manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22611_0/ukb-d-22611_0_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:11:47.269085",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"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-22611_0/ukb-d-22611_0.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22611_0/ukb-d-22611_0_data.vcf.gz; Date=Mon Nov 25 15:37:45 2019",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-22611_0/ukb-d-22611_0.vcf.gz; Date=Sun May 10 11:02:29 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-22611_0/ukb-d-22611_0.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-22611_0/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 16:34:12 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22611_0/ukb-d-22611_0.vcf.gz ...
Read summary statistics for 13566863 SNPs.
Dropped 12681 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, 1283503 SNPs remain.
After merging with regression SNP LD, 1283503 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0119 (0.0046)
Lambda GC: 1.0244
Mean Chi^2: 1.0288
Intercept: 1.0079 (0.0057)
Ratio: 0.2733 (0.1966)
Analysis finished at Mon Nov 25 16:36:57 2019
Total time elapsed: 2.0m:44.64s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0168,
"mean_EFFECT": -3.7189e-06,
"n": 89714,
"n_snps": 13566863,
"n_clumped_hits": 0,
"n_p_sig": 1,
"n_mono": 0,
"n_ns": 1251230,
"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": 563191,
"n_est": 90036.2474,
"ratio_se_n": 1.0018,
"mean_diff": -9.4984e-06,
"ratio_diff": 3.5294,
"sd_y_est1": 0.3527,
"sd_y_est2": 0.3533,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1283503,
"ldsc_nsnp_merge_regression_ld": 1283503,
"ldsc_observed_scale_h2_beta": 0.0119,
"ldsc_observed_scale_h2_se": 0.0046,
"ldsc_intercept_beta": 1.0079,
"ldsc_intercept_se": 0.0057,
"ldsc_lambda_gc": 1.0244,
"ldsc_mean_chisq": 1.0288,
"ldsc_ratio": 0.2743
}
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 | 13554846 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57044 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33332 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051329e+00 | 6.184968e+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 | 7.902489e+07 | 5.591644e+07 | 3.02000e+02 | 3.292812e+07 | 7.013467e+07 | 1.148620e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -3.700000e-06 | 9.685200e-03 | -1.23795e-01 | -2.555900e-03 | 1.710000e-05 | 2.612200e-03 | 1.025320e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.968400e-03 | 6.715600e-03 | 1.37360e-03 | 1.991000e-03 | 3.662200e-03 | 1.000610e-02 | 3.383630e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.969576e-01 | 2.898275e-01 | 0.00000e+00 | 2.446628e-01 | 4.964151e-01 | 7.484176e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.969558e-01 | 2.898285e-01 | 0.00000e+00 | 2.446595e-01 | 4.964124e-01 | 7.484177e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.910684e-01 | 2.544751e-01 | 1.00000e-03 | 7.499400e-03 | 6.030120e-02 | 2.957645e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 563191 | 0.9584878 | NA | NA | NA | NA | NA | 1.965245e-01 | 2.471463e-01 | 0.00000e+00 | 5.790700e-03 | 8.446490e-02 | 3.085060e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.971400e+04 | 0.000000e+00 | 8.97140e+04 | 8.971400e+04 | 8.971400e+04 | 8.971400e+04 | 8.971400e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0020187 | 0.0029046 | 0.4870584 | 0.4870560 | 0.1116230 | 0.1894970 | 89714 |
1 | 693731 | rs12238997 | A | G | 0.0027915 | 0.0027513 | 0.3103002 | 0.3102982 | 0.1166320 | 0.1417730 | 89714 |
1 | 707522 | rs371890604 | G | C | 0.0030644 | 0.0030927 | 0.3217548 | 0.3217513 | 0.0980012 | 0.1293930 | 89714 |
1 | 717587 | rs144155419 | G | A | -0.0017244 | 0.0073603 | 0.8147711 | 0.8147703 | 0.0158424 | 0.0045926 | 89714 |
1 | 723329 | rs189787166 | A | T | -0.0479839 | 0.0216444 | 0.0266312 | 0.0266286 | 0.0017596 | 0.0003994 | 89714 |
