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"file_date": "2019-11-25T16:20:28.869392",
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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-5001/ukb-d-5001.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5001/ukb-d-5001_data.vcf.gz; Date=Mon Nov 25 16:53:47 2019",
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}
*********************************************************************
* 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-5001/ukb-d-5001.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-5001/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 17:19:59 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5001/ukb-d-5001.vcf.gz ...
Read summary statistics for 13562422 SNPs.
Dropped 12682 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0519 (0.0069)
Lambda GC: 1.0945
Mean Chi^2: 1.0959
Intercept: 1.009 (0.0067)
Ratio: 0.0936 (0.0696)
Analysis finished at Mon Nov 25 17:22:34 2019
Total time elapsed: 2.0m:34.73s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0564,
"mean_EFFECT": -0,
"n": 84560,
"n_snps": 13562422,
"n_clumped_hits": 1,
"n_p_sig": 4,
"n_mono": 0,
"n_ns": 1251044,
"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": 561700,
"n_est": 84918.6656,
"ratio_se_n": 1.0021,
"mean_diff": -0.0001,
"ratio_diff": 36.2459,
"sd_y_est1": 0.3312,
"sd_y_est2": 0.3319,
"r2_sum1": 0,
"r2_sum2": 0.0004,
"r2_sum3": 0.0004,
"r2_sum4": 0.0004,
"ldsc_nsnp_merge_refpanel_ld": 1283502,
"ldsc_nsnp_merge_regression_ld": 1283502,
"ldsc_observed_scale_h2_beta": 0.0519,
"ldsc_observed_scale_h2_se": 0.0069,
"ldsc_intercept_beta": 1.009,
"ldsc_intercept_se": 0.0067,
"ldsc_lambda_gc": 1.0945,
"ldsc_mean_chisq": 1.0959,
"ldsc_ratio": 0.0938
}
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 | 13550404 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57048 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33325 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051606e+00 | 6.185015e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.902533e+07 | 5.591631e+07 | 3.0200e+02 | 3.292938e+07 | 7.013786e+07 | 1.148565e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -3.320000e-05 | 9.410000e-03 | -1.4600e-01 | -2.539500e-03 | 6.900000e-06 | 2.569000e-03 | 1.011260e-01 | ▁▁▇▃▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.734100e-03 | 6.487600e-03 | 1.3242e-03 | 1.925300e-03 | 3.539200e-03 | 9.668400e-03 | 3.320140e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.912087e-01 | 2.907072e-01 | 0.0000e+00 | 2.371488e-01 | 4.881587e-01 | 7.429404e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.912068e-01 | 2.907083e-01 | 0.0000e+00 | 2.371459e-01 | 4.881566e-01 | 7.429404e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.911313e-01 | 2.544796e-01 | 1.0000e-03 | 7.522600e-03 | 6.039180e-02 | 2.959520e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 561700 | 0.9585841 | NA | NA | NA | NA | NA | 1.965649e-01 | 2.471540e-01 | 0.0000e+00 | 5.790700e-03 | 8.446490e-02 | 3.085060e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.456000e+04 | 0.000000e+00 | 8.4560e+04 | 8.456000e+04 | 8.456000e+04 | 8.456000e+04 | 8.456000e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0013076 | 0.0028139 | 0.6421493 | 0.6421487 | 0.1121560 | 0.1894970 | 84560 |
1 | 693731 | rs12238997 | A | G | 0.0024167 | 0.0026619 | 0.3639410 | 0.3639388 | 0.1175570 | 0.1417730 | 84560 |
1 | 707522 | rs371890604 | G | C | 0.0024680 | 0.0029869 | 0.4086571 | 0.4086543 | 0.0985902 | 0.1293930 | 84560 |
1 | 717587 | rs144155419 | G | A | 0.0027291 | 0.0071657 | 0.7033087 | 0.7033078 | 0.0157686 | 0.0045926 | 84560 |
1 | 723329 | rs189787166 | A | T | -0.0153198 | 0.0210321 | 0.4663726 | 0.4663682 | 0.0017291 | 0.0003994 | 84560 |
1 | 730087 | rs148120343 | T | C | 0.0003885 | 0.0037052 | 0.9164840 | 0.9164840 | 0.0572239 | 0.0127796 | 84560 |
