044724 | 0.0141872 | 0.7525823 | 0.7525807 | 0.0017777 | 0.0003994 | 117763 |
1 | 730087 | rs148120343 | T | C | -0.0003924 | 0.0025195 | 0.8762360 | 0.8762357 | 0.0568966 | 0.0127796 | 117763 |
1 | 731718 | rs142557973 | T | C | 0.0015743 | 0.0017178 | 0.3594090 | 0.3594069 | 0.1226470 | 0.1543530 | 117763 |
1 | 732032 | rs61770163 | A | C | 0.0021776 | 0.0018309 | 0.2342928 | 0.2342928 | 0.1222350 | 0.1555510 | 117763 |
1 | 734349 | rs141242758 | T | C | 0.0016600 | 0.0017187 | 0.3340981 | 0.3340953 | 0.1219010 | 0.1525560 | 117763 |
1 | 740284 | rs61770167 | C | T | -0.0005766 | 0.0078437 | 0.9414030 | 0.9414031 | 0.0058608 | 0.0023962 | 117763 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0014206 | 0.0020197 | 0.4818468 | 0.4818460 | 0.0554823 | 0.0309934 | 117763 |
23 | 154923374 | rs111332691 | T | A | -0.0026211 | 0.0022023 | 0.2339888 | 0.2339873 | 0.0447339 | 0.0116556 | 117763 |
23 | 154925045 | rs509981 | C | T | 0.0000915 | 0.0010601 | 0.9312511 | 0.9312511 | 0.2447530 | 0.3634440 | 117763 |
23 | 154925895 | rs538470 | C | T | 0.0001093 | 0.0010840 | 0.9196769 | 0.9196764 | 0.2411730 | 0.3634440 | 117763 |
23 | 154927581 | rs644138 | G | A | 0.0004003 | 0.0009975 | 0.6882227 | 0.6882210 | 0.3005980 | 0.4635760 | 117763 |
23 | 154929412 | rs557132 | C | T | 0.0000730 | 0.0010603 | 0.9451499 | 0.9451493 | 0.2446280 | 0.3568210 | 117763 |
23 | 154929637 | rs35185538 | CT | C | 0.0003974 | 0.0011077 | 0.7197373 | 0.7197362 | 0.2288620 | 0.3011920 | 117763 |
23 | 154929952 | rs4012982 | CAA | C | 0.0002999 | 0.0011159 | 0.7881266 | 0.7881247 | 0.2387120 | 0.3165560 | 117763 |
23 | 154930230 | rs781880 | A | G | 0.0000911 | 0.0010600 | 0.9315031 | 0.9315030 | 0.2450460 | 0.3618540 | 117763 |
23 | 154930487 | rs781879 | T | A | -0.0036768 | 0.0036034 | 0.3075559 | 0.3075532 | 0.0196777 | 0.1263580 | 117763 |
1 692794 rs530212009 CA C . PASS AF=0.111695 ES:SE:LP:AF:SS:ID 0.00072687:0.00191181:0.152552:0.111695:117763:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116715 ES:SE:LP:AF:SS:ID 0.00248688:0.00181046:0.770666:0.116715:117763:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0983485 ES:SE:LP:AF:SS:ID 0.00120773:0.00203132:0.257949:0.0983485:117763:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157583 ES:SE:LP:AF:SS:ID 0.0114555:0.00486771:1.73036:0.0157583:117763:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00177766 ES:SE:LP:AF:SS:ID -0.00447235:0.0141872:0.123446:0.00177766:117763:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0568966 ES:SE:LP:AF:SS:ID -0.000392399:0.00251953:0.0573789:0.0568966:117763:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122647 ES:SE:LP:AF:SS:ID 0.00157432:0.00171776:0.444411:0.122647:117763:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122235 ES:SE:LP:AF:SS:ID 0.0021776:0.00183088:0.630241:0.122235:117763:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121901 ES:SE:LP:AF:SS:ID 0.00166005:0.00171866:0.476126:0.121901:117763:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00586084 ES:SE:LP:AF:SS:ID -0.000576561:0.00784368:0.0262244:0.00586084:117763:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00183204 ES:SE:LP:AF:SS:ID -0.00950807:0.0150556:0.277617:0.00183204:117763:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869013 ES:SE:LP:AF:SS:ID -0.00216643:0.00169336:0.697299:0.869013:117763:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00158489 ES:SE:LP:AF:SS:ID 0.0175528:0.0150542:0.613271:0.00158489:117763:rs190826124
