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-20405_1/ukb-d-20405_1_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:10:57.837573",
"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-20405_1/ukb-d-20405_1.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20405_1/ukb-d-20405_1_data.vcf.gz; Date=Mon Nov 25 15:36:26 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-20405_1/ukb-d-20405_1.vcf.gz; Date=Sun May 10 12:27:25 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-20405_1/ukb-d-20405_1.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-20405_1/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 16:46:32 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20405_1/ukb-d-20405_1.vcf.gz ...
Read summary statistics for 12203570 SNPs.
Dropped 10750 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, 1283152 SNPs remain.
After merging with regression SNP LD, 1283152 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0155 (0.0038)
Lambda GC: 1.0318
Mean Chi^2: 1.0359
Intercept: 1.0001 (0.0059)
Ratio: 0.0021 (0.1658)
Analysis finished at Mon Nov 25 16:48:36 2019
Total time elapsed: 2.0m:4.38s
{
"af_correlation": 0.9495,
"inflation_factor": 1.0275,
"mean_EFFECT": 5.3818e-06,
"n": 117880,
"n_snps": 12203570,
"n_clumped_hits": 1,
"n_p_sig": 7,
"n_mono": 0,
"n_ns": 1193524,
"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": 305359,
"n_est": 118224.7906,
"ratio_se_n": 1.0015,
"mean_diff": 0,
"ratio_diff": 117.3921,
"sd_y_est1": 0.21,
"sd_y_est2": 0.2103,
"r2_sum1": 0,
"r2_sum2": 0.0005,
"r2_sum3": 0.0005,
"r2_sum4": 0.0005,
"ldsc_nsnp_merge_refpanel_ld": 1283152,
"ldsc_nsnp_merge_regression_ld": 1283152,
"ldsc_observed_scale_h2_beta": 0.0155,
"ldsc_observed_scale_h2_se": 0.0038,
"ldsc_intercept_beta": 1.0001,
"ldsc_intercept_se": 0.0059,
"ldsc_lambda_gc": 1.0318,
"ldsc_mean_chisq": 1.0359,
"ldsc_ratio": 0.0028
}
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 | 12193445 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 53881 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 32312 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.066137e+00 | 6.184643e+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 | 7.891620e+07 | 5.596936e+07 | 3.02000e+02 | 3.273128e+07 | 6.995246e+07 | 1.147852e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.400000e-06 | 3.586500e-03 | -4.01029e-02 | -1.196400e-03 | -4.600000e-06 | 1.178000e-03 | 4.643290e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.726900e-03 | 2.306900e-03 | 7.17000e-04 | 9.998000e-04 | 1.615100e-03 | 3.783900e-03 | 1.344190e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.956539e-01 | 2.898865e-01 | 0.00000e+00 | 2.439782e-01 | 4.941741e-01 | 7.467909e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.956525e-01 | 2.898873e-01 | 0.00000e+00 | 2.439762e-01 | 4.941724e-01 | 7.467907e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.112675e-01 | 2.587944e-01 | 2.28020e-03 | 1.399520e-02 | 8.751840e-02 | 3.349500e-01 | 9.977200e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 305359 | 0.9749779 | NA | NA | NA | NA | NA | 2.130041e-01 | 2.503878e-01 | 0.00000e+00 | 1.078270e-02 | 1.076280e-01 | 3.382590e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.178800e+05 | 0.000000e+00 | 1.17880e+05 | 1.178800e+05 | 1.178800e+05 | 1.178800e+05 | 1.178800e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0017256 | 0.0015077 | 0.2524103 | 0.2524077 | 0.1116960 | 0.1894970 | 117880 |
1 | 693731 | rs12238997 | A | G | -0.0011374 | 0.0014278 | 0.4256729 | 0.4256717 | 0.1167130 | 0.1417730 | 117880 |
1 | 707522 | rs371890604 | G | C | -0.0007689 | 0.0016022 | 0.6312916 | 0.6312916 | 0.0983344 | 0.1293930 | 117880 |
1 | 717587 | rs144155419 | G | A | -0.0031232 | 0.0038397 | 0.4159978 | 0.4159960 | 0.0157581 | 0.0045926 | 117880 |
1 | 730087 | rs148120343 | T | C | -0.0012390 | 0.0019871 | 0.5329421 | 0.5329413 | 0.0568842 | 0.0127796 | 117880 |
