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-22601_24423108/ukb-d-22601_24423108_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T13:25:33.519992",
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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-22601_24423108/ukb-d-22601_24423108.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_24423108/ukb-d-22601_24423108_data.vcf.gz; Date=Mon Nov 25 14:14:59 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-22601_24423108/ukb-d-22601_24423108.vcf.gz; Date=Sun May 10 06:16:26 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-22601_24423108/ukb-d-22601_24423108.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-22601_24423108/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 14:59:38 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_24423108/ukb-d-22601_24423108.vcf.gz ...
Read summary statistics for 9954297 SNPs.
Dropped 7676 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, 1277743 SNPs remain.
After merging with regression SNP LD, 1277743 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0045 (0.0049)
Lambda GC: 1.0119
Mean Chi^2: 1.0176
Intercept: 1.0096 (0.0064)
Ratio: 0.5446 (0.3659)
Analysis finished at Mon Nov 25 15:01:18 2019
Total time elapsed: 1.0m:40.9s
{
"af_correlation": 0.9414,
"inflation_factor": 1.004,
"mean_EFFECT": -4.6886e-07,
"n": 89866,
"n_snps": 9954297,
"n_clumped_hits": 1,
"n_p_sig": 26,
"n_mono": 0,
"n_ns": 1080008,
"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": 196971,
"n_est": 89876.7293,
"ratio_se_n": 1.0001,
"mean_diff": -3.9315e-06,
"ratio_diff": 5.3774,
"sd_y_est1": 0.1278,
"sd_y_est2": 0.1278,
"r2_sum1": 6.8462e-06,
"r2_sum2": 0.0004,
"r2_sum3": 0.0004,
"r2_sum4": 0.0004,
"ldsc_nsnp_merge_refpanel_ld": 1277743,
"ldsc_nsnp_merge_regression_ld": 1277743,
"ldsc_observed_scale_h2_beta": 0.0045,
"ldsc_observed_scale_h2_se": 0.0049,
"ldsc_intercept_beta": 1.0096,
"ldsc_intercept_se": 0.0064,
"ldsc_lambda_gc": 1.0119,
"ldsc_mean_chisq": 1.0176,
"ldsc_ratio": 0.5455
}
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 | TRUE |
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 | 9947171 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 98 | 0 | 48025 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 30064 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.080813e+00 | 6.177043e+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 | 7.875659e+07 | 5.609364e+07 | 3.02000e+02 | 3.246955e+07 | 6.965739e+07 | 1.147371e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -5.000000e-07 | 1.441300e-03 | -1.30348e-02 | -6.750000e-04 | -8.400000e-06 | 6.559000e-04 | 1.544640e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.233400e-03 | 7.425000e-04 | 4.98400e-04 | 6.632000e-04 | 9.002000e-04 | 1.593600e-03 | 4.273600e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.989533e-01 | 2.885973e-01 | 0.00000e+00 | 2.490090e-01 | 4.991511e-01 | 7.483418e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.989515e-01 | 2.885984e-01 | 0.00000e+00 | 2.490064e-01 | 4.991486e-01 | 7.483412e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.556051e-01 | 2.629493e-01 | 8.40060e-03 | 3.926980e-02 | 1.508390e-01 | 4.076420e-01 | 9.915990e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 196971 | 0.9802125 | NA | NA | NA | NA | NA | 2.552368e-01 | 2.537796e-01 | 0.00000e+00 | 4.392970e-02 | 1.667330e-01 | 4.037540e-01 | 1.000000e+00 | ▇▃▂▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.986600e+04 | 0.000000e+00 | 8.98660e+04 | 8.986600e+04 | 8.986600e+04 | 8.986600e+04 | 8.986600e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0004888 | 0.0010529 | 0.6424894 | 0.6424871 | 0.1114870 | 0.1894970 | 89866 |
1 | 693731 | rs12238997 | A | G | 0.0004662 | 0.0009974 | 0.6401636 | 0.6401628 | 0.1164980 | 0.1417730 | 89866 |
1 | 707522 | rs371890604 | G | C | 0.0017905 | 0.0011212 | 0.1102900 | 0.1102848 | 0.0978285 | 0.1293930 | 89866 |
1 | 717587 | rs144155419 | G | A | -0.0003387 | 0.0026708 | 0.8990760 | 0.8990760 | 0.0158090 | 0.0045926 | 89866 |
