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"file_date": "2019-11-25T16:08:38.712757",
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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-20528/ukb-d-20528.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20528/ukb-d-20528_data.vcf.gz; Date=Mon Nov 25 16:40:21 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-20528/ukb-d-20528.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-20528/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 17:15:53 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20528/ukb-d-20528.vcf.gz ...
Read summary statistics for 13571578 SNPs.
Dropped 12695 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: 0.0152 (0.0041)
Lambda GC: 1.0384
Mean Chi^2: 1.04
Intercept: 1.0052 (0.006)
Ratio: 0.1301 (0.1509)
Analysis finished at Mon Nov 25 17:17:45 2019
Total time elapsed: 1.0m:51.85s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0277,
"mean_EFFECT": 0,
"n": 117617,
"n_snps": 13571578,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1251348,
"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": 564638,
"n_est": 118040.9616,
"ratio_se_n": 1.0018,
"mean_diff": 0,
"ratio_diff": 9.8831,
"sd_y_est1": 0.3684,
"sd_y_est2": 0.3691,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1283502,
"ldsc_nsnp_merge_regression_ld": 1283502,
"ldsc_observed_scale_h2_beta": 0.0152,
"ldsc_observed_scale_h2_se": 0.0041,
"ldsc_intercept_beta": 1.0052,
"ldsc_intercept_se": 0.006,
"ldsc_lambda_gc": 1.0384,
"ldsc_mean_chisq": 1.04,
"ldsc_ratio": 0.13
}
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 | 13559547 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57056 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33331 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051435e+00 | 6.185079e+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 | 7.902519e+07 | 5.591595e+07 | 3.02000e+02 | 3.292804e+07 | 7.013918e+07 | 1.148590e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.490000e-05 | 8.854300e-03 | -9.89774e-02 | -2.381300e-03 | 3.000000e-07 | 2.356600e-03 | 1.126920e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.364800e-03 | 6.135200e-03 | 1.25770e-03 | 1.816600e-03 | 3.343200e-03 | 9.138700e-03 | 3.055400e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.958131e-01 | 2.897249e-01 | 1.00000e-07 | 2.439102e-01 | 4.941275e-01 | 7.469697e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.958117e-01 | 2.897257e-01 | 1.00000e-07 | 2.439074e-01 | 4.941258e-01 | 7.469685e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.909976e-01 | 2.544493e-01 | 1.00000e-03 | 7.483700e-03 | 6.026270e-02 | 2.956740e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 564638 | 0.9583956 | NA | NA | NA | NA | NA | 1.964733e-01 | 2.471295e-01 | 0.00000e+00 | 5.790700e-03 | 8.446490e-02 | 3.083070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.176170e+05 | 0.000000e+00 | 1.17617e+05 | 1.176170e+05 | 1.176170e+05 | 1.176170e+05 | 1.176170e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0053958 | 0.0026457 | 0.0414038 | 0.0414018 | 0.1116920 | 0.1894970 | 117617 |
1 | 693731 | rs12238997 | A | G | 0.0034661 | 0.0025058 | 0.1665900 | 0.1665868 | 0.1167120 | 0.1417730 | 117617 |
1 | 707522 | rs371890604 | G | C | 0.0035772 | 0.0028112 | 0.2031959 | 0.2031928 | 0.0983350 | 0.1293930 | 117617 |
1 | 717587 | rs144155419 | G | A | 0.0005977 | 0.0067473 | 0.9294140 | 0.9294139 | 0.0157344 | 0.0045926 | 117617 |
1 | 723329 | rs189787166 | A | T | -0.0068424 | 0.0196215 | 0.7273024 | 0.7273018 | 0.0017799 | 0.0003994 | 117617 |
1 | 730087 | rs148120343 | T | C | 0.0035957 | 0.0034844 | 0.3020967 | 0.3020951 | 0.0569456 | 0.0127796 | 117617 |
1 | 731718 | rs142557973 | T | C | 0.0036078 | 0.0023774 | 0.1291300 | 0.1291276 | 0.1226310 | 0.1543530 | 117617 |
