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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-283/ukb-a-283_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2020-02-16T02:06:07.074210",
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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-a-import/processed/ukb-a-283/ukb-a-283.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-283/ukb-a-283_data.vcf.gz; Date=Sun Feb 16 02:23:54 2020",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-a-283/ukb-a-283.vcf.gz; Date=Sat May 9 18:59:09 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-a-import/processed/ukb-a-283/ukb-a-283.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-a-import/processed/ukb-a-283/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Sun Feb 16 02:49:25 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-283/ukb-a-283.vcf.gz ...
Read summary statistics for 10877936 SNPs.
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, 1281483 SNPs remain.
After merging with regression SNP LD, 1281483 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2157 (0.007)
Lambda GC: 2.0243
Mean Chi^2: 2.5411
Intercept: 1.1187 (0.0143)
Ratio: 0.077 (0.0093)
Analysis finished at Sun Feb 16 02:51:10 2020
Total time elapsed: 1.0m:44.99s
{
"af_correlation": 0.9533,
"inflation_factor": 1.582,
"mean_EFFECT": 0,
"n": 331226,
"n_snps": 10877936,
"n_clumped_hits": 277,
"n_p_sig": 29298,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 356865,
"n_est": 329750.825,
"ratio_se_n": 0.9978,
"mean_diff": -1.0141e-06,
"ratio_diff": 0.4975,
"sd_y_est1": 0.9744,
"sd_y_est2": 0.9722,
"r2_sum1": 0.0444,
"r2_sum2": 0.0467,
"r2_sum3": 0.0469,
"r2_sum4": 0.047,
"ldsc_nsnp_merge_refpanel_ld": 1281483,
"ldsc_nsnp_merge_regression_ld": 1281483,
"ldsc_observed_scale_h2_beta": 0.2157,
"ldsc_observed_scale_h2_se": 0.007,
"ldsc_intercept_beta": 1.1187,
"ldsc_intercept_se": 0.0143,
"ldsc_lambda_gc": 2.0243,
"ldsc_mean_chisq": 2.5411,
"ldsc_ratio": 0.077
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | TRUE |
n | FALSE |
is_snpid_non_unique | FALSE |
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 | 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 | 58 | 0 | 10877936 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.598638e+00 | 5.745666e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.911383e+07 | 5.624931e+07 | 8.28000e+02 | 3.287294e+07 | 6.988889e+07 | 1.148258e+08 | 2.492251e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.580000e-05 | 1.524870e-02 | -1.74028e-01 | -5.115200e-03 | 1.690000e-05 | 5.158300e-03 | 1.838770e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.031100e-02 | 9.765900e-03 | 2.36560e-03 | 2.921600e-03 | 5.611600e-03 | 1.499450e-02 | 5.358860e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.252528e-01 | 3.073154e-01 | 0.00000e+00 | 1.403440e-01 | 3.962397e-01 | 6.904623e-01 | 1.000000e+00 | ▇▅▅▅▅ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.252523e-01 | 3.073156e-01 | 0.00000e+00 | 1.403431e-01 | 3.962393e-01 | 6.904629e-01 | 1.000000e+00 | ▇▅▅▅▅ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.820865e-01 | 2.503832e-01 | 1.00090e-03 | 6.878700e-03 | 5.191440e-02 | 2.739880e-01 | 9.989990e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 356865 | 0.9671937 | NA | NA | NA | NA | NA | 1.877709e-01 | 2.439191e-01 | 0.00000e+00 | 5.191700e-03 | 7.468050e-02 | 2.873400e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.312260e+05 | 0.000000e+00 | 3.31226e+05 | 3.312260e+05 | 3.312260e+05 | 3.312260e+05 | 3.312260e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 693731 | rs12238997 | A | G | 0.0008269 | 0.0039515 | 0.8342390 | 0.8342390 | 0.1169260 | 0.1417730 | 331226 |
1 | 717587 | rs144155419 | G | A | -0.0049356 | 0.0106144 | 0.6419379 | 0.6419373 | 0.0143862 | 0.0045926 | 331226 |
