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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-298/ukb-a-298_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2020-02-16T00:22:22.971885",
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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-298/ukb-a-298.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-298/ukb-a-298_data.vcf.gz; Date=Sun Feb 16 01:00:20 2020",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-a-298/ukb-a-298.vcf.gz; Date=Sun May 10 12:49:29 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-a-import/processed/ukb-a-298/ukb-a-298.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-298/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 01:55:38 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-298/ukb-a-298.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: 0.0329 (0.0033)
Lambda GC: 1.0921
Mean Chi^2: 1.1009
Intercept: 1.0053 (0.0065)
Ratio: 0.0529 (0.0644)
Analysis finished at Sun Feb 16 01:57:22 2020
Total time elapsed: 1.0m:44.74s
{
"af_correlation": 0.9533,
"inflation_factor": 1.0602,
"mean_EFFECT": -0,
"n": 147970,
"n_snps": 10877936,
"n_clumped_hits": 2,
"n_p_sig": 8,
"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": 147457.6615,
"ratio_se_n": 0.9983,
"mean_diff": -0,
"ratio_diff": 44.1724,
"sd_y_est1": 0.4669,
"sd_y_est2": 0.4661,
"r2_sum1": 0.0001,
"r2_sum2": 0.0004,
"r2_sum3": 0.0004,
"r2_sum4": 0.0004,
"ldsc_nsnp_merge_refpanel_ld": 1281483,
"ldsc_nsnp_merge_regression_ld": 1281483,
"ldsc_observed_scale_h2_beta": 0.0329,
"ldsc_observed_scale_h2_se": 0.0033,
"ldsc_intercept_beta": 1.0053,
"ldsc_intercept_se": 0.0065,
"ldsc_lambda_gc": 1.0921,
"ldsc_mean_chisq": 1.1009,
"ldsc_ratio": 0.0525
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
is_snpid_non_unique | FALSE |
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 | 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 | -2.700000e-05 | 1.024600e-02 | -1.15556e-01 | -2.868700e-03 | -2.130000e-05 | 2.799700e-03 | 1.336510e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.394100e-03 | 7.006900e-03 | 1.69380e-03 | 2.094400e-03 | 4.023100e-03 | 1.075100e-02 | 3.996470e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.905274e-01 | 2.913709e-01 | 0.00000e+00 | 2.358479e-01 | 4.873758e-01 | 7.428960e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.905264e-01 | 2.913715e-01 | 0.00000e+00 | 2.358465e-01 | 4.873753e-01 | 7.428955e-01 | 9.999997e-01 | ▇▇▇▇▇ |
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 | 1.479700e+05 | 0.000000e+00 | 1.47970e+05 | 1.479700e+05 | 1.479700e+05 | 1.479700e+05 | 1.479700e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 693731 | rs12238997 | A | G | 0.0027369 | 0.0028383 | 0.3349061 | 0.3349047 | 0.1169260 | 0.1417730 | 147970 |
1 | 717587 | rs144155419 | G | A | 0.0014950 | 0.0076237 | 0.8445339 | 0.8445333 | 0.0143862 | 0.0045926 | 147970 |
1 | 730087 | rs148120343 | T | C | -0.0017466 | 0.0039505 | 0.6584003 | 0.6583994 | 0.0554733 | 0.0127796 | 147970 |
1 | 731718 | rs142557973 | T | C | 0.0030131 | 0.0026941 | 0.2633941 | 0.2633931 | 0.1216580 | 0.1543530 | 147970 |
1 | 734349 | rs141242758 | T | C | 0.0028095 | 0.0026955 | 0.2972829 | 0.2972796 | 0.1215130 | 0.1525560 | 147970 |
1 | 740284 | rs61770167 | C | T | 0.0317890 | 0.0124245 | 0.0105111 | 0.0105103 | 0.0058556 | 0.0023962 | 147970 |
1 | 742813 | rs112573343 | C | T | -0.0216383 | 0.0228784 | 0.3442532 | 0.3442526 | 0.0015525 | 0.1030350 | 147970 |
1 | 753405 | rs3115860 | C | A | -0.0022535 | 0.0025592 | 0.3785480 | 0.3785486 | 0.8706760 | 0.7517970 | 147970 |
1 | 753541 | rs2073813 | G | A | 0.0024304 | 0.0025656 | 0.3434883 | 0.3434869 | 0.1288330 | 0.3019170 | 147970 |