1 751343 rs28544273 T A . PASS AF=0.123679 ES:SE:LP:AF:SS:ID 0.00267492:0.00167788:0.955112:0.123679:117763:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143308 ES:SE:LP:AF:SS:ID 0.00249108:0.00165948:0.875085:0.143308:117763:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123801 ES:SE:LP:AF:SS:ID 0.00266429:0.00167557:0.951484:0.123801:117763:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869786 ES:SE:LP:AF:SS:ID -0.00235951:0.00163172:0.829231:0.869786:117763:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874576 ES:SE:LP:AF:SS:ID -0.00260244:0.0016592:0.932672:0.874576:117763:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129674 ES:SE:LP:AF:SS:ID 0.00224655:0.00163629:0.770136:0.129674:117763:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0365183 ES:SE:LP:AF:SS:ID 0.00048554:0.0029717:0.0603744:0.0365183:117763:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869381 ES:SE:LP:AF:SS:ID -0.00231505:0.00163018:0.80806:0.869381:117763:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869453 ES:SE:LP:AF:SS:ID -0.00232434:0.00163078:0.812265:0.869453:117763:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869381 ES:SE:LP:AF:SS:ID -0.00232202:0.00163013:0.811569:0.869381:117763:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00512144 ES:SE:LP:AF:SS:ID 0.0143736:0.00833511:1.07249:0.00512144:117763:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00509053 ES:SE:LP:AF:SS:ID 0.0143948:0.00835342:1.07135:0.00509053:117763:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00568601 ES:SE:LP:AF:SS:ID -0.00272822:0.00803485:0.134187:0.00568601:117763:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869452 ES:SE:LP:AF:SS:ID -0.00236715:0.00162712:0.836466:0.869452:117763:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126951 ES:SE:LP:AF:SS:ID 0.00253185:0.00166097:0.894725:0.126951:117763:rs61768170
1 756604 rs3131962 A G . PASS AF=0.86897 ES:SE:LP:AF:SS:ID -0.00237442:0.00162284:0.843348:0.86897:117763:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868378 ES:SE:LP:AF:SS:ID -0.00231577:0.00162229:0.814036:0.868378:117763:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869162 ES:SE:LP:AF:SS:ID -0.00243388:0.00162445:0.872688:0.869162:117763:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869169 ES:SE:LP:AF:SS:ID -0.00243385:0.00162457:0.872587:0.869169:117763:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869171 ES:SE:LP:AF:SS:ID -0.00243373:0.00162457:0.872516:0.869171:117763:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869607 ES:SE:LP:AF:SS:ID -0.002421:0.00162874:0.862741:0.869607:117763:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0995777 ES:SE:LP:AF:SS:ID 0.00118713:0.00189343:0.275168:0.0995777:117763:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00654643 ES:SE:LP:AF:SS:ID -0.00222528:0.0072936:0.119021:0.00654643:117763:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873674 ES:SE:LP:AF:SS:ID -0.00272356:0.00165378:1.00179:0.873674:117763:rs3115851
1 761732 rs2286139 C T . PASS AF=0.862966 ES:SE:LP:AF:SS:ID -0.00246729:0.00162185:0.892136:0.862966:117763:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868361 ES:SE:LP:AF:SS:ID -0.00244971:0.00163745:0.870819:0.868361:117763:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865361 ES:SE:LP:AF:SS:ID -0.00247285:0.00163766:0.882566:0.865361:117763:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0997465 ES:SE:LP:AF:SS:ID 0.00426796:0.001957:1.53469:0.0997465:117763:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870665 ES:SE:LP:AF:SS:ID -0.00288286:0.00165706:1.08668:0.870665:117763:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870665 ES:SE:LP:AF:SS:ID -0.00288269:0.00165706:1.08658:0.870665:117763:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870663 ES:SE:LP:AF:SS:ID -0.00288231:0.00165707:1.08637:0.870663:117763:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870985 ES:SE:LP:AF:SS:ID -0.00280889:0.00165777:1.04482:0.870985:117763:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126537 ES:SE:LP:AF:SS:ID 0.00261357:0.00165919:0.93851:0.126537:117763:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106315 ES:SE:LP:AF:SS:ID 0.000699473:0.00180316:0.156095:0.106315:117763:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854401 ES:SE:LP:AF:SS:ID -0.00230846:0.00162145:0.810968:0.854401:117763:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00168927 ES:SE:LP:AF:SS:ID -0.00361803:0.0142504:0.097137:0.00168927:117763:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.839108 ES:SE:LP:AF:SS:ID -0.000974079:0.00160637:0.264194:0.839108:117763:rs376645387