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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-364/ukb-a-364_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2020-02-16T01:01:30.247001",
"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-a-import/processed/ukb-a-364/ukb-a-364.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-364/ukb-a-364_data.vcf.gz; Date=Sun Feb 16 01:48:49 2020",
"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-a-364/ukb-a-364.vcf.gz; Date=Sun May 10 14:19:58 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-364/ukb-a-364.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-364/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 02:23:14 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-364/ukb-a-364.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: 0.0555 (0.0052)
Lambda GC: 1.1171
Mean Chi^2: 1.1268
Intercept: 1.0053 (0.0074)
Ratio: 0.0415 (0.0586)
Analysis finished at Sun Feb 16 02:25:03 2020
Total time elapsed: 1.0m:48.92s
{
"af_correlation": 0.9533,
"inflation_factor": 1.0747,
"mean_EFFECT": 0.0001,
"n": 110153,
"n_snps": 10877936,
"n_clumped_hits": 2,
"n_p_sig": 44,
"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": 109805.7585,
"ratio_se_n": 0.9984,
"mean_diff": 3.6092e-06,
"ratio_diff": 3.6537,
"sd_y_est1": 0.9591,
"sd_y_est2": 0.9575,
"r2_sum1": 0.0007,
"r2_sum2": 0.0008,
"r2_sum3": 0.0008,
"r2_sum4": 0.0008,
"ldsc_nsnp_merge_refpanel_ld": 1281483,
"ldsc_nsnp_merge_regression_ld": 1281483,
"ldsc_observed_scale_h2_beta": 0.0555,
"ldsc_observed_scale_h2_se": 0.0052,
"ldsc_intercept_beta": 1.0053,
"ldsc_intercept_se": 0.0074,
"ldsc_lambda_gc": 1.1171,
"ldsc_mean_chisq": 1.1268,
"ldsc_ratio": 0.0418
}
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 | 1.037000e-04 | 2.446140e-02 | -3.32037e-01 | -6.748100e-03 | 3.050000e-05 | 6.855800e-03 | 2.969180e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.760700e-02 | 1.669590e-02 | 4.03240e-03 | 4.987300e-03 | 9.577900e-03 | 2.558140e-02 | 9.503650e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.884248e-01 | 2.918056e-01 | 0.00000e+00 | 2.329732e-01 | 4.844038e-01 | 7.413632e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.884233e-01 | 2.918064e-01 | 0.00000e+00 | 2.329700e-01 | 4.844019e-01 | 7.413616e-01 | 9.999999e-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 | 1.101530e+05 | 0.000000e+00 | 1.10153e+05 | 1.101530e+05 | 1.101530e+05 | 1.101530e+05 | 1.101530e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 693731 | rs12238997 | A | G | -0.0028107 | 0.0067484 | 0.6770457 | 0.6770448 | 0.1169260 | 0.1417730 | 110153 |
1 | 717587 | rs144155419 | G | A | 0.0027350 | 0.0182130 | 0.8806311 | 0.8806312 | 0.0143862 | 0.0045926 | 110153 |
1 | 730087 | rs148120343 | T | C | -0.0118016 | 0.0094085 | 0.2097128 | 0.2097110 | 0.0554733 | 0.0127796 | 110153 |
1 | 731718 | rs142557973 | T | C | -0.0041478 | 0.0064085 | 0.5174841 | 0.5174834 | 0.1216580 | 0.1543530 | 110153 |
1 | 734349 | rs141242758 | T | C | -0.0043952 | 0.0064135 | 0.4931488 | 0.4931479 | 0.1215130 | 0.1525560 | 110153 |
1 | 740284 | rs61770167 | C | T | 0.0070307 | 0.0284383 | 0.8047330 | 0.8047330 | 0.0058556 | 0.0023962 | 110153 |
1 | 742813 | rs112573343 | C | T | -0.0368742 | 0.0573012 | 0.5198906 | 0.5198898 | 0.0015525 | 0.1030350 | 110153 |
1 | 753405 | rs3115860 | C | A | 0.0040979 | 0.0060903 | 0.5010442 | 0.5010429 | 0.8706760 | 0.7517970 | 110153 |
1 | 753541 | rs2073813 | G | A | -0.0040757 | 0.0061031 | 0.5042582 | 0.5042568 | 0.1288330 | 0.3019170 | 110153 |