1 | 731718 | rs142557973 | T | C | 0.0015867 | 0.0025283 | 0.5302846 | 0.5302821 | 0.1233210 | 0.1543530 | 84560 |
1 | 732032 | rs61770163 | A | C | 0.0026554 | 0.0026927 | 0.3240530 | 0.3240497 | 0.1226810 | 0.1555510 | 84560 |
1 | 734349 | rs141242758 | T | C | 0.0016252 | 0.0025300 | 0.5206502 | 0.5206479 | 0.1225210 | 0.1525560 | 84560 |
1 | 740284 | rs61770167 | C | T | 0.0002943 | 0.0114042 | 0.9794120 | 0.9794120 | 0.0059528 | 0.0023962 | 84560 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0058971 | 0.0029453 | 0.0452616 | 0.0452588 | 0.0553391 | 0.0309934 | 84560 |
23 | 154923374 | rs111332691 | T | A | -0.0019959 | 0.0032156 | 0.5348057 | 0.5348036 | 0.0445246 | 0.0116556 | 84560 |
23 | 154925045 | rs509981 | C | T | -0.0004939 | 0.0015485 | 0.7497872 | 0.7497869 | 0.2439760 | 0.3634440 | 84560 |
23 | 154925895 | rs538470 | C | T | -0.0006445 | 0.0015830 | 0.6838975 | 0.6838975 | 0.2404630 | 0.3634440 | 84560 |
23 | 154927581 | rs644138 | G | A | -0.0019092 | 0.0014561 | 0.1898021 | 0.1897989 | 0.2997000 | 0.4635760 | 84560 |
23 | 154929412 | rs557132 | C | T | -0.0004520 | 0.0015492 | 0.7704545 | 0.7704538 | 0.2437950 | 0.3568210 | 84560 |
23 | 154929637 | rs35185538 | CT | C | -0.0006314 | 0.0016141 | 0.6956391 | 0.6956390 | 0.2283320 | 0.3011920 | 84560 |
23 | 154929952 | rs4012982 | CAA | C | -0.0003005 | 0.0016293 | 0.8536959 | 0.8536949 | 0.2379300 | 0.3165560 | 84560 |
23 | 154930230 | rs781880 | A | G | -0.0004339 | 0.0015488 | 0.7793508 | 0.7793482 | 0.2442420 | 0.3618540 | 84560 |
23 | 154930487 | rs781879 | T | A | -0.0009497 | 0.0053265 | 0.8584860 | 0.8584855 | 0.0192211 | 0.1263580 | 84560 |
1 692794 rs530212009 CA C . PASS AF=0.112156 ES:SE:LP:AF:SS:ID 0.00130761:0.0028139:0.192364:0.112156:84560:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.117557 ES:SE:LP:AF:SS:ID 0.0024167:0.0026619:0.438969:0.117557:84560:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0985902 ES:SE:LP:AF:SS:ID 0.00246796:0.00298689:0.388641:0.0985902:84560:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157686 ES:SE:LP:AF:SS:ID 0.00272913:0.00716572:0.152854:0.0157686:84560:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00172909 ES:SE:LP:AF:SS:ID -0.0153198:0.0210321:0.331267:0.00172909:84560:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0572239 ES:SE:LP:AF:SS:ID 0.000388542:0.00370521:0.0378751:0.0572239:84560:rs148120343
1 731718 rs58276399 T C . PASS AF=0.123321 ES:SE:LP:AF:SS:ID 0.00158668:0.00252827:0.275491:0.123321:84560:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122681 ES:SE:LP:AF:SS:ID 0.00265545:0.00269269:0.489384:0.122681:84560:rs61770163
1 734349 rs141242758 T C . PASS AF=0.122521 ES:SE:LP:AF:SS:ID 0.00162517:0.00253005:0.283454:0.122521:84560:rs141242758
1 740284 rs61770167 C T . PASS AF=0.0059528 ES:SE:LP:AF:SS:ID 0.000294298:0.0114042:0.00903458:0.0059528:84560:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0018425 ES:SE:LP:AF:SS:ID -0.0267375:0.0223094:0.636894:0.0018425:84560:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.868238 ES:SE:LP:AF:SS:ID -0.00167178:0.00249506:0.298575:0.868238:84560:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00164427 ES:SE:LP:AF:SS:ID 0.0289137:0.0216449:0.74086:0.00164427:84560:rs190826124
1 751343 rs28544273 T A . PASS AF=0.124395 ES:SE:LP:AF:SS:ID 0.00203061:0.00247069:0.386002:0.124395:84560:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.144 ES:SE:LP:AF:SS:ID 0.0018814:0.00244683:0.354629:0.144:84560:rs200141114
1 751756 rs28527770 T C . PASS AF=0.124533 ES:SE:LP:AF:SS:ID 0.00208612:0.00246689:0.400389:0.124533:84560:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869246 ES:SE:LP:AF:SS:ID -0.00150943:0.0024029:0.27581:0.869246:84560:rs3115860
1 753425 rs3131970 T C . PASS AF=0.873942 ES:SE:LP:AF:SS:ID -0.00170544:0.00244277:0.314187:0.873942:84560:rs3131970