1 | 754182 | rs3131969 | A | G | -0.0024252 | 0.0025559 | 0.3426920 | 0.3426905 | 0.8703180 | 0.6785140 | 147970 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51219387 | rs9616832 | T | C | 0.0000057 | 0.0032913 | 0.9986110 | 0.9986109 | 0.0729806 | 0.0654952 | 147970 |
22 | 51219704 | rs147475742 | G | A | -0.0028009 | 0.0044096 | 0.5253104 | 0.5253087 | 0.0418225 | 0.0473243 | 147970 |
22 | 51219766 | rs182321900 | C | T | 0.0281992 | 0.0222215 | 0.2044410 | 0.2044392 | 0.0014546 | NA | 147970 |
22 | 51220088 | rs566371895 | G | A | -0.0178441 | 0.0147065 | 0.2250002 | 0.2249969 | 0.0039843 | 0.0003994 | 147970 |
22 | 51220146 | rs868950473 | C | T | 0.0268708 | 0.0219039 | 0.2199161 | 0.2199133 | 0.0015139 | NA | 147970 |
22 | 51221731 | rs115055839 | T | C | 0.0000887 | 0.0032945 | 0.9785210 | 0.9785206 | 0.0728101 | 0.0625000 | 147970 |
22 | 51223637 | rs375798137 | G | A | -0.0015708 | 0.0038841 | 0.6858987 | 0.6858986 | 0.0540289 | 0.0788738 | 147970 |
22 | 51226692 | rs150189434 | G | A | 0.0256319 | 0.0229442 | 0.2639368 | 0.2639342 | 0.0013983 | 0.0155751 | 147970 |
22 | 51229805 | rs9616985 | T | C | -0.0004327 | 0.0033073 | 0.8959100 | 0.8959099 | 0.0727671 | 0.0730831 | 147970 |
22 | 51237063 | rs3896457 | T | C | -0.0016735 | 0.0020111 | 0.4053293 | 0.4053285 | 0.2968410 | 0.2050720 | 147970 |
1 693731 rs12238997 A G . PASS AF=0.116926 ES:SE:LP:AF:SS:ID 0.00273694:0.00283832:0.475077:0.116926:147970:rs12238997
1 717587 rs144155419 G A . PASS AF=0.0143862 ES:SE:LP:AF:SS:ID 0.001495:0.00762373:0.0733829:0.0143862:147970:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0554733 ES:SE:LP:AF:SS:ID -0.00174662:0.00395052:0.18151:0.0554733:147970:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121658 ES:SE:LP:AF:SS:ID 0.00301309:0.00269409:0.579394:0.121658:147970:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121513 ES:SE:LP:AF:SS:ID 0.0028095:0.00269552:0.52683:0.121513:147970:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00585559 ES:SE:LP:AF:SS:ID 0.031789:0.0124245:1.97835:0.00585559:147970:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0015525 ES:SE:LP:AF:SS:ID -0.0216383:0.0228784:0.463122:0.0015525:147970:rs112573343
1 753405 rs3115860 C A . PASS AF=0.870676 ES:SE:LP:AF:SS:ID -0.00225352:0.00255915:0.421879:0.870676:147970:rs3115860
1 753541 rs2073813 G A . PASS AF=0.128833 ES:SE:LP:AF:SS:ID 0.00243035:0.00256556:0.464088:0.128833:147970:rs2073813
1 754182 rs3131969 A G . PASS AF=0.870318 ES:SE:LP:AF:SS:ID -0.00242516:0.00255586:0.465096:0.870318:147970:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870409 ES:SE:LP:AF:SS:ID -0.00252437:0.00255719:0.490044:0.870409:147970:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870037 ES:SE:LP:AF:SS:ID -0.00240762:0.00255581:0.46069:0.870037:147970:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00465304 ES:SE:LP:AF:SS:ID -0.00197027:0.0129402:0.05602:0.00465304:147970:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00464711 ES:SE:LP:AF:SS:ID -0.00201306:0.0129766:0.0571396:0.00464711:147970:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00590897 ES:SE:LP:AF:SS:ID 0.0125753:0.0127118:0.491422:0.00590897:147970:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870329 ES:SE:LP:AF:SS:ID -0.00229688:0.00255187:0.434055:0.870329:147970:rs3115858
1 756604 rs3131962 A G . PASS AF=0.87002 ES:SE:LP:AF:SS:ID -0.0022111:0.00254577:0.414425:0.87002:147970:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869421 ES:SE:LP:AF:SS:ID -0.00199055:0.00254247:0.362834:0.869421:147970:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870219 ES:SE:LP:AF:SS:ID -0.00216744:0.00254784:0.40347:0.870219:147970:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870219 ES:SE:LP:AF:SS:ID -0.00216607:0.00254803:0.403103:0.870219:147970:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870222 ES:SE:LP:AF:SS:ID -0.00216076:0.00254813:0.401812:0.870222:147970:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870396 ES:SE:LP:AF:SS:ID -0.00226919:0.00255478:0.426631:0.870396:147970:rs3131954