1 | 731718 | rs142557973 | T | C | -0.0011306 | 0.0013547 | 0.4039727 | 0.4039704 | 0.1226360 | 0.1543530 | 117880 |
1 | 732032 | rs61770163 | A | C | -0.0013464 | 0.0014439 | 0.3511018 | 0.3510990 | 0.1222430 | 0.1555510 | 117880 |
1 | 734349 | rs141242758 | T | C | -0.0011064 | 0.0013554 | 0.4143773 | 0.4143724 | 0.1218910 | 0.1525560 | 117880 |
1 | 740284 | rs61770167 | C | T | 0.0076225 | 0.0061850 | 0.2177950 | 0.2177921 | 0.0058634 | 0.0023962 | 117880 |
1 | 749963 | rs529266287 | T | TAA | 0.0016061 | 0.0013356 | 0.2291638 | 0.2291603 | 0.8690250 | 0.7641770 | 117880 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0007475 | 0.0015930 | 0.6388766 | 0.6388752 | 0.0555055 | 0.0309934 | 117880 |
23 | 154923374 | rs111332691 | T | A | 0.0010637 | 0.0017364 | 0.5401595 | 0.5401609 | 0.0447871 | 0.0116556 | 117880 |
23 | 154925045 | rs509981 | C | T | 0.0001428 | 0.0008363 | 0.8644270 | 0.8644258 | 0.2446550 | 0.3634440 | 117880 |
23 | 154925895 | rs538470 | C | T | -0.0000585 | 0.0008552 | 0.9455049 | 0.9455047 | 0.2410780 | 0.3634440 | 117880 |
23 | 154927581 | rs644138 | G | A | 0.0003103 | 0.0007869 | 0.6933316 | 0.6933302 | 0.3005220 | 0.4635760 | 117880 |
23 | 154929412 | rs557132 | C | T | 0.0001462 | 0.0008365 | 0.8612380 | 0.8612375 | 0.2445300 | 0.3568210 | 117880 |
23 | 154929637 | rs35185538 | CT | C | 0.0004355 | 0.0008738 | 0.6182085 | 0.6182077 | 0.2287520 | 0.3011920 | 117880 |
23 | 154929952 | rs4012982 | CAA | C | -0.0001965 | 0.0008804 | 0.8233900 | 0.8233900 | 0.2386140 | 0.3165560 | 117880 |
23 | 154930230 | rs781880 | A | G | 0.0000670 | 0.0008363 | 0.9361771 | 0.9361773 | 0.2449530 | 0.3618540 | 117880 |
23 | 154930487 | rs781879 | T | A | 0.0013390 | 0.0028414 | 0.6374630 | 0.6374633 | 0.0196917 | 0.1263580 | 117880 |
1 692794 rs530212009 CA C . PASS AF=0.111696 ES:SE:LP:AF:SS:ID -0.00172564:0.00150774:0.597893:0.111696:117880:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116713 ES:SE:LP:AF:SS:ID -0.00113743:0.00142782:0.370924:0.116713:117880:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0983344 ES:SE:LP:AF:SS:ID -0.000768897:0.00160217:0.19977:0.0983344:117880:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157581 ES:SE:LP:AF:SS:ID -0.00312318:0.00383972:0.380909:0.0157581:117880:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0568842 ES:SE:LP:AF:SS:ID -0.00123902:0.00198713:0.27332:0.0568842:117880:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122636 ES:SE:LP:AF:SS:ID -0.0011306:0.00135474:0.393648:0.122636:117880:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122243 ES:SE:LP:AF:SS:ID -0.00134636:0.00144388:0.454567:0.122243:117880:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121891 ES:SE:LP:AF:SS:ID -0.00110635:0.00135545:0.382604:0.121891:117880:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00586344 ES:SE:LP:AF:SS:ID 0.00762252:0.006185:0.661952:0.00586344:117880:rs61770167
1 749963 rs529266287 T TAA . PASS AF=0.869025 ES:SE:LP:AF:SS:ID 0.00160608:0.00133559:0.639854:0.869025:117880:rs529266287
1 751343 rs28544273 T A . PASS AF=0.123676 ES:SE:LP:AF:SS:ID -0.002115:0.00132329:0.958686:0.123676:117880:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143312 ES:SE:LP:AF:SS:ID -0.00117937:0.00130874:0.434727:0.143312:117880:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123798 ES:SE:LP:AF:SS:ID -0.00207371:0.00132146:0.933342:0.123798:117880:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869794 ES:SE:LP:AF:SS:ID 0.0017697:0.00128691:0.77189:0.869794:117880:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874573 ES:SE:LP:AF:SS:ID 0.00195728:0.00130853:0.870591:0.874573:117880:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129665 ES:SE:LP:AF:SS:ID -0.00169786:0.00129051:0.725164:0.129665:117880:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0365244 ES:SE:LP:AF:SS:ID 0.00255632:0.00234372:0.560031:0.0365244:117880:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869388 ES:SE:LP:AF:SS:ID 0.00175563:0.00128569:0.764239:0.869388:117880:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869459 ES:SE:LP:AF:SS:ID 0.0017675:0.00128617:0.771164:0.869459:117880:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869387 ES:SE:LP:AF:SS:ID 0.00176082:0.00128565:0.767466:0.869387:117880:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00511644 ES:SE:LP:AF:SS:ID -0.00339226:0.00657747:0.217501:0.00511644:117880:rs150578204