1 | 730087 | rs148120343 | T | C | -0.0006562 | 0.0013830 | 0.6351715 | 0.6351714 | 0.0569661 | 0.0127796 | 89866 |
1 | 731718 | rs142557973 | T | C | 0.0006069 | 0.0009465 | 0.5213531 | 0.5213510 | 0.1223780 | 0.1543530 | 89866 |
1 | 732032 | rs61770163 | A | C | 0.0013242 | 0.0010090 | 0.1893948 | 0.1893922 | 0.1220530 | 0.1555510 | 89866 |
1 | 734349 | rs141242758 | T | C | 0.0005715 | 0.0009472 | 0.5462482 | 0.5462467 | 0.1216170 | 0.1525560 | 89866 |
1 | 749963 | rs529266287 | T | TAA | -0.0003673 | 0.0009319 | 0.6934721 | 0.6934712 | 0.8689590 | 0.7641770 | 89866 |
1 | 751343 | rs28544273 | T | A | 0.0008424 | 0.0009238 | 0.3618462 | 0.3618437 | 0.1236780 | 0.2426120 | 89866 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0003933 | 0.0011078 | 0.7225868 | 0.7225849 | 0.0553576 | 0.0309934 | 89866 |
23 | 154923374 | rs111332691 | T | A | -0.0008159 | 0.0012060 | 0.4987065 | 0.4987029 | 0.0449113 | 0.0116556 | 89866 |
23 | 154925045 | rs509981 | C | T | 0.0004095 | 0.0005816 | 0.4814199 | 0.4814189 | 0.2444280 | 0.3634440 | 89866 |
23 | 154925895 | rs538470 | C | T | 0.0003803 | 0.0005947 | 0.5225634 | 0.5225611 | 0.2408760 | 0.3634440 | 89866 |
23 | 154927581 | rs644138 | G | A | 0.0004719 | 0.0005471 | 0.3884320 | 0.3884295 | 0.3001910 | 0.4635760 | 89866 |
23 | 154929412 | rs557132 | C | T | 0.0003769 | 0.0005818 | 0.5170934 | 0.5170908 | 0.2442750 | 0.3568210 | 89866 |
23 | 154929637 | rs35185538 | CT | C | 0.0003583 | 0.0006075 | 0.5553055 | 0.5553039 | 0.2286930 | 0.3011920 | 89866 |
23 | 154929952 | rs4012982 | CAA | C | 0.0004331 | 0.0006123 | 0.4793525 | 0.4793508 | 0.2381980 | 0.3165560 | 89866 |
23 | 154930230 | rs781880 | A | G | 0.0003396 | 0.0005816 | 0.5593324 | 0.5593325 | 0.2447120 | 0.3618540 | 89866 |
23 | 154930487 | rs781879 | T | A | -0.0021649 | 0.0019730 | 0.2725323 | 0.2725288 | 0.0196791 | 0.1263580 | 89866 |
1 692794 rs530212009 CA C . PASS AF=0.111487 ES:SE:LP:AF:SS:ID 0.000488777:0.00105289:0.192134:0.111487:89866:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116498 ES:SE:LP:AF:SS:ID 0.000466245:0.000997377:0.193709:0.116498:89866:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0978285 ES:SE:LP:AF:SS:ID 0.00179054:0.00112125:0.957464:0.0978285:89866:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015809 ES:SE:LP:AF:SS:ID -0.000338734:0.0026708:0.0462036:0.015809:89866:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0569661 ES:SE:LP:AF:SS:ID -0.000656184:0.00138301:0.197109:0.0569661:89866:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122378 ES:SE:LP:AF:SS:ID 0.000606931:0.00094646:0.282868:0.122378:89866:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122053 ES:SE:LP:AF:SS:ID 0.00132423:0.00100903:0.722632:0.122053:89866:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121617 ES:SE:LP:AF:SS:ID 0.000571513:0.000947164:0.26261:0.121617:89866:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.868959 ES:SE:LP:AF:SS:ID -0.000367295:0.000931869:0.158971:0.868959:89866:rs529266287
1 751343 rs28544273 T A . PASS AF=0.123678 ES:SE:LP:AF:SS:ID 0.000842384:0.000923811:0.441476:0.123678:89866:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143191 ES:SE:LP:AF:SS:ID 0.000319069:0.000914628:0.138345:0.143191:89866:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123813 ES:SE:LP:AF:SS:ID 0.000853203:0.000922478:0.449748:0.123813:89866:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869927 ES:SE:LP:AF:SS:ID -0.000699147:0.000898824:0.359855:0.869927:89866:rs3115860
1 753425 rs3131970 T C . PASS AF=0.87461 ES:SE:LP:AF:SS:ID -0.000988021:0.000913475:0.553725:0.87461:89866:rs3131970
1 753541 rs2073813 G A . PASS AF=0.12951 ES:SE:LP:AF:SS:ID 0.000631791:0.000901572:0.315648:0.12951:89866:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0357365 ES:SE:LP:AF:SS:ID 0.000385105:0.00164944:0.0886336:0.0357365:89866:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869574 ES:SE:LP:AF:SS:ID -0.000738031:0.000898032:0.385973:0.869574:89866:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869652 ES:SE:LP:AF:SS:ID -0.000749439:0.000898431:0.393413:0.869652:89866:rs3131968
