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"file_date": "2019-11-25T13:09:50.649105",
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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-30830_raw/ukb-d-30830_raw.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30830_raw/ukb-d-30830_raw_data.vcf.gz; Date=Mon Nov 25 14:09:37 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-30830_raw/ukb-d-30830_raw.vcf.gz; Date=Sat May 9 17:48:50 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-30830_raw/ukb-d-30830_raw.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-30830_raw/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 14:54:56 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30830_raw/ukb-d-30830_raw.vcf.gz ...
Read summary statistics for 13585246 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1801 (0.0474)
Lambda GC: 1.4621
Mean Chi^2: 2.149
Intercept: 1.0991 (0.0173)
Ratio: 0.0863 (0.0151)
Analysis finished at Mon Nov 25 14:57:00 2019
Total time elapsed: 2.0m:4.36s
{
"af_correlation": 0.9521,
"inflation_factor": 1.2719,
"mean_EFFECT": -0.001,
"n": 312215,
"n_snps": 13585246,
"n_clumped_hits": 216,
"n_p_sig": 36292,
"n_mono": 0,
"n_ns": 1251735,
"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": 568991,
"n_est": 313452.6917,
"ratio_se_n": 1.002,
"mean_diff": 0.0009,
"ratio_diff": 607.0045,
"sd_y_est1": 25.1684,
"sd_y_est2": 25.2183,
"r2_sum1": 48.1893,
"r2_sum2": 0.0761,
"r2_sum3": 0.0758,
"r2_sum4": 0.0753,
"ldsc_nsnp_merge_refpanel_ld": 1283502,
"ldsc_nsnp_merge_regression_ld": 1283502,
"ldsc_observed_scale_h2_beta": 0.1801,
"ldsc_observed_scale_h2_se": 0.0474,
"ldsc_intercept_beta": 1.0991,
"ldsc_intercept_se": 0.0173,
"ldsc_lambda_gc": 1.4621,
"ldsc_mean_chisq": 2.149,
"ldsc_ratio": 0.0862
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | TRUE |
n | FALSE |
is_snpid_non_unique | TRUE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | TRUE |
n_p_sig | TRUE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | FALSE |
ldsc_intercept_beta | FALSE |
n_clumped_hits | FALSE |
r2_sum1 | TRUE |
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 | 1.000000 | 3 | 94 | 0 | 13573198 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.000000 | 1 | 100 | 0 | 57081 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.000000 | 1 | 342 | 0 | 33334 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | 9.051262e+00 | 6.184964e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.902551e+07 | 5.591508e+07 | 3.02000e+02 | 3.293070e+07 | 7.013916e+07 | 1.148601e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | -9.637000e-04 | 3.893770e-01 | -2.54060e+01 | -1.162100e-01 | -1.593000e-04 | 1.145100e-01 | 1.306400e+01 | ▁▁▁▇▁ |
numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | 2.675995e-01 | 2.581252e-01 | 5.22840e-02 | 7.620200e-02 | 1.404000e-01 | 3.845200e-01 | 1.301000e+00 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.596128e-01 | 3.008662e-01 | 0.00000e+00 | 1.891398e-01 | 4.468502e-01 | 7.206294e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.596122e-01 | 3.008664e-01 | 0.00000e+00 | 1.891379e-01 | 4.468510e-01 | 7.206325e-01 | 9.999999e-01 | ▇▆▆▆▆ |
numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | 1.908184e-01 | 2.544052e-01 | 1.00000e-03 | 7.433900e-03 | 6.004500e-02 | 2.953300e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 568991 | 0.958117 | NA | NA | NA | NA | NA | 1.963451e-01 | 2.471029e-01 | 0.00000e+00 | 5.591000e-03 | 8.426520e-02 | 3.081070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.122150e+05 | 0.000000e+00 | 3.12215e+05 | 3.122150e+05 | 3.122150e+05 | 3.122150e+05 | 3.122150e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.133170 | 0.111590 | 0.2327298 | 0.2327180 | 0.1104600 | 0.1894970 | 312215 |
1 | 693731 | rs12238997 | A | G | 0.024617 | 0.105420 | 0.8153600 | 0.8153626 | 0.1157500 | 0.1417730 | 312215 |
1 | 707522 | rs371890604 | G | C | -0.046790 | 0.118610 | 0.6932294 | 0.6932222 | 0.0971530 | 0.1293930 | 312215 |
1 | 717587 | rs144155419 | G | A | 0.614980 | 0.282640 | 0.0295699 | 0.0295671 | 0.0156810 | 0.0045926 | 312215 |
1 | 723329 | rs189787166 | A | T | -0.680170 | 0.834240 | 0.4148996 | 0.4148909 | 0.0017330 | 0.0003994 | 312215 |
1 | 730087 | rs148120343 | T | C | 0.056586 | 0.146870 | 0.7000193 | 0.7000303 | 0.0564350 | 0.0127796 | 312215 |
1 | 731718 | rs142557973 | T | C | 0.013986 | 0.099994 | 0.8887600 | 0.8887640 | 0.1216400 | 0.1543530 | 312215 |
1 | 732032 | rs61770163 | A | C | 0.034475 | 0.106710 | 0.7466499 | 0.7466408 | 0.1210100 | 0.1555510 | 312215 |
1 | 734349 | rs141242758 | T | C | 0.013654 | 0.100050 | 0.8914500 | 0.8914483 | 0.1208600 | 0.1525560 | 312215 |
1 | 740284 | rs61770167 | C | T | -0.211590 | 0.459590 | 0.6452396 | 0.6452373 | 0.0057346 | 0.0023962 | 312215 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.118590 | 0.115380 | 0.3040402 | 0.3040340 | 0.056128 | 0.0309934 | 312215 |
23 | 154923374 | rs111332691 | T | A | -0.056379 | 0.126400 | 0.6555805 | 0.6555710 | 0.044947 | 0.0116556 | 312215 |
23 | 154925045 | rs509981 | C | T | 0.128470 | 0.060956 | 0.0350663 | 0.0350668 | 0.245800 | 0.3634440 | 312215 |
23 | 154925895 | rs538470 | C | T | 0.122950 | 0.062354 | 0.0486306 | 0.0486317 | 0.242090 | 0.3634440 | 312215 |
23 | 154927581 | rs644138 | G | A | 0.143600 | 0.057335 | 0.0122611 | 0.0122597 | 0.302300 | 0.4635760 | 312215 |
23 | 154929412 | rs557132 | C | T | 0.127950 | 0.060973 | 0.0358641 | 0.0358637 | 0.245650 | 0.3568210 | 312215 |
23 | 154929637 | rs35185538 | CT | C | 0.133650 | 0.063625 | 0.0356739 | 0.0356770 | 0.230020 | 0.3011920 | 312215 |
23 | 154929952 | rs4012982 | CAA | C | 0.153920 | 0.064119 | 0.0163712 | 0.0163711 | 0.239600 | 0.3165560 | 312215 |
23 | 154930230 | rs781880 | A | G | 0.120300 | 0.060966 | 0.0484619 | 0.0484693 | 0.246030 | 0.3618540 | 312215 |
