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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-N90/ukb-d-N90_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T17:15:19.569861",
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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-N90/ukb-d-N90.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-N90/ukb-d-N90_data.vcf.gz; Date=Mon Nov 25 17:28:43 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-N90/ukb-d-N90.vcf.gz; Date=Sat May 9 18:07:32 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-N90/ukb-d-N90.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-N90/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 17:52:42 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-N90/ukb-d-N90.vcf.gz ...
Read summary statistics for 9452871 SNPs.
Dropped 6975 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, 1272361 SNPs remain.
After merging with regression SNP LD, 1272361 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0001 (0.0012)
Lambda GC: 1.0161
Mean