1 754458 rs142682604 G T . PASS AF=0.0050855 ES:SE:LP:AF:SS:ID -0.00343873:0.006592:0.220466:0.0050855:117880:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00568415 ES:SE:LP:AF:SS:ID 0.000557733:0.00633875:0.0315703:0.00568415:117880:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869461 ES:SE:LP:AF:SS:ID 0.00175338:0.0012833:0.764858:0.869461:117880:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126942 ES:SE:LP:AF:SS:ID -0.00173871:0.00130996:0.734216:0.126942:117880:rs61768170
1 756604 rs3131962 A G . PASS AF=0.868981 ES:SE:LP:AF:SS:ID 0.00174929:0.00127993:0.765182:0.868981:117880:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868381 ES:SE:LP:AF:SS:ID 0.00174877:0.00127944:0.765275:0.868381:117880:rs3115853
1 757734 rs4951929 C T . PASS AF=0.86917 ES:SE:LP:AF:SS:ID 0.00174794:0.0012812:0.763271:0.86917:117880:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869177 ES:SE:LP:AF:SS:ID 0.00174934:0.00128129:0.76406:0.869177:117880:rs4951862
1 758144 rs3131956 A G . PASS AF=0.86918 ES:SE:LP:AF:SS:ID 0.00174828:0.0012813:0.763402:0.86918:117880:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869615 ES:SE:LP:AF:SS:ID 0.00175845:0.00128458:0.76691:0.869615:117880:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0995696 ES:SE:LP:AF:SS:ID -0.00152508:0.00149326:0.512706:0.0995696:117880:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00653662 ES:SE:LP:AF:SS:ID 0.00229988:0.00575777:0.161422:0.00653662:117880:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873673 ES:SE:LP:AF:SS:ID 0.00186359:0.00130425:0.81517:0.873673:117880:rs3115851
1 761732 rs2286139 C T . PASS AF=0.862961 ES:SE:LP:AF:SS:ID 0.00143805:0.00127908:0.583536:0.862961:117880:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868361 ES:SE:LP:AF:SS:ID 0.00158114:0.0012914:0.655964:0.868361:117880:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865372 ES:SE:LP:AF:SS:ID 0.00173747:0.00129159:0.748218:0.865372:117880:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0997403 ES:SE:LP:AF:SS:ID -0.00187092:0.00154341:0.646971:0.0997403:117880:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870662 ES:SE:LP:AF:SS:ID 0.00189509:0.00130685:0.832603:0.870662:117880:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870662 ES:SE:LP:AF:SS:ID 0.00189466:0.00130685:0.832331:0.870662:117880:rs3131950
1 762601 rs3131949 T C . PASS AF=0.87066 ES:SE:LP:AF:SS:ID 0.00189397:0.00130685:0.831892:0.87066:117880:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870982 ES:SE:LP:AF:SS:ID 0.00182348:0.0013074:0.787549:0.870982:117880:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126535 ES:SE:LP:AF:SS:ID -0.00180958:0.00130853:0.778077:0.126535:117880:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106314 ES:SE:LP:AF:SS:ID -0.00139846:0.00142204:0.487578:0.106314:117880:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854398 ES:SE:LP:AF:SS:ID 0.00194134:0.00127871:0.889525:0.854398:117880:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.83908 ES:SE:LP:AF:SS:ID 0.000449104:0.001267:0.140866:0.83908:117880:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763032 ES:SE:LP:AF:SS:ID 0.000909545:0.00101546:0.43131:0.763032:117880:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105264 ES:SE:LP:AF:SS:ID 0.000327217:0.00140478:0.0884078:0.105264:117880:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00774254 ES:SE:LP:AF:SS:ID 0.0117388:0.00518507:1.62749:0.00774254:117880:rs12562811
1 769138 rs59306077 CAT C . PASS AF=0.129947 ES:SE:LP:AF:SS:ID -0.00172384:0.00128983:0.741382:0.129947:117880:rs762168062