1 753541 rs2073813 G A . PASS AF=0.130314 ES:SE:LP:AF:SS:ID 0.00211806:0.00240843:0.421168:0.130314:84560:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0369737 ES:SE:LP:AF:SS:ID 0.000499579:0.00433577:0.0417855:0.0369737:84560:rs12184325
1 754182 rs3131969 A G . PASS AF=0.868843 ES:SE:LP:AF:SS:ID -0.00167501:0.00240047:0.313976:0.868843:84560:rs3131969
1 754192 rs3131968 A G . PASS AF=0.868982 ES:SE:LP:AF:SS:ID -0.00157918:0.00240183:0.291691:0.868982:84560:rs3131968
1 754334 rs3131967 T C . PASS AF=0.868843 ES:SE:LP:AF:SS:ID -0.0016785:0.00240034:0.314812:0.868843:84560:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00518321 ES:SE:LP:AF:SS:ID 0.0186504:0.0121682:0.901883:0.00518321:84560:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00514894 ES:SE:LP:AF:SS:ID 0.0183387:0.0122019:0.876616:0.00514894:84560:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0053731 ES:SE:LP:AF:SS:ID 0.00280916:0.0122065:0.0872541:0.0053731:84560:rs184270342
1 755890 rs3115858 A T . PASS AF=0.868963 ES:SE:LP:AF:SS:ID -0.00158367:0.00239655:0.293508:0.868963:84560:rs3115858
1 756434 rs61768170 G C . PASS AF=0.127547 ES:SE:LP:AF:SS:ID 0.00221394:0.00244579:0.43728:0.127547:84560:rs61768170
1 756604 rs3131962 A G . PASS AF=0.868537 ES:SE:LP:AF:SS:ID -0.00169757:0.00239094:0.320839:0.868537:84560:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867698 ES:SE:LP:AF:SS:ID -0.00192014:0.00238768:0.375418:0.867698:84560:rs3115853
1 757734 rs4951929 C T . PASS AF=0.868689 ES:SE:LP:AF:SS:ID -0.00162274:0.00239291:0.303048:0.868689:84560:rs4951929
1 757936 rs4951862 C A . PASS AF=0.868696 ES:SE:LP:AF:SS:ID -0.0016256:0.00239309:0.303681:0.868696:84560:rs4951862
1 758144 rs3131956 A G . PASS AF=0.868706 ES:SE:LP:AF:SS:ID -0.00165464:0.00239318:0.31041:0.868706:84560:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869131 ES:SE:LP:AF:SS:ID -0.00156734:0.00239929:0.289377:0.869131:84560:rs3131954
1 759293 rs10157329 T A . PASS AF=0.100096 ES:SE:LP:AF:SS:ID 0.00218572:0.0027837:0.364168:0.100096:84560:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00617499 ES:SE:LP:AF:SS:ID 0.00342158:0.0110722:0.12073:0.00617499:84560:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873113 ES:SE:LP:AF:SS:ID -0.0016021:0.00243546:0.291872:0.873113:84560:rs3115851
1 761732 rs2286139 C T . PASS AF=0.862393 ES:SE:LP:AF:SS:ID -0.00168177:0.00238884:0.317468:0.862393:84560:rs2286139
1 761752 rs1057213 C T . PASS AF=0.867919 ES:SE:LP:AF:SS:ID -0.00167542:0.00241128:0.312323:0.867919:84560:rs1057213
1 762273 rs3115849 G A . PASS AF=0.864685 ES:SE:LP:AF:SS:ID -0.00119316:0.00241116:0.207113:0.864685:84560:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0997324 ES:SE:LP:AF:SS:ID 0.00132163:0.00289192:0.18865:0.0997324:84560:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870023 ES:SE:LP:AF:SS:ID -0.00145882:0.00243906:0.259819:0.870023:84560:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870022 ES:SE:LP:AF:SS:ID -0.00145892:0.00243905:0.259843:0.870022:84560:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870025 ES:SE:LP:AF:SS:ID -0.00145031:0.00243922:0.25796:0.870025:84560:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870385 ES:SE:LP:AF:SS:ID -0.00145639:0.00244051:0.259108:0.870385:84560:rs3131948
1 764191 rs7515915 T G . PASS AF=0.127086 ES:SE:LP:AF:SS:ID 0.00209017:0.00244281:0.406492:0.127086:84560:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106665 ES:SE:LP:AF:SS:ID 0.00125976:0.00265521:0.197103:0.106665:84560:rs61768174
1 766105 rs2519015 T A . PASS AF=0.85369 ES:SE:LP:AF:SS:ID -0.00187098:0.00238712:0.363342:0.85369:84560:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00162574 ES:SE:LP:AF:SS:ID -0.0199926:0.0212058:0.461188:0.00162574:84560:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.837496 ES:SE:LP:AF:SS:ID 0.00149859:0.00234886:0.281107:0.837496:84560:rs376645387