1 | 754182 | rs3131969 | A | G | 0.0040473 | 0.0060840 | 0.5059027 | 0.5059012 | 0.8703180 | 0.6785140 | 110153 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51219387 | rs9616832 | T | C | -0.0100183 | 0.0078884 | 0.2040892 | 0.2040861 | 0.0729806 | 0.0654952 | 110153 |
22 | 51219704 | rs147475742 | G | A | -0.0167540 | 0.0105364 | 0.1118129 | 0.1118108 | 0.0418225 | 0.0473243 | 110153 |
22 | 51219766 | rs182321900 | C | T | -0.1105230 | 0.0558463 | 0.0478112 | 0.0478096 | 0.0014546 | NA | 110153 |
22 | 51220088 | rs566371895 | G | A | -0.0304485 | 0.0364565 | 0.4036073 | 0.4036046 | 0.0039843 | 0.0003994 | 110153 |
22 | 51220146 | rs868950473 | C | T | -0.0879720 | 0.0544648 | 0.1062681 | 0.1062656 | 0.0015139 | NA | 110153 |
22 | 51221731 | rs115055839 | T | C | -0.0093743 | 0.0078952 | 0.2350932 | 0.2350904 | 0.0728101 | 0.0625000 | 110153 |
22 | 51223637 | rs375798137 | G | A | 0.0034108 | 0.0092460 | 0.7122082 | 0.7122085 | 0.0540289 | 0.0788738 | 110153 |
22 | 51226692 | rs150189434 | G | A | -0.0985116 | 0.0574130 | 0.0861946 | 0.0861911 | 0.0013983 | 0.0155751 | 110153 |
22 | 51229805 | rs9616985 | T | C | -0.0096399 | 0.0079246 | 0.2238139 | 0.2238124 | 0.0727671 | 0.0730831 | 110153 |
22 | 51237063 | rs3896457 | T | C | 0.0006318 | 0.0047860 | 0.8949789 | 0.8949789 | 0.2968410 | 0.2050720 | 110153 |
1 693731 rs12238997 A G . PASS AF=0.116926 ES:SE:LP:AF:SS:ID -0.00281069:0.00674837:0.169382:0.116926:110153:rs12238997
1 717587 rs144155419 G A . PASS AF=0.0143862 ES:SE:LP:AF:SS:ID 0.00273503:0.018213:0.055206:0.0143862:110153:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0554733 ES:SE:LP:AF:SS:ID -0.0118016:0.00940846:0.678375:0.0554733:110153:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121658 ES:SE:LP:AF:SS:ID -0.00414777:0.0064085:0.286103:0.121658:110153:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121513 ES:SE:LP:AF:SS:ID -0.00439524:0.0064135:0.307022:0.121513:110153:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00585559 ES:SE:LP:AF:SS:ID 0.0070307:0.0284383:0.0943482:0.00585559:110153:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0015525 ES:SE:LP:AF:SS:ID -0.0368742:0.0573012:0.284088:0.0015525:110153:rs112573343
1 753405 rs3115860 C A . PASS AF=0.870676 ES:SE:LP:AF:SS:ID 0.00409789:0.00609035:0.300124:0.870676:110153:rs3115860
1 753541 rs2073813 G A . PASS AF=0.128833 ES:SE:LP:AF:SS:ID -0.0040757:0.00610311:0.297347:0.128833:110153:rs2073813
1 754182 rs3131969 A G . PASS AF=0.870318 ES:SE:LP:AF:SS:ID 0.00404726:0.00608397:0.295933:0.870318:110153:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870409 ES:SE:LP:AF:SS:ID 0.00413536:0.00608752:0.303697:0.870409:110153:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870037 ES:SE:LP:AF:SS:ID 0.00404193:0.00608352:0.29548:0.870037:110153:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00465304 ES:SE:LP:AF:SS:ID 0.00290851:0.0309775:0.0337663:0.00465304:110153:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00464711 ES:SE:LP:AF:SS:ID 0.00226027:0.0310602:0.0259542:0.00464711:110153:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00590897 ES:SE:LP:AF:SS:ID 0.0376849:0.0304791:0.664929:0.00590897:110153:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870329 ES:SE:LP:AF:SS:ID 0.00392746:0.00607388:0.285769:0.870329:110153:rs3115858
1 756604 rs3131962 A G . PASS AF=0.87002 ES:SE:LP:AF:SS:ID 0.00355884:0.00606:0.254125:0.87002:110153:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869421 ES:SE:LP:AF:SS:ID 0.00374491:0.00605245:0.270765:0.869421:110153:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870219 ES:SE:LP:AF:SS:ID 0.00361873:0.00606449:0.259082:0.870219:110153:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870219 ES:SE:LP:AF:SS:ID 0.00363204:0.00606492:0.260217:0.870219:110153:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870222 ES:SE:LP:AF:SS:ID 0.00367799:0.00606511:0.26421:0.870222:110153:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870396 ES:SE:LP:AF:SS:ID 0.00371086:0.00608071:0.266252:0.870396:110153:rs3131954