23 | 154930487 | rs781879 | T | A | -0.256470 | 0.209400 | 0.2206500 | 0.2206562 | 0.019488 | 0.1263580 | 312215 |
1 692794 rs530212009 CA C . PASS AF=0.11046 ES:SE:LP:AF:SS:ID 0.13317:0.11159:0.633148:0.11046:312215:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11575 ES:SE:LP:AF:SS:ID 0.024617:0.10542:0.0886506:0.11575:312215:rs12238997
1 707522 rs371890604 G C . PASS AF=0.097153 ES:SE:LP:AF:SS:ID -0.04679:0.11861:0.159123:0.097153:312215:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015681 ES:SE:LP:AF:SS:ID 0.61498:0.28264:1.52915:0.015681:312215:rs144155419
1 723329 rs189787166 A T . PASS AF=0.001733 ES:SE:LP:AF:SS:ID -0.68017:0.83424:0.382057:0.001733:312215:rs189787166
1 730087 rs148120343 T C . PASS AF=0.056435 ES:SE:LP:AF:SS:ID 0.056586:0.14687:0.15489:0.056435:312215:rs148120343
1 731718 rs58276399 T C . PASS AF=0.12164 ES:SE:LP:AF:SS:ID 0.013986:0.099994:0.0512155:0.12164:312215:rs58276399
1 732032 rs61770163 A C . PASS AF=0.12101 ES:SE:LP:AF:SS:ID 0.034475:0.10671:0.126883:0.12101:312215:rs61770163
1 734349 rs141242758 T C . PASS AF=0.12086 ES:SE:LP:AF:SS:ID 0.013654:0.10005:0.049903:0.12086:312215:rs141242758
1 740284 rs61770167 C T . PASS AF=0.0057346 ES:SE:LP:AF:SS:ID -0.21159:0.45959:0.190279:0.0057346:312215:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0018613 ES:SE:LP:AF:SS:ID -1.5893:0.86898:1.17129:0.0018613:312215:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.86983 ES:SE:LP:AF:SS:ID -0.056523:0.098625:0.246746:0.86983:312215:rs529266287
1 750230 rs190826124 G C . PASS AF=0.0015162 ES:SE:LP:AF:SS:ID -0.97135:0.89709:0.554536:0.0015162:312215:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12283 ES:SE:LP:AF:SS:ID 0.061088:0.097682:0.274309:0.12283:312215:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.14262 ES:SE:LP:AF:SS:ID 0.057754:0.096529:0.25993:0.14262:312215:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12295 ES:SE:LP:AF:SS:ID 0.060513:0.097545:0.27163:0.12295:312215:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87104 ES:SE:LP:AF:SS:ID -0.0322:0.095078:0.133795:0.87104:312215:rs3115860
1 753425 rs3131970 T C . PASS AF=0.87558 ES:SE:LP:AF:SS:ID -0.049886:0.096627:0.217771:0.87558:312215:rs3131970
1 753541 rs2073813 G A . PASS AF=0.12851 ES:SE:LP:AF:SS:ID 0.045699:0.095307:0.199565:0.12851:312215:rs2073813
1 754105 rs12184325 C T . PASS AF=0.036292 ES:SE:LP:AF:SS:ID 0.11663:0.17299:0.300874:0.036292:312215:rs12184325
1 754182 rs3131969 A G . PASS AF=0.87063 ES:SE:LP:AF:SS:ID -0.033163:0.094974:0.138489:0.87063:312215:rs3131969
1 754192 rs3131968 A G . PASS AF=0.87074 ES:SE:LP:AF:SS:ID -0.03712:0.095022:0.157353:0.87074:312215:rs3131968
1 754334 rs3131967 T C . PASS AF=0.87062 ES:SE:LP:AF:SS:ID -0.03282:0.094971:0.136879:0.87062:312215:rs3131967
1 754433 rs150578204 G A . PASS AF=0.0050365 ES:SE:LP:AF:SS:ID 0.39903:0.48714:0.384344:0.0050365:312215:rs150578204
