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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-20550_3/ukb-d-20550_3.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20550_3/ukb-d-20550_3_data.vcf.gz; Date=Mon Nov 25 16:01:18 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-20550_3/ukb-d-20550_3.vcf.gz; Date=Sat May 9 14:38:16 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-20550_3/ukb-d-20550_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-20550_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 16:45:50 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20550_3/ukb-d-20550_3.vcf.gz ...
Read summary statistics for 12282662 SNPs.
Dropped 10855 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, 1283183 SNPs remain.
After merging with regression SNP LD, 1283183 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0283 (0.0047)
Lambda GC: 1.0499
Mean Chi^2: 1.0517
Intercept: 0.9963 (0.0058)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:48:10 2019
Total time elapsed: 2.0m:19.8s
{
"af_correlation": 0.9497,
"inflation_factor": 1.0297,
"mean_EFFECT": 4.3711e-06,
"n": 98990,
"n_snps": 12282662,
"n_clumped_hits": 0,
"n_p_sig": 1,
"n_mono": 0,
"n_ns": 1197017,
"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": 314970,
"n_est": 99286.715,
"ratio_se_n": 1.0015,
"mean_diff": 0,
"ratio_diff": 10.0848,
"sd_y_est1": 0.2324,
"sd_y_est2": 0.2327,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1283183,
"ldsc_nsnp_merge_regression_ld": 1283183,
"ldsc_observed_scale_h2_beta": 0.0283,
"ldsc_observed_scale_h2_se": 0.0047,
"ldsc_intercept_beta": 0.9963,
"ldsc_intercept_se": 0.0058,
"ldsc_lambda_gc": 1.0499,
"ldsc_mean_chisq": 1.0517,
"ldsc_ratio": -0.0716
}
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 | 12272433 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 54058 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 32370 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.064951e+00 | 6.184448e+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 | 7.892096e+07 | 5.596648e+07 | 3.02000e+02 | 3.274165e+07 | 6.995838e+07 | 1.147843e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.400000e-06 | 4.411600e-03 | -4.53206e-02 | -1.469700e-03 | -5.400000e-06 | 1.431500e-03 | 5.889790e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.345900e-03 | 2.855500e-03 | 8.63300e-04 | 1.209300e-03 | 1.967900e-03 | 4.654500e-03 | 1.708240e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.954093e-01 | 2.898798e-01 | 0.00000e+00 | 2.436049e-01 | 4.936964e-01 | 7.466533e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.954077e-01 | 2.898807e-01 | 0.00000e+00 | 2.436022e-01 | 4.936955e-01 | 7.466524e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.099715e-01 | 2.585573e-01 | 2.17960e-03 | 1.349380e-02 | 8.574600e-02 | 3.325900e-01 | 9.978200e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 314970 | 0.9743565 | NA | NA | NA | NA | NA | 2.118647e-01 | 2.501946e-01 | 0.00000e+00 | 1.018370e-02 | 1.060300e-01 | 3.362620e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.899000e+04 | 0.000000e+00 | 9.89900e+04 | 9.899000e+04 | 9.899000e+04 | 9.899000e+04 | 9.899000e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0014607 | 0.0018227 | 0.4229081 | 0.4229064 | 0.1115540 | 0.1894970 | 98990 |
1 | 693731 | rs12238997 | A | G | 0.0010951 | 0.0017259 | 0.5257642 | 0.5257607 | 0.1164250 | 0.1417730 | 98990 |
1 | 707522 | rs371890604 | G | C | 0.0004007 | 0.0019400 | 0.8363520 | 0.8363516 | 0.0981163 | 0.1293930 | 98990 |
1 | 717587 | rs144155419 | G | A | 0.0089621 | 0.0046185 | 0.0523239 | 0.0523211 | 0.0158461 | 0.0045926 | 98990 |
1 | 730087 | rs148120343 | T | C | -0.0006312 | 0.0024048 | 0.7929723 | 0.7929712 | 0.0566111 | 0.0127796 | 98990 |
1 | 731718 | rs142557973 | T | C | 0.0007773 | 0.0016382 | 0.6351554 | 0.6351551 | 0.1223630 | 0.1543530 | 98990 |
