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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1448_2/ukb-d-1448_2_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:38:59.899997",
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"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/ukb-d-import/processed/ukb-d-1448_2/ukb-d-1448_2.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1448_2/ukb-d-1448_2_data.vcf.gz; Date=Mon Nov 25 16:28:57 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-1448_2/ukb-d-1448_2.vcf.gz; Date=Sun May 10 09:07:34 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-1448_2/ukb-d-1448_2.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-1448_2/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 17:10:13 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-1448_2/ukb-d-1448_2.vcf.gz ...
Read summary statistics for 13586246 SNPs.
Dropped 12712 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0118 (0.0015)
Lambda GC: 1.072
Mean Chi^2: 1.0775
Intercept: 0.9958 (0.0063)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:12:16 2019
Total time elapsed: 2.0m:3.1s
{
"af_correlation": 0.9521,
"inflation_factor": 1.044,
"mean_EFFECT": 3.3622e-06,
"n": 348424,
"n_snps": 13586246,
"n_clumped_hits": 0,
"n_p_sig": 2,
"n_mono": 0,
"n_ns": 1251794,
"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": 569238,
"n_est": 349808.7036,
"ratio_se_n": 1.002,
"mean_diff": 6.3683e-06,
"ratio_diff": 10.5354,
"sd_y_est1": 0.3247,
"sd_y_est2": 0.3253,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1283504,
"ldsc_nsnp_merge_regression_ld": 1283504,
"ldsc_observed_scale_h2_beta": 0.0118,
"ldsc_observed_scale_h2_se": 0.0015,
"ldsc_intercept_beta": 0.9958,
"ldsc_intercept_se": 0.0063,
"ldsc_lambda_gc": 1.072,
"ldsc_mean_chisq": 1.0775,
"ldsc_ratio": -0.0542
}
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 | 13574198 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57084 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33337 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051300e+00 | 6.184955e+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 | 7.902529e+07 | 5.591512e+07 | 3.02000e+02 | 3.293080e+07 | 7.013840e+07 | 1.148599e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.400000e-06 | 4.553300e-03 | -5.68252e-02 | -1.235300e-03 | 3.000000e-07 | 1.228200e-03 | 6.580330e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.268500e-03 | 3.152900e-03 | 6.38000e-04 | 9.306000e-04 | 1.714800e-03 | 4.696800e-03 | 1.592210e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.929402e-01 | 2.907034e-01 | 0.00000e+00 | 2.392522e-01 | 4.907124e-01 | 7.447423e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.929397e-01 | 2.907037e-01 | 0.00000e+00 | 2.392512e-01 | 4.907117e-01 | 7.447419e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.908060e-01 | 2.544035e-01 | 1.00000e-03 | 7.430600e-03 | 6.003200e-02 | 2.953218e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 569238 | 0.9581019 | NA | NA | NA | NA | NA | 1.963368e-01 | 2.471016e-01 | 0.00000e+00 | 5.591000e-03 | 8.426520e-02 | 3.081070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.484240e+05 | 0.000000e+00 | 3.48424e+05 | 3.484240e+05 | 3.484240e+05 | 3.484240e+05 | 3.484240e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0018144 | 0.0013626 | 0.1829911 | 0.1829912 | 0.1105660 | 0.1894970 | 348424 |
1 | 693731 | rs12238997 | A | G | 0.0015669 | 0.0012874 | 0.2235430 | 0.2235443 | 0.1157510 | 0.1417730 | 348424 |
1 | 707522 | rs371890604 | G | C | 0.0014515 | 0.0014472 | 0.3158668 | 0.3158647 | 0.0972257 | 0.1293930 | 348424 |
1 | 717587 | rs144155419 | G | A | 0.0043402 | 0.0034585 | 0.2094990 | 0.2094976 | 0.0156497 | 0.0045926 | 348424 |
1 | 723329 | rs189787166 | A | T | 0.0039823 | 0.0101868 | 0.6958490 | 0.6958494 | 0.0017334 | 0.0003994 | 348424 |
1 | 730087 | rs148120343 | T | C | 0.0019002 | 0.0017940 | 0.2895010 | 0.2894992 | 0.0564055 | 0.0127796 | 348424 |