1 754334 rs3131967 T C . PASS AF=0.86957 ES:SE:LP:AF:SS:ID -0.000737164:0.000897996:0.385413:0.86957:89866:rs3131967
1 755890 rs3115858 A T . PASS AF=0.869566 ES:SE:LP:AF:SS:ID -0.000695068:0.000896216:0.358514:0.869566:89866:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126879 ES:SE:LP:AF:SS:ID 0.000628852:0.000914897:0.308153:0.126879:89866:rs61768170
1 756604 rs3131962 A G . PASS AF=0.869094 ES:SE:LP:AF:SS:ID -0.000690958:0.000893892:0.357004:0.869094:89866:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868498 ES:SE:LP:AF:SS:ID -0.000794505:0.000893345:0.427347:0.868498:89866:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869245 ES:SE:LP:AF:SS:ID -0.00071117:0.000894709:0.369881:0.869245:89866:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869251 ES:SE:LP:AF:SS:ID -0.000710807:0.00089477:0.369609:0.869251:89866:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869252 ES:SE:LP:AF:SS:ID -0.000710663:0.000894776:0.369511:0.869252:89866:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869724 ES:SE:LP:AF:SS:ID -0.000718539:0.000897156:0.373468:0.869724:89866:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0991203 ES:SE:LP:AF:SS:ID 0.000907188:0.00104444:0.414456:0.0991203:89866:rs10157329
1 759837 rs3115851 T A . PASS AF=0.873732 ES:SE:LP:AF:SS:ID -0.000915352:0.000910481:0.50206:0.873732:89866:rs3115851
1 761732 rs2286139 C T . PASS AF=0.863116 ES:SE:LP:AF:SS:ID -0.000813587:0.000893043:0.440952:0.863116:89866:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868511 ES:SE:LP:AF:SS:ID -0.000762754:0.000901965:0.400394:0.868511:89866:rs1057213
1 762273 rs3115849 G A . PASS AF=0.86539 ES:SE:LP:AF:SS:ID -0.000682434:0.000902098:0.347411:0.86539:89866:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0994301 ES:SE:LP:AF:SS:ID 0.00152532:0.00108026:0.801472:0.0994301:89866:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870696 ES:SE:LP:AF:SS:ID -0.000819353:0.000912474:0.432718:0.870696:89866:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870695 ES:SE:LP:AF:SS:ID -0.000819336:0.000912474:0.432708:0.870695:89866:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870693 ES:SE:LP:AF:SS:ID -0.000818916:0.000912477:0.432417:0.870693:89866:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871061 ES:SE:LP:AF:SS:ID -0.000820554:0.000912908:0.433276:0.871061:89866:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126484 ES:SE:LP:AF:SS:ID 0.000776317:0.000913831:0.40275:0.126484:89866:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106022 ES:SE:LP:AF:SS:ID 0.00090936:0.000993408:0.443712:0.106022:89866:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854451 ES:SE:LP:AF:SS:ID -0.000838932:0.00089283:0.459159:0.854451:89866:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.839008 ES:SE:LP:AF:SS:ID -0.000572343:0.000882025:0.287008:0.839008:89866:rs376645387
1 768253 rs2977608 A C . PASS AF=0.76317 ES:SE:LP:AF:SS:ID -0.000851378:0.000709139:0.638429:0.76317:89866:rs2977608
1 768448 rs12562034 G A . PASS AF=0.10519 ES:SE:LP:AF:SS:ID 0.000670962:0.000977307:0.307706:0.10519:89866:rs12562034
1 769138 rs59306077 CAT C . PASS AF=0.129876 ES:SE:LP:AF:SS:ID 0.000646332:0.000901031:0.324977:0.129876:89866:rs762168062
1 769223 rs60320384 C G . PASS AF=0.129602 ES:SE:LP:AF:SS:ID 0.000537923:0.000899853:0.259652:0.129602:89866:rs60320384
1 769963 rs7518545 G A . PASS AF=0.104469 ES:SE:LP:AF:SS:ID 0.000764149:0.000984843:0.358719:0.104469:89866:rs7518545
1 770181 rs146076599 A G . PASS AF=0.00900456 ES:SE:LP:AF:SS:ID 0.00188937:0.00347535:0.231595:0.00900456:89866:rs146076599
1 770886 rs371458725 G A . PASS AF=0.103468 ES:SE:LP:AF:SS:ID 0.000674397:0.000993389:0.303458:0.103468:89866:rs371458725
1 771410 rs2519006 C T . PASS AF=0.829371 ES:SE:LP:AF:SS:ID -0.000675479:0.000878324:0.354712:0.829371:89866:rs2519006
1 771823 rs2977605 T C . PASS AF=0.869112 ES:SE:LP:AF:SS:ID -0.000726002:0.00089551:0.37931:0.869112:89866:rs2977605