1 761732 rs2286139 C T . PASS AF=0.867743 ES:SE:LP:AF:SS:ID -0.00217922:0.00254137:0.407636:0.867743:147970:rs2286139
1 766007 rs61768174 A C . PASS AF=0.106958 ES:SE:LP:AF:SS:ID 0.00233142:0.00283429:0.386422:0.106958:147970:rs61768174
1 768253 rs2977608 A C . PASS AF=0.763932 ES:SE:LP:AF:SS:ID -0.00156097:0.0020141:0.3582:0.763932:147970:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105257 ES:SE:LP:AF:SS:ID 0.00087419:0.00277154:0.123525:0.105257:147970:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00692766 ES:SE:LP:AF:SS:ID 0.00329492:0.0103175:0.125251:0.00692766:147970:rs12562811
1 769223 rs60320384 C G . PASS AF=0.128651 ES:SE:LP:AF:SS:ID 0.00173125:0.00256278:0.301607:0.128651:147970:rs60320384
1 769224 rs141644775 G A . PASS AF=0.00143239 ES:SE:LP:AF:SS:ID -0.0120575:0.0236503:0.214546:0.00143239:147970:rs141644775
1 770181 rs146076599 A G . PASS AF=0.00907328 ES:SE:LP:AF:SS:ID -0.0106309:0.00972316:0.561874:0.00907328:147970:rs146076599
1 770377 rs112563271 A T . PASS AF=0.00692321 ES:SE:LP:AF:SS:ID 0.00236935:0.0103641:0.0866254:0.00692321:147970:rs112563271
1 771823 rs2977605 T C . PASS AF=0.869934 ES:SE:LP:AF:SS:ID -0.00171316:0.00255113:0.299397:0.869934:147970:rs2977605
1 771967 rs59066358 G A . PASS AF=0.128709 ES:SE:LP:AF:SS:ID 0.00175501:0.0025619:0.306873:0.128709:147970:rs59066358
1 772755 rs2905039 A C . PASS AF=0.870112 ES:SE:LP:AF:SS:ID -0.00171884:0.0025514:0.300586:0.870112:147970:rs2905039
1 774736 rs28830877 A C . PASS AF=0.998797 ES:SE:LP:AF:SS:ID 0.0146732:0.0262624:0.239309:0.998797:147970:rs28830877
1 776556 rs151160018 C T . PASS AF=0.00851871 ES:SE:LP:AF:SS:ID 0.00154301:0.00955405:0.0596344:0.00851871:147970:rs151160018
1 777122 rs2980319 A T . PASS AF=0.871122 ES:SE:LP:AF:SS:ID -0.00170871:0.00255582:0.29776:0.871122:147970:rs2980319
1 777232 rs112618790 C T . PASS AF=0.0961319 ES:SE:LP:AF:SS:ID 0.0007159:0.00294092:0.0927634:0.0961319:147970:rs112618790
1 778745 rs1055606 A G . PASS AF=0.127871 ES:SE:LP:AF:SS:ID 0.00182592:0.00256472:0.321933:0.127871:147970:rs1055606
1 779322 rs4040617 A G . PASS AF=0.127984 ES:SE:LP:AF:SS:ID 0.00192917:0.00256117:0.345526:0.127984:147970:rs4040617
1 780785 rs2977612 T A . PASS AF=0.870455 ES:SE:LP:AF:SS:ID -0.00177475:0.0025508:0.312848:0.870455:147970:rs2977612
1 781367 rs149821290 A C . PASS AF=0.00989772 ES:SE:LP:AF:SS:ID -0.00159316:0.00900093:0.0657496:0.00989772:147970:rs149821290
1 781845 rs61768199 A G . PASS AF=0.1044 ES:SE:LP:AF:SS:ID 0.00234489:0.00287159:0.382823:0.1044:147970:rs61768199
1 782721 rs185280546 G A . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.00528668:0.00773844:0.305834:0.0143713:147970:rs185280546
1 782981 rs6594026 C T . PASS AF=0.128338 ES:SE:LP:AF:SS:ID 0.00173611:0.00256163:0.302823:0.128338:147970:rs6594026
1 783193 rs145767270 G C . PASS AF=0.0143639 ES:SE:LP:AF:SS:ID 0.00661383:0.00777011:0.40377:0.0143639:147970:rs145767270
1 783194 rs138555831 G T . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.00653503:0.00776912:0.397655:0.0143713:147970:rs138555831
1 783711 rs184266993 G A . PASS AF=0.00541372 ES:SE:LP:AF:SS:ID -0.0121559:0.0124618:0.482358:0.00541372:147970:rs184266993
1 785050 rs2905062 G A . PASS AF=0.87014 ES:SE:LP:AF:SS:ID -0.00167171:0.00255144:0.290443:0.87014:147970:rs2905062
1 785989 rs2980300 T C . PASS AF=0.87009 ES:SE:LP:AF:SS:ID -0.00168836:0.00255325:0.293754:0.87009:147970:rs2980300