1 761732 rs2286139 C T . PASS AF=0.867743 ES:SE:LP:AF:SS:ID 0.00426426:0.00605316:0.317727:0.867743:110153:rs2286139
1 766007 rs61768174 A C . PASS AF=0.106958 ES:SE:LP:AF:SS:ID -0.00521205:0.00673033:0.357843:0.106958:110153:rs61768174
1 768253 rs2977608 A C . PASS AF=0.763932 ES:SE:LP:AF:SS:ID -0.00492827:0.00479234:0.517439:0.763932:110153:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105257 ES:SE:LP:AF:SS:ID 0.0140275:0.00659552:1.47577:0.105257:110153:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00692766 ES:SE:LP:AF:SS:ID 0.0596798:0.025031:1.76659:0.00692766:110153:rs12562811
1 769223 rs60320384 C G . PASS AF=0.128651 ES:SE:LP:AF:SS:ID -0.003808:0.00609578:0.273947:0.128651:110153:rs60320384
1 769224 rs141644775 G A . PASS AF=0.00143239 ES:SE:LP:AF:SS:ID -0.134065:0.0585372:1.65741:0.00143239:110153:rs141644775
1 770181 rs146076599 A G . PASS AF=0.00907328 ES:SE:LP:AF:SS:ID -0.026413:0.0229931:0.600901:0.00907328:110153:rs146076599
1 770377 rs112563271 A T . PASS AF=0.00692321 ES:SE:LP:AF:SS:ID 0.0619048:0.0251626:1.85737:0.00692321:110153:rs112563271
1 771823 rs2977605 T C . PASS AF=0.869934 ES:SE:LP:AF:SS:ID 0.00415265:0.00607107:0.306298:0.869934:110153:rs2977605
1 771967 rs59066358 G A . PASS AF=0.128709 ES:SE:LP:AF:SS:ID -0.00404647:0.00609265:0.295342:0.128709:110153:rs59066358
1 772755 rs2905039 A C . PASS AF=0.870112 ES:SE:LP:AF:SS:ID 0.00424226:0.0060715:0.314499:0.870112:110153:rs2905039
1 774736 rs28830877 A C . PASS AF=0.998797 ES:SE:LP:AF:SS:ID 0.0476494:0.0664587:0.324781:0.998797:110153:rs28830877
1 776556 rs151160018 C T . PASS AF=0.00851871 ES:SE:LP:AF:SS:ID -0.023673:0.0224648:0.534638:0.00851871:110153:rs151160018
1 777122 rs2980319 A T . PASS AF=0.871122 ES:SE:LP:AF:SS:ID 0.0043712:0.00608192:0.325768:0.871122:110153:rs2980319
1 777232 rs112618790 C T . PASS AF=0.0961319 ES:SE:LP:AF:SS:ID 0.010823:0.00698904:0.915459:0.0961319:110153:rs112618790
1 778745 rs1055606 A G . PASS AF=0.127871 ES:SE:LP:AF:SS:ID -0.0041905:0.00609909:0.308:0.127871:110153:rs1055606
1 779322 rs4040617 A G . PASS AF=0.127984 ES:SE:LP:AF:SS:ID -0.00436658:0.0060906:0.324759:0.127984:110153:rs4040617
1 780785 rs2977612 T A . PASS AF=0.870455 ES:SE:LP:AF:SS:ID 0.005137:0.00607197:0.400614:0.870455:110153:rs2977612
1 781367 rs149821290 A C . PASS AF=0.00989772 ES:SE:LP:AF:SS:ID -0.00423806:0.0215521:0.073602:0.00989772:110153:rs149821290
1 781845 rs61768199 A G . PASS AF=0.1044 ES:SE:LP:AF:SS:ID -0.0058825:0.00682106:0.410645:0.1044:110153:rs61768199
1 782721 rs185280546 G A . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.0060812:0.0187899:0.127139:0.0143713:110153:rs185280546
1 782981 rs6594026 C T . PASS AF=0.128338 ES:SE:LP:AF:SS:ID -0.00473523:0.00609522:0.359286:0.128338:110153:rs6594026
1 783193 rs145767270 G C . PASS AF=0.0143639 ES:SE:LP:AF:SS:ID 0.00687182:0.0188696:0.145251:0.0143639:110153:rs145767270
1 783194 rs138555831 G T . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.00702981:0.0188676:0.149074:0.0143713:110153:rs138555831
1 783711 rs184266993 G A . PASS AF=0.00541372 ES:SE:LP:AF:SS:ID -0.0229235:0.0289781:0.367636:0.00541372:110153:rs184266993
1 785050 rs2905062 G A . PASS AF=0.87014 ES:SE:LP:AF:SS:ID 0.0048025:0.00607236:0.367525:0.87014:110153:rs2905062
1 785989 rs2980300 T C . PASS AF=0.87009 ES:SE:LP:AF:SS:ID 0.00473538:0.00607632:0.360719:0.87009:110153:rs2980300