1 | 730087 | rs148120343 | T | C | 0.0057075 | 0.0038150 | 0.1346421 | 0.1346386 | 0.0570389 | 0.0127796 | 89714 |
1 | 731718 | rs142557973 | T | C | 0.0028308 | 0.0026108 | 0.2782403 | 0.2782365 | 0.1225270 | 0.1543530 | 89714 |
1 | 732032 | rs61770163 | A | C | 0.0017954 | 0.0027840 | 0.5190008 | 0.5189999 | 0.1221950 | 0.1555510 | 89714 |
1 | 734349 | rs141242758 | T | C | 0.0028898 | 0.0026127 | 0.2687089 | 0.2687062 | 0.1217590 | 0.1525560 | 89714 |
1 | 740284 | rs61770167 | C | T | 0.0161706 | 0.0120280 | 0.1788191 | 0.1788149 | 0.0057274 | 0.0023962 | 89714 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0048942 | 0.0030569 | 0.1093810 | 0.1093777 | 0.0552893 | 0.0309934 | 89714 |
23 | 154923374 | rs111332691 | T | A | -0.0021648 | 0.0033244 | 0.5149286 | 0.5149262 | 0.0448982 | 0.0116556 | 89714 |
23 | 154925045 | rs509981 | C | T | 0.0008731 | 0.0016026 | 0.5858872 | 0.5858849 | 0.2447410 | 0.3634440 | 89714 |
23 | 154925895 | rs538470 | C | T | 0.0012593 | 0.0016382 | 0.4420862 | 0.4420858 | 0.2412510 | 0.3634440 | 89714 |
23 | 154927581 | rs644138 | G | A | 0.0020163 | 0.0015074 | 0.1810369 | 0.1810330 | 0.3004360 | 0.4635760 | 89714 |
23 | 154929412 | rs557132 | C | T | 0.0008961 | 0.0016030 | 0.5761745 | 0.5761729 | 0.2446020 | 0.3568210 | 89714 |
23 | 154929637 | rs35185538 | CT | C | 0.0010365 | 0.0016737 | 0.5357288 | 0.5357281 | 0.2289830 | 0.3011920 | 89714 |
23 | 154929952 | rs4012982 | CAA | C | 0.0007643 | 0.0016872 | 0.6505355 | 0.6505360 | 0.2384720 | 0.3165560 | 89714 |
23 | 154930230 | rs781880 | A | G | 0.0008541 | 0.0016025 | 0.5940664 | 0.5940666 | 0.2450560 | 0.3618540 | 89714 |
23 | 154930487 | rs781879 | T | A | -0.0025545 | 0.0054316 | 0.6381430 | 0.6381422 | 0.0196698 | 0.1263580 | 89714 |
1 692794 rs530212009 CA C . PASS AF=0.111623 ES:SE:LP:AF:SS:ID 0.00201868:0.00290458:0.312419:0.111623:89714:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116632 ES:SE:LP:AF:SS:ID 0.00279149:0.00275133:0.508218:0.116632:89714:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0980012 ES:SE:LP:AF:SS:ID 0.00306442:0.00309267:0.492475:0.0980012:89714:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0158424 ES:SE:LP:AF:SS:ID -0.00172435:0.00736032:0.0889644:0.0158424:89714:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00175956 ES:SE:LP:AF:SS:ID -0.0479839:0.0216444:1.57461:0.00175956:89714:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0570389 ES:SE:LP:AF:SS:ID 0.00570749:0.00381502:0.870819:0.0570389:89714:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122527 ES:SE:LP:AF:SS:ID 0.00283083:0.00261077:0.55558:0.122527:89714:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122195 ES:SE:LP:AF:SS:ID 0.0017954:0.00278405:0.284832:0.122195:89714:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121759 ES:SE:LP:AF:SS:ID 0.00288978:0.00261271:0.570718:0.121759:89714:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00572742 ES:SE:LP:AF:SS:ID 0.0161706:0.012028:0.747586:0.00572742:89714:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00183221 ES:SE:LP:AF:SS:ID -0.0181797:0.0229046:0.369204:0.00183221:89714:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.868769 ES:SE:LP:AF:SS:ID -0.00199002:0.00257039:0.357725:0.868769:89714:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00162108 ES:SE:LP:AF:SS:ID 0.00533221:0.022573:0.0897695:0.00162108:89714:rs190826124
1 751343 rs28544273 T A . PASS AF=0.123875 ES:SE:LP:AF:SS:ID 0.00181851:0.00254806:0.322918:0.123875:89714:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143391 ES:SE:LP:AF:SS:ID 0.00241736:0.0025229:0.471106:0.143391:89714:rs200141114
1 751756 rs28527770 T C . PASS AF=0.124012 ES:SE:LP:AF:SS:ID 0.0018562:0.00254436:0.331916:0.124012:89714:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869705 ES:SE:LP:AF:SS:ID -0.00164997:0.00247916:0.296098:0.869705:89714:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874365 ES:SE:LP:AF:SS:ID -0.00204303:0.00251947:0.379419:0.874365:89714:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129721 ES:SE:LP:AF:SS:ID 0.00178967:0.0024869:0.326289:0.129721:89714:rs2073813