1 | 732032 | rs61770163 | A | C | 0.0037846 | 0.0025340 | 0.1353050 | 0.1353021 | 0.1222120 | 0.1555510 | 117617 |
1 | 734349 | rs141242758 | T | C | 0.0036940 | 0.0023786 | 0.1204220 | 0.1204198 | 0.1218860 | 0.1525560 | 117617 |
1 | 740284 | rs61770167 | C | T | -0.0013531 | 0.0108503 | 0.9007579 | 0.9007583 | 0.0058652 | 0.0023962 | 117617 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0030211 | 0.0027944 | 0.2796443 | 0.2796427 | 0.0554994 | 0.0309934 | 117617 |
23 | 154923374 | rs111332691 | T | A | 0.0011311 | 0.0030440 | 0.7101956 | 0.7101930 | 0.0448320 | 0.0116556 | 117617 |
23 | 154925045 | rs509981 | C | T | 0.0014155 | 0.0014669 | 0.3345569 | 0.3345549 | 0.2447470 | 0.3634440 | 117617 |
23 | 154925895 | rs538470 | C | T | 0.0016524 | 0.0015000 | 0.2706207 | 0.2706176 | 0.2411690 | 0.3634440 | 117617 |
23 | 154927581 | rs644138 | G | A | 0.0005639 | 0.0013802 | 0.6828464 | 0.6828445 | 0.3006040 | 0.4635760 | 117617 |
23 | 154929412 | rs557132 | C | T | 0.0014678 | 0.0014672 | 0.3171407 | 0.3171390 | 0.2446210 | 0.3568210 | 117617 |
23 | 154929637 | rs35185538 | CT | C | 0.0014006 | 0.0015326 | 0.3607971 | 0.3607939 | 0.2288870 | 0.3011920 | 117617 |
23 | 154929952 | rs4012982 | CAA | C | 0.0018024 | 0.0015442 | 0.2431151 | 0.2431135 | 0.2387050 | 0.3165560 | 117617 |
23 | 154930230 | rs781880 | A | G | 0.0015193 | 0.0014668 | 0.3002998 | 0.3002961 | 0.2450460 | 0.3618540 | 117617 |
23 | 154930487 | rs781879 | T | A | -0.0007270 | 0.0049866 | 0.8840911 | 0.8840908 | 0.0196746 | 0.1263580 | 117617 |
1 692794 rs530212009 CA C . PASS AF=0.111692 ES:SE:LP:AF:SS:ID 0.00539584:0.00264569:1.38296:0.111692:117617:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116712 ES:SE:LP:AF:SS:ID 0.00346609:0.00250575:0.778351:0.116712:117617:rs12238997
1 707522 rs371890604 G C . PASS AF=0.098335 ES:SE:LP:AF:SS:ID 0.00357721:0.00281115:0.692085:0.098335:117617:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157344 ES:SE:LP:AF:SS:ID 0.00059769:0.00674729:0.0317908:0.0157344:117617:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00177987 ES:SE:LP:AF:SS:ID -0.00684235:0.0196215:0.138285:0.00177987:117617:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0569456 ES:SE:LP:AF:SS:ID 0.00359573:0.0034844:0.519854:0.0569456:117617:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122631 ES:SE:LP:AF:SS:ID 0.00360775:0.00237735:0.888973:0.122631:117617:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122212 ES:SE:LP:AF:SS:ID 0.00378463:0.00253404:0.868686:0.122212:117617:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121886 ES:SE:LP:AF:SS:ID 0.00369403:0.00237862:0.919294:0.121886:117617:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00586515 ES:SE:LP:AF:SS:ID -0.00135307:0.0108503:0.0453919:0.00586515:117617:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0018387 ES:SE:LP:AF:SS:ID 0.00278725:0.0207947:0.0489667:0.0018387:117617:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.86904 ES:SE:LP:AF:SS:ID -0.00347254:0.00234369:0.858757:0.86904:117617:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00158497 ES:SE:LP:AF:SS:ID -0.00490444:0.0208369:0.0894183:0.00158497:117617:rs190826124
1 751343 rs28544273 T A . PASS AF=0.123664 ES:SE:LP:AF:SS:ID 0.00350722:0.00232211:0.882878:0.123664:117617:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143291 ES:SE:LP:AF:SS:ID 0.00442413:0.00229673:1.26702:0.143291:117617:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123786 ES:SE:LP:AF:SS:ID 0.00351427:0.00231889:0.887231:0.123786:117617:rs28527770