1 | 730087 | rs148120343 | T | C | -0.0075918 | 0.0055058 | 0.1679380 | 0.1679375 | 0.0554733 | 0.0127796 | 331226 |
1 | 731718 | rs142557973 | T | C | -0.0002497 | 0.0037486 | 0.9468960 | 0.9468958 | 0.1216580 | 0.1543530 | 331226 |
1 | 734349 | rs141242758 | T | C | 0.0001752 | 0.0037508 | 0.9627440 | 0.9627437 | 0.1215130 | 0.1525560 | 331226 |
1 | 740284 | rs61770167 | C | T | 0.0242297 | 0.0170556 | 0.1554240 | 0.1554243 | 0.0058556 | 0.0023962 | 331226 |
1 | 742813 | rs112573343 | C | T | 0.0047042 | 0.0321292 | 0.8835941 | 0.8835942 | 0.0015525 | 0.1030350 | 331226 |
1 | 753405 | rs3115860 | C | A | -0.0008420 | 0.0035631 | 0.8131881 | 0.8131877 | 0.8706760 | 0.7517970 | 331226 |
1 | 753541 | rs2073813 | G | A | 0.0000150 | 0.0035722 | 0.9966590 | 0.9966594 | 0.1288330 | 0.3019170 | 331226 |
1 | 754182 | rs3131969 | A | G | -0.0003520 | 0.0035594 | 0.9212169 | 0.9212172 | 0.8703180 | 0.6785140 | 331226 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51219387 | rs9616832 | T | C | 0.0044478 | 0.0045857 | 0.3320802 | 0.3320800 | 0.0729806 | 0.0654952 | 331226 |
22 | 51219704 | rs147475742 | G | A | 0.0059022 | 0.0061467 | 0.3369388 | 0.3369384 | 0.0418225 | 0.0473243 | 331226 |
22 | 51219766 | rs182321900 | C | T | -0.0207496 | 0.0315146 | 0.5102735 | 0.5102732 | 0.0014546 | NA | 331226 |
22 | 51220088 | rs566371895 | G | A | 0.0108655 | 0.0207393 | 0.6003438 | 0.6003420 | 0.0039843 | 0.0003994 | 331226 |
22 | 51220146 | rs868950473 | C | T | -0.0234337 | 0.0310392 | 0.4502658 | 0.4502663 | 0.0015139 | NA | 331226 |
22 | 51221731 | rs115055839 | T | C | 0.0040492 | 0.0045886 | 0.3775383 | 0.3775377 | 0.0728101 | 0.0625000 | 331226 |
22 | 51223637 | rs375798137 | G | A | -0.0005504 | 0.0054045 | 0.9188851 | 0.9188852 | 0.0540289 | 0.0788738 | 331226 |
22 | 51226692 | rs150189434 | G | A | -0.0267025 | 0.0322060 | 0.4070399 | 0.4070389 | 0.0013983 | 0.0155751 | 331226 |
22 | 51229805 | rs9616985 | T | C | 0.0042062 | 0.0046059 | 0.3611353 | 0.3611345 | 0.0727671 | 0.0730831 | 331226 |
22 | 51237063 | rs3896457 | T | C | 0.0045490 | 0.0028044 | 0.1047840 | 0.1047835 | 0.2968410 | 0.2050720 | 331226 |
1 693731 rs12238997 A G . PASS AF=0.116926 ES:SE:LP:AF:SS:ID 0.000826927:0.00395152:0.0787095:0.116926:331226:rs12238997
1 717587 rs144155419 G A . PASS AF=0.0143862 ES:SE:LP:AF:SS:ID -0.00493561:0.0106144:0.192507:0.0143862:331226:rs144155419
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1 731718 rs58276399 T C . PASS AF=0.121658 ES:SE:LP:AF:SS:ID -0.000249675:0.00374857:0.0236977:0.121658:331226:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121513 ES:SE:LP:AF:SS:ID 0.000175202:0.00375078:0.0164892:0.121513:331226:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00585559 ES:SE:LP:AF:SS:ID 0.0242297:0.0170556:0.808482:0.00585559:331226:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0015525 ES:SE:LP:AF:SS:ID 0.00470418:0.0321292:0.0537472:0.0015525:331226:rs112573343
1 753405 rs3115860 C A . PASS AF=0.870676 ES:SE:LP:AF:SS:ID -0.000842019:0.00356311:0.089809:0.870676:331226:rs3115860
1 753541 rs2073813 G A . PASS AF=0.128833 ES:SE:LP:AF:SS:ID 1.49562e-05:0.00357219:0.00145341:0.128833:331226:rs2073813
1 754182 rs3131969 A G . PASS AF=0.870318 ES:SE:LP:AF:SS:ID -0.000352022:0.00355935:0.0356381:0.870318:331226:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870409 ES:SE:LP:AF:SS:ID -0.00030991:0.00356104:0.0312141:0.870409:331226:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870037 ES:SE:LP:AF:SS:ID -0.000359298:0.00355922:0.0364053:0.870037:331226:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00465304 ES:SE:LP:AF:SS:ID 0.00180934:0.0181387:0.0359559:0.00465304:331226:rs150578204
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1 755435 rs184270342 T G . PASS AF=0.00590897 ES:SE:LP:AF:SS:ID 0.00798828:0.017727:0.185581:0.00590897:331226:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870329 ES:SE:LP:AF:SS:ID -0.000923956:0.00355302:0.0997274:0.870329:331226:rs3115858