1 | 732032 | rs61770163 | A | C | 0.0011833 | 0.0017472 | 0.4982634 | 0.4982587 | 0.1219830 | 0.1555510 | 98990 |
1 | 734349 | rs141242758 | T | C | 0.0006985 | 0.0016392 | 0.6700142 | 0.6700143 | 0.1216130 | 0.1525560 | 98990 |
1 | 740284 | rs61770167 | C | T | -0.0092589 | 0.0074784 | 0.2156920 | 0.2156887 | 0.0058414 | 0.0023962 | 98990 |
1 | 749963 | rs529266287 | T | TAA | -0.0007837 | 0.0016145 | 0.6273704 | 0.6273699 | 0.8692740 | 0.7641770 | 98990 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0030390 | 0.0019079 | 0.1111960 | 0.1111927 | 0.0559291 | 0.0309934 | 98990 |
23 | 154923374 | rs111332691 | T | A | -0.0049453 | 0.0020889 | 0.0179122 | 0.0179101 | 0.0448985 | 0.0116556 | 98990 |
23 | 154925045 | rs509981 | C | T | -0.0005357 | 0.0010082 | 0.5951576 | 0.5951566 | 0.2441810 | 0.3634440 | 98990 |
23 | 154925895 | rs538470 | C | T | -0.0006829 | 0.0010310 | 0.5077489 | 0.5077472 | 0.2406180 | 0.3634440 | 98990 |
23 | 154927581 | rs644138 | G | A | -0.0012211 | 0.0009474 | 0.1974390 | 0.1974344 | 0.3004650 | 0.4635760 | 98990 |
23 | 154929412 | rs557132 | C | T | -0.0005550 | 0.0010084 | 0.5820818 | 0.5820803 | 0.2440640 | 0.3568210 | 98990 |
23 | 154929637 | rs35185538 | CT | C | -0.0006880 | 0.0010541 | 0.5139431 | 0.5139425 | 0.2281060 | 0.3011920 | 98990 |
23 | 154929952 | rs4012982 | CAA | C | -0.0002351 | 0.0010614 | 0.8247380 | 0.8247370 | 0.2381730 | 0.3165560 | 98990 |
23 | 154930230 | rs781880 | A | G | -0.0005948 | 0.0010081 | 0.5552096 | 0.5552066 | 0.2444650 | 0.3618540 | 98990 |
23 | 154930487 | rs781879 | T | A | -0.0053709 | 0.0034240 | 0.1167449 | 0.1167413 | 0.0196595 | 0.1263580 | 98990 |
1 692794 rs530212009 CA C . PASS AF=0.111554 ES:SE:LP:AF:SS:ID -0.00146066:0.00182266:0.373754:0.111554:98990:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116425 ES:SE:LP:AF:SS:ID 0.00109508:0.00172592:0.279209:0.116425:98990:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0981163 ES:SE:LP:AF:SS:ID 0.000400725:0.00193997:0.0776109:0.0981163:98990:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0158461 ES:SE:LP:AF:SS:ID 0.00896206:0.00461847:1.2813:0.0158461:98990:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0566111 ES:SE:LP:AF:SS:ID -0.00063115:0.0024048:0.100742:0.0566111:98990:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122363 ES:SE:LP:AF:SS:ID 0.00077728:0.00163816:0.19712:0.122363:98990:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121983 ES:SE:LP:AF:SS:ID 0.00118326:0.0017472:0.302541:0.121983:98990:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121613 ES:SE:LP:AF:SS:ID 0.000698531:0.00163925:0.173916:0.121613:98990:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00584141 ES:SE:LP:AF:SS:ID -0.00925886:0.00747844:0.666166:0.00584141:98990:rs61770167
1 749963 rs529266287 T TAA . PASS AF=0.869274 ES:SE:LP:AF:SS:ID -0.00078373:0.0016145:0.202476:0.869274:98990:rs529266287
1 751343 rs28544273 T A . PASS AF=0.123375 ES:SE:LP:AF:SS:ID 0.000998151:0.00160064:0.273358:0.123375:98990:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143107 ES:SE:LP:AF:SS:ID 0.00192379:0.00158188:0.649882:0.143107:98990:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123485 ES:SE:LP:AF:SS:ID 0.00103487:0.00159847:0.2862:0.123485:98990:rs28527770
1 753405 rs3115860 C A . PASS AF=0.870138 ES:SE:LP:AF:SS:ID -0.00132121:0.0015565:0.40233:0.870138:98990:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874947 ES:SE:LP:AF:SS:ID -0.000820644:0.00158308:0.218826:0.874947:98990:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129331 ES:SE:LP:AF:SS:ID 0.00141749:0.00156093:0.43911:0.129331:98990:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0365845 ES:SE:LP:AF:SS:ID -0.00141363:0.00282744:0.209644:0.0365845:98990:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869745 ES:SE:LP:AF:SS:ID -0.00132152:0.00155514:0.402907:0.869745:98990:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869813 