1 754105 rs12184325 C T . PASS AF=0.035825 ES:SE:LP:AF:SS:ID -0.00930288:0.00454711:1.38966:0.035825:89714:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869349 ES:SE:LP:AF:SS:ID -0.00169612:0.0024771:0.306693:0.869349:89714:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869427 ES:SE:LP:AF:SS:ID -0.00173222:0.0024782:0.314649:0.869427:89714:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869345 ES:SE:LP:AF:SS:ID -0.0016929:0.002477:0.305987:0.869345:89714:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00533064 ES:SE:LP:AF:SS:ID -0.0107387:0.0123674:0.414283:0.00533064:89714:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00529572 ES:SE:LP:AF:SS:ID -0.0108233:0.0123982:0.417162:0.00529572:89714:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00567704 ES:SE:LP:AF:SS:ID -0.031813:0.012191:2.0425:0.00567704:89714:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869328 ES:SE:LP:AF:SS:ID -0.00184333:0.00247186:0.341191:0.869328:89714:rs3115858
1 756434 rs61768170 G C . PASS AF=0.127114 ES:SE:LP:AF:SS:ID 0.00186276:0.00252319:0.336903:0.127114:89714:rs61768170
1 756604 rs3131962 A G . PASS AF=0.86885 ES:SE:LP:AF:SS:ID -0.00172139:0.00246541:0.314218:0.86885:89714:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868235 ES:SE:LP:AF:SS:ID -0.00197106:0.00246384:0.372926:0.868235:89714:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869004 ES:SE:LP:AF:SS:ID -0.00169718:0.00246767:0.308387:0.869004:89714:rs4951929
1 757936 rs4951862 C A . PASS AF=0.86901 ES:SE:LP:AF:SS:ID -0.00169658:0.00246784:0.308225:0.86901:89714:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869012 ES:SE:LP:AF:SS:ID -0.00169467:0.00246786:0.307792:0.869012:89714:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869497 ES:SE:LP:AF:SS:ID -0.00177977:0.0024745:0.326064:0.869497:89714:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0992799 ES:SE:LP:AF:SS:ID 0.00274427:0.00288055:0.467564:0.0992799:89714:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00652131 ES:SE:LP:AF:SS:ID -0.0237302:0.0110996:1.48778:0.00652131:89714:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873488 ES:SE:LP:AF:SS:ID -0.00171809:0.00251114:0.306396:0.873488:89714:rs3115851
1 761732 rs2286139 C T . PASS AF=0.862845 ES:SE:LP:AF:SS:ID -0.00153244:0.00246314:0.272586:0.862845:89714:rs2286139
1 761752 rs1057213 C T . PASS AF=0.86828 ES:SE:LP:AF:SS:ID -0.00169843:0.00248758:0.305608:0.86828:89714:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865153 ES:SE:LP:AF:SS:ID -0.00158686:0.002488:0.280997:0.865153:89714:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0996835 ES:SE:LP:AF:SS:ID 0.000993256:0.00297825:0.1315:0.0996835:89714:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870449 ES:SE:LP:AF:SS:ID -0.00132462:0.00251642:0.222849:0.870449:89714:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870449 ES:SE:LP:AF:SS:ID -0.00132456:0.00251642:0.222838:0.870449:89714:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870446 ES:SE:LP:AF:SS:ID -0.00132485:0.00251643:0.222894:0.870446:89714:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870814 ES:SE:LP:AF:SS:ID -0.00132075:0.00251762:0.22195:0.870814:89714:rs3131948
1 764191 rs7515915 T G . PASS AF=0.12671 ES:SE:LP:AF:SS:ID 0.00171085:0.0025204:0.303412:0.12671:89714:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106163 ES:SE:LP:AF:SS:ID 0.00333753:0.00274014:0.651265:0.106163:89714:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854165 ES:SE:LP:AF:SS:ID -0.00156787:0.00246228:0.280433:0.854165:89714:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00167172 ES:SE:LP:AF:SS:ID -0.0451346:0.0217114:1.42442:0.00167172:89714:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.839232 ES:SE:LP:AF:SS:ID 0.00440387:0.00243524:1.15151:0.839232:89714:rs376645387