1 | 731718 | rs142557973 | T | C | 0.0014421 | 0.0012209 | 0.2375451 | 0.2375469 | 0.1216490 | 0.1543530 | 348424 |
1 | 732032 | rs61770163 | A | C | 0.0016404 | 0.0013024 | 0.2078299 | 0.2078303 | 0.1210850 | 0.1555510 | 348424 |
1 | 734349 | rs141242758 | T | C | 0.0014808 | 0.0012216 | 0.2254592 | 0.2254589 | 0.1208790 | 0.1525560 | 348424 |
1 | 740284 | rs61770167 | C | T | -0.0096910 | 0.0055818 | 0.0825335 | 0.0825336 | 0.0057964 | 0.0023962 | 348424 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0012272 | 0.0014084 | 0.3835474 | 0.3835444 | 0.0560551 | 0.0309934 | 348424 |
23 | 154923374 | rs111332691 | T | A | -0.0008849 | 0.0015481 | 0.5675851 | 0.5675856 | 0.0446955 | 0.0116556 | 348424 |
23 | 154925045 | rs509981 | C | T | 0.0016078 | 0.0007437 | 0.0306309 | 0.0306305 | 0.2457460 | 0.3634440 | 348424 |
23 | 154925895 | rs538470 | C | T | 0.0016331 | 0.0007608 | 0.0318229 | 0.0318220 | 0.2420510 | 0.3634440 | 348424 |
23 | 154927581 | rs644138 | G | A | 0.0016973 | 0.0006996 | 0.0152588 | 0.0152580 | 0.3021920 | 0.4635760 | 348424 |
23 | 154929412 | rs557132 | C | T | 0.0016023 | 0.0007439 | 0.0312594 | 0.0312583 | 0.2455970 | 0.3568210 | 348424 |
23 | 154929637 | rs35185538 | CT | C | 0.0011016 | 0.0007764 | 0.1559448 | 0.1559430 | 0.2297910 | 0.3011920 | 348424 |
23 | 154929952 | rs4012982 | CAA | C | 0.0018674 | 0.0007824 | 0.0169989 | 0.0169981 | 0.2395410 | 0.3165560 | 348424 |
23 | 154930230 | rs781880 | A | G | 0.0015732 | 0.0007438 | 0.0344247 | 0.0344244 | 0.2460140 | 0.3618540 | 348424 |
23 | 154930487 | rs781879 | T | A | 0.0041548 | 0.0025509 | 0.1033661 | 0.1033641 | 0.0195723 | 0.1263580 | 348424 |
1 692794 rs530212009 CA C . PASS AF=0.110566 ES:SE:LP:AF:SS:ID 0.00181444:0.0013626:0.73757:0.110566:348424:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.115751 ES:SE:LP:AF:SS:ID 0.00156692:0.00128736:0.650639:0.115751:348424:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0972257 ES:SE:LP:AF:SS:ID 0.00145149:0.00144716:0.500496:0.0972257:348424:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0156497 ES:SE:LP:AF:SS:ID 0.0043402:0.00345847:0.678818:0.0156497:348424:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00173336 ES:SE:LP:AF:SS:ID 0.00398232:0.0101868:0.157485:0.00173336:348424:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0564055 ES:SE:LP:AF:SS:ID 0.0019002:0.00179396:0.53835:0.0564055:348424:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121649 ES:SE:LP:AF:SS:ID 0.00144209:0.00122093:0.624254:0.121649:348424:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121085 ES:SE:LP:AF:SS:ID 0.00164038:0.00130235:0.682292:0.121085:348424:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120879 ES:SE:LP:AF:SS:ID 0.00148075:0.0012216:0.646932:0.120879:348424:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00579641 ES:SE:LP:AF:SS:ID -0.00969096:0.0055818:1.08337:0.00579641:348424:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00188398 ES:SE:LP:AF:SS:ID 0.0019158:0.0105187:0.0677912:0.00188398:348424:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869838 ES:SE:LP:AF:SS:ID -0.00153836:0.00120433:0.695772:0.869838:348424:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00153811 ES:SE:LP:AF:SS:ID -0.0156043:0.0108674:0.82092:0.00153811:348424:rs190826124
1 751343 rs28544273 T A . PASS AF=0.122804 ES:SE:LP:AF:SS:ID 0.00151168:0.00119286:0.688121:0.122804:348424:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142609 ES:SE:LP:AF:SS:ID 0.00131328:0.00117895:0.576255:0.142609:348424:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12292 ES:SE:LP:AF:SS:ID 0.00146664:0.0011912:0.661072:0.12292:348424:rs28527770
1 753405 rs3115860 C A . PASS AF=0.870978 ES:SE:LP:AF:SS:ID -0.00166721:0.00116069:0.821342:0.870978:348424:rs3115860
1 753425 rs3131970 T C . PASS AF=0.87557 ES:SE:LP:AF:SS:ID -0.0015393:0.00117998:0.716563:0.87557:348424:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128532 ES:SE:LP:AF:SS:ID 0.00159427:0.00116359:0.767901:0.128532:348424:rs2073813