ES:SE:LP:AF:SS:ID -0.00135821:0.00155561:0.417247:0.869813:98990:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869745 ES:SE:LP:AF:SS:ID -0.00132947:0.0015551:0.406044:0.869745:98990:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00512664 ES:SE:LP:AF:SS:ID 0.0169813:0.00793804:1.48919:0.00512664:98990:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00509715 ES:SE:LP:AF:SS:ID 0.0171092:0.0079557:1.50151:0.00509715:98990:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00565755 ES:SE:LP:AF:SS:ID -0.000855622:0.00767921:0.0403467:0.00565755:98990:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869823 ES:SE:LP:AF:SS:ID -0.00133124:0.00155223:0.407713:0.869823:98990:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126603 ES:SE:LP:AF:SS:ID 0.00146583:0.00158453:0.449868:0.126603:98990:rs61768170
1 756604 rs3131962 A G . PASS AF=0.86935 ES:SE:LP:AF:SS:ID -0.00135607:0.00154822:0.41897:0.86935:98990:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868773 ES:SE:LP:AF:SS:ID -0.00138793:0.00154761:0.432014:0.868773:98990:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869537 ES:SE:LP:AF:SS:ID -0.00137947:0.00154972:0.427836:0.869537:98990:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869544 ES:SE:LP:AF:SS:ID -0.00137695:0.00154983:0.42678:0.869544:98990:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869546 ES:SE:LP:AF:SS:ID -0.0013764:0.00154984:0.426556:0.869546:98990:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869975 ES:SE:LP:AF:SS:ID -0.00133087:0.00155378:0.407045:0.869975:98990:rs3131954
1 759293 rs10157329 T A . PASS AF=0.09923 ES:SE:LP:AF:SS:ID -0.000362681:0.0018079:0.0752019:0.09923:98990:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00652328 ES:SE:LP:AF:SS:ID 0.00138711:0.00696129:0.0746575:0.00652328:98990:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874033 ES:SE:LP:AF:SS:ID -0.000980758:0.00157784:0.272281:0.874033:98990:rs3115851
1 761732 rs2286139 C T . PASS AF=0.863358 ES:SE:LP:AF:SS:ID -0.00148909:0.00154731:0.47384:0.863358:98990:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868717 ES:SE:LP:AF:SS:ID -0.00131022:0.00156211:0.396191:0.868717:98990:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865738 ES:SE:LP:AF:SS:ID -0.0015052:0.00156206:0.474634:0.865738:98990:rs3115849
1 762485 rs12095200 C A . PASS AF=0.09949 ES:SE:LP:AF:SS:ID 0.000761976:0.00186564:0.165603:0.09949:98990:rs12095200
1 762589 rs3115848 G C . PASS AF=0.87108 ES:SE:LP:AF:SS:ID -0.00144914:0.00158096:0.44449:0.87108:98990:rs3115848
1 762592 rs3131950 C G . PASS AF=0.87108 ES:SE:LP:AF:SS:ID -0.00144895:0.00158096:0.444411:0.87108:98990:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871079 ES:SE:LP:AF:SS:ID -0.00144796:0.00158097:0.444016:0.871079:98990:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871404 ES:SE:LP:AF:SS:ID -0.00126177:0.00158165:0.371596:0.871404:98990:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126213 ES:SE:LP:AF:SS:ID 0.00127534:0.00158271:0.376376:0.126213:98990:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105813 ES:SE:LP:AF:SS:ID -0.000578791:0.00172181:0.132676:0.105813:98990:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854841 ES:SE:LP:AF:SS:ID -0.000823947:0.0015471:0.225973:0.854841:98990:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.839409 ES:SE:LP:AF:SS:ID -0.00240616:0.00153061:0.935737:0.839409:98990:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763643 ES:SE:LP:AF:SS:ID -0.00168359:0.00122759:0.768956:0.763643:98990:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105051 ES:SE:LP:AF:SS:ID 0.00161272:0.00169746:0.465877:0.105051:98990:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00769385 ES:SE:LP:AF:SS:ID -0.00525483:0.00627881:0.39508:0.00769385:98990:rs12562811
1 769138 rs59306077 CAT C . PASS AF=0.129579 ES:SE:LP:AF:SS:ID 0.00153331:0.00156011:0.487186:0.129579:98990:rs762168062