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1 757734 rs4951929 C T . PASS AF=0.870219 ES:SE:LP:AF:SS:ID -0.00104136:0.00354745:0.114017:0.870219:331226:rs4951929
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1 758626 rs3131954 C T . PASS AF=0.870396 ES:SE:LP:AF:SS:ID -0.000802759:0.00355692:0.0854226:0.870396:331226:rs3131954
1 761732 rs2286139 C T . PASS AF=0.867743 ES:SE:LP:AF:SS:ID 0.000225339:0.00353996:0.0226221:0.867743:331226:rs2286139
1 766007 rs61768174 A C . PASS AF=0.106958 ES:SE:LP:AF:SS:ID -0.000105981:0.00394211:0.00941609:0.106958:331226:rs61768174
1 768253 rs2977608 A C . PASS AF=0.763932 ES:SE:LP:AF:SS:ID -0.00423626:0.0028073:0.881752:0.763932:331226:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105257 ES:SE:LP:AF:SS:ID 0.00719404:0.00387452:1.19827:0.105257:331226:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00692766 ES:SE:LP:AF:SS:ID -0.0154058:0.0143865:0.546322:0.00692766:331226:rs12562811
1 769223 rs60320384 C G . PASS AF=0.128651 ES:SE:LP:AF:SS:ID 0.00054155:0.00356696:0.0558501:0.128651:331226:rs60320384
1 769224 rs141644775 G A . PASS AF=0.00143239 ES:SE:LP:AF:SS:ID 0.0448967:0.0335242:0.743532:0.00143239:331226:rs141644775
1 770181 rs146076599 A G . PASS AF=0.00907328 ES:SE:LP:AF:SS:ID -0.0113423:0.0136538:0.391322:0.00907328:331226:rs146076599
1 770377 rs112563271 A T . PASS AF=0.00692321 ES:SE:LP:AF:SS:ID -0.0156921:0.0144478:0.556854:0.00692321:331226:rs112563271
1 771823 rs2977605 T C . PASS AF=0.869934 ES:SE:LP:AF:SS:ID -0.000760576:0.00355095:0.0807127:0.869934:331226:rs2977605
1 771967 rs59066358 G A . PASS AF=0.128709 ES:SE:LP:AF:SS:ID 0.000413335:0.00356531:0.0420548:0.128709:331226:rs59066358
1 772755 rs2905039 A C . PASS AF=0.870112 ES:SE:LP:AF:SS:ID -0.000643989:0.00355112:0.067478:0.870112:331226:rs2905039
1 774736 rs28830877 A C . PASS AF=0.998797 ES:SE:LP:AF:SS:ID -0.0197619:0.0368866:0.227581:0.998797:331226:rs28830877
1 776556 rs151160018 C T . PASS AF=0.00851871 ES:SE:LP:AF:SS:ID 0.0179829:0.0133212:0.751943:0.00851871:331226:rs151160018
1 777122 rs2980319 A T . PASS AF=0.871122 ES:SE:LP:AF:SS:ID -0.000240465:0.00355712:0.0240616:0.871122:331226:rs2980319
1 777232 rs112618790 C T . PASS AF=0.0961319 ES:SE:LP:AF:SS:ID 0.00854149:0.0041038:1.42711:0.0961319:331226:rs112618790
1 778745 rs1055606 A G . PASS AF=0.127871 ES:SE:LP:AF:SS:ID -0.000127718:0.0035689:0.0125782:0.127871:331226:rs1055606
1 779322 rs4040617 A G . PASS AF=0.127984 ES:SE:LP:AF:SS:ID -0.000251808:0.00356407:0.0251775:0.127984:331226:rs4040617
1 780785 rs2977612 T A . PASS AF=0.870455 ES:SE:LP:AF:SS:ID 0.00025598:0.00355129:0.0257011:0.870455:331226:rs2977612
1 781367 rs149821290 A C . PASS AF=0.00989772 ES:SE:LP:AF:SS:ID 0.00366553:0.0126168:0.112714:0.00989772:331226:rs149821290
1 781845 rs61768199 A G . PASS AF=0.1044 ES:SE:LP:AF:SS:ID -0.000418188:0.003994:0.0378149:0.1044:331226:rs61768199
1 782721 rs185280546 G A . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.00442176:0.0108039:0.166:0.0143713:331226:rs185280546
1 782981 rs6594026 C T . PASS AF=0.128338 ES:SE:LP:AF:SS:ID -0.000854488:0.00356608:0.0911784:0.128338:331226:rs6594026
1 783193 rs145767270 G C . PASS AF=0.0143639 ES:SE:LP:AF:SS:ID 0.00321383:0.0108497:0.115167:0.0143639:331226:rs145767270
1 783194 rs138555831 G T . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.00318564:0.0108485:0.114058:0.0143713:331226:rs138555831
1 783711 rs184266993 G A . PASS AF=0.00541372 ES:SE:LP:AF:SS:ID -0.00671285:0.0173357:0.155778:0.00541372:331226:rs184266993
1 785050 rs2905062 G A . PASS AF=0.87014 ES:SE:LP:AF:SS:ID 0.00035605:0.00355189:0.0361404:0.87014:331226:rs2905062
1 785989 rs2980300 T C . PASS AF=0.87009 ES:SE:LP:AF:SS:ID 0.000425263:0.00355415:0.0434676:0.87009:331226:rs2980300