1 754105 rs12184325 C T . PASS AF=0.036325 ES:SE:LP:AF:SS:ID 0.00217687:0.0021116:0.519156:0.036325:348424:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870576 ES:SE:LP:AF:SS:ID -0.00167773:0.00115951:0.829985:0.870576:348424:rs3131969
1 754192 rs3131968 A G . PASS AF=0.87068 ES:SE:LP:AF:SS:ID -0.00165652:0.00116004:0.814466:0.87068:348424:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870573 ES:SE:LP:AF:SS:ID -0.00167218:0.00115946:0.8261:0.870573:348424:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00504313 ES:SE:LP:AF:SS:ID 0.000838193:0.00595136:0.051589:0.00504313:348424:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00501098 ES:SE:LP:AF:SS:ID 0.000943782:0.00596703:0.0583266:0.00501098:348424:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0055674 ES:SE:LP:AF:SS:ID 0.0116367:0.00577612:1.3571:0.0055674:348424:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870647 ES:SE:LP:AF:SS:ID -0.00174513:0.0011574:0.880724:0.870647:348424:rs3115858
1 756434 rs61768170 G C . PASS AF=0.12589 ES:SE:LP:AF:SS:ID 0.00156186:0.00118099:0.730478:0.12589:348424:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870217 ES:SE:LP:AF:SS:ID -0.00173431:0.00115464:0.875858:0.870217:348424:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869504 ES:SE:LP:AF:SS:ID -0.0017147:0.00115356:0.862766:0.869504:348424:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870367 ES:SE:LP:AF:SS:ID -0.00172643:0.00115561:0.869065:0.870367:348424:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870372 ES:SE:LP:AF:SS:ID -0.00172392:0.00115569:0.867151:0.870372:348424:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870381 ES:SE:LP:AF:SS:ID -0.00173132:0.00115573:0.87249:0.870381:348424:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870823 ES:SE:LP:AF:SS:ID -0.00179554:0.00115867:0.916408:0.870823:348424:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID 0.00101027:0.00134621:0.343922:0.0987831:348424:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00644687 ES:SE:LP:AF:SS:ID 0.0137076:0.00521999:2.06346:0.00644687:348424:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874731 ES:SE:LP:AF:SS:ID -0.00156593:0.00117601:0.737542:0.874731:348424:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864126 ES:SE:LP:AF:SS:ID -0.00190331:0.00115314:1.0051:0.864126:348424:rs2286139
1 761752 rs1057213 C T . PASS AF=0.8695 ES:SE:LP:AF:SS:ID -0.00151299:0.00116434:0.712657:0.8695:348424:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866446 ES:SE:LP:AF:SS:ID -0.00158514:0.00116458:0.760763:0.866446:348424:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987204 ES:SE:LP:AF:SS:ID 0.00177918:0.00139443:0.694681:0.0987204:348424:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871633 ES:SE:LP:AF:SS:ID -0.00149585:0.00117791:0.690127:0.871633:348424:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871633 ES:SE:LP:AF:SS:ID -0.00149574:0.00117791:0.690057:0.871633:348424:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871633 ES:SE:LP:AF:SS:ID -0.0014973:0.00117793:0.691041:0.871633:348424:rs3131949
1 762632 rs3131948 T A . PASS AF=0.872009 ES:SE:LP:AF:SS:ID -0.00150205:0.00117862:0.693536:0.872009:348424:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125467 ES:SE:LP:AF:SS:ID 0.00165652:0.00117956:0.795305:0.125467:348424:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105397 ES:SE:LP:AF:SS:ID 0.00102236:0.00128374:0.370788:0.105397:348424:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855446 ES:SE:LP:AF:SS:ID -0.00116445:0.00115267:0.505304:0.855446:348424:rs2519015
1 767393 rs538667473 A C . PASS AF=0.0016537 ES:SE:LP:AF:SS:ID 0.00467026:0.0102103:0.188841:0.0016537:348424:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.838377 ES:SE:LP:AF:SS:ID -0.00230388:0.00113589:1.37126:0.838377:348424:rs376645387