1 754458 rs142682604 G T . PASS AF=0.0050039 ES:SE:LP:AF:SS:ID 0.40833:0.48843:0.394533:0.0050039:312215:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0055192 ES:SE:LP:AF:SS:ID 0.42571:0.47469:0.432021:0.0055192:312215:rs184270342
1 755890 rs3115858 A T . PASS AF=0.87072 ES:SE:LP:AF:SS:ID -0.037091:0.094813:0.157609:0.87072:312215:rs3115858
1 756434 rs61768170 G C . PASS AF=0.12584 ES:SE:LP:AF:SS:ID 0.060765:0.096732:0.275814:0.12584:312215:rs61768170
1 756604 rs3131962 A G . PASS AF=0.87029 ES:SE:LP:AF:SS:ID -0.044187:0.094587:0.193555:0.87029:312215:rs3131962
1 757640 rs3115853 G A . PASS AF=0.86956 ES:SE:LP:AF:SS:ID -0.027875:0.094502:0.114627:0.86956:312215:rs3115853
1 757734 rs4951929 C T . PASS AF=0.87044 ES:SE:LP:AF:SS:ID -0.038078:0.094667:0.162721:0.87044:312215:rs4951929
1 757936 rs4951862 C A . PASS AF=0.87044 ES:SE:LP:AF:SS:ID -0.038235:0.094674:0.16348:0.87044:312215:rs4951862
1 758144 rs3131956 A G . PASS AF=0.87045 ES:SE:LP:AF:SS:ID -0.039312:0.094677:0.168783:0.87045:312215:rs3131956
1 758626 rs3131954 C T . PASS AF=0.8709 ES:SE:LP:AF:SS:ID -0.03394:0.094917:0.142264:0.8709:312215:rs3131954
1 759293 rs10157329 T A . PASS AF=0.098742 ES:SE:LP:AF:SS:ID -0.030308:0.11031:0.105967:0.098742:312215:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.0063972 ES:SE:LP:AF:SS:ID 0.57371:0.42928:0.741363:0.0063972:312215:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.87475 ES:SE:LP:AF:SS:ID -0.057265:0.096308:0.257974:0.87475:312215:rs3115851
1 761732 rs2286139 C T . PASS AF=0.86418 ES:SE:LP:AF:SS:ID -0.042835:0.094472:0.18692:0.86418:312215:rs2286139
1 761752 rs1057213 C T . PASS AF=0.86957 ES:SE:LP:AF:SS:ID -0.043413:0.09537:0.187782:0.86957:312215:rs1057213
1 762273 rs3115849 G A . PASS AF=0.86651 ES:SE:LP:AF:SS:ID -0.054637:0.095389:0.246578:0.86651:312215:rs3115849
1 762485 rs12095200 C A . PASS AF=0.09874 ES:SE:LP:AF:SS:ID 0.035614:0.11416:0.122019:0.09874:312215:rs12095200
1 762589 rs3115848 G C . PASS AF=0.87168 ES:SE:LP:AF:SS:ID -0.070057:0.09647:0.330023:0.87168:312215:rs3115848
1 762592 rs3131950 C G . PASS AF=0.87168 ES:SE:LP:AF:SS:ID -0.070063:0.09647:0.330051:0.87168:312215:rs3131950
1 762601 rs3131949 T C . PASS AF=0.87168 ES:SE:LP:AF:SS:ID -0.070186:0.096472:0.330767:0.87168:312215:rs3131949
1 762632 rs3131948 T A . PASS AF=0.87204 ES:SE:LP:AF:SS:ID -0.062653:0.096525:0.287115:0.87204:312215:rs3131948
1 764191 rs7515915 T G . PASS AF=0.12546 ES:SE:LP:AF:SS:ID 0.068511:0.096599:0.320409:0.12546:312215:rs7515915
1 766007 rs61768174 A C . PASS AF=0.10531 ES:SE:LP:AF:SS:ID -0.047166:0.10522:0.184455:0.10531:312215:rs61768174
1 766105 rs2519015 T A . PASS AF=0.8555 ES:SE:LP:AF:SS:ID -0.064546:0.09443:0.306036:0.8555:312215:rs2519015
1 767393 rs538667473 A C . PASS AF=0.0016517 ES:SE:LP:AF:SS:ID -0.4892:0.83622:0.252946:0.0016517:312215:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.83831 ES:SE:LP:AF:SS:ID -0.22184:0.092879:1.77163:0.83831:312215:rs376645387