1 753405 rs3115860 C A . PASS AF=0.8698 ES:SE:LP:AF:SS:ID -0.00373401:0.0022582:1.00778:0.8698:117617:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874585 ES:SE:LP:AF:SS:ID -0.00362468:0.00229616:0.941441:0.874585:117617:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129655 ES:SE:LP:AF:SS:ID 0.00374315:0.00226455:1.00724:0.129655:117617:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0365593 ES:SE:LP:AF:SS:ID 0.00122386:0.00411023:0.115835:0.0365593:117617:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869395 ES:SE:LP:AF:SS:ID -0.00383254:0.00225605:1.04884:0.869395:117617:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869467 ES:SE:LP:AF:SS:ID -0.00382489:0.00225689:1.04516:0.869467:117617:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869395 ES:SE:LP:AF:SS:ID -0.00383466:0.00225599:1.04975:0.869395:117617:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00512041 ES:SE:LP:AF:SS:ID 0.0102347:0.0115332:0.426137:0.00512041:117617:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00508968 ES:SE:LP:AF:SS:ID 0.0103123:0.0115586:0.429101:0.00508968:117617:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0056706 ES:SE:LP:AF:SS:ID -0.00877665:0.0111386:0.365799:0.0056706:117617:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869467 ES:SE:LP:AF:SS:ID -0.00371478:0.00225185:1.0043:0.869467:117617:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126927 ES:SE:LP:AF:SS:ID 0.00374266:0.00229875:0.985064:0.126927:117617:rs61768170
1 756604 rs3131962 A G . PASS AF=0.86899 ES:SE:LP:AF:SS:ID -0.00383811:0.00224594:1.05814:0.86899:117617:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868386 ES:SE:LP:AF:SS:ID -0.00387862:0.00224506:1.07542:0.868386:117617:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869177 ES:SE:LP:AF:SS:ID -0.00378983:0.00224816:1.03693:0.869177:117617:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869183 ES:SE:LP:AF:SS:ID -0.0037883:0.00224832:1.0362:0.869183:117617:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869186 ES:SE:LP:AF:SS:ID -0.0037927:0.00224834:1.03798:0.869186:117617:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869621 ES:SE:LP:AF:SS:ID -0.00368118:0.00225409:0.989492:0.869621:117617:rs3131954
1 759293 rs10157329 T A . PASS AF=0.099573 ES:SE:LP:AF:SS:ID 0.00310924:0.0026202:0.628247:0.099573:117617:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.0065294 ES:SE:LP:AF:SS:ID -0.00719631:0.0101098:0.321863:0.0065294:117617:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873686 ES:SE:LP:AF:SS:ID -0.00348635:0.0022887:0.893847:0.873686:117617:rs3115851
1 761732 rs2286139 C T . PASS AF=0.86297 ES:SE:LP:AF:SS:ID -0.00364558:0.00224452:0.981578:0.86297:117617:rs2286139
1 761752 rs1057213 C T . PASS AF=0.86837 ES:SE:LP:AF:SS:ID -0.00340843:0.00226614:0.877568:0.86837:117617:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865379 ES:SE:LP:AF:SS:ID -0.00374827:0.00226649:1.008:0.865379:117617:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0997227 ES:SE:LP:AF:SS:ID 0.00422742:0.00270864:0.925937:0.0997227:117617:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870674 ES:SE:LP:AF:SS:ID -0.00376194:0.00229316:0.996096:0.870674:117617:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870674 ES:SE:LP:AF:SS:ID -0.00376199:0.00229316:0.996113:0.870674:117617:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870673 ES:SE:LP:AF:SS:ID -0.00376514:0.00229317:0.997342:0.870673:117617:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870994 ES:SE:LP:AF:SS:ID -0.00368316:0.00229414:0.964991:0.870994:117617:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126519 ES:SE:LP:AF:SS:ID 0.00351113:0.00229624:0.898779:0.126519:117617:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106337 ES:SE:LP:AF:SS:ID 0.00422379:0.00249506:1.04343:0.106337:117617:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854424 ES:SE:LP:AF:SS:ID -0.00379437:0.00224405:1.04159:0.854424:117617:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00169138 ES:SE:LP:AF:SS:ID -0.00965501:0.0197089:0.204663:0.00169138:117617:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.839135 ES:SE:LP:AF:SS:ID -0.00288546:0.00222336:0.711391:0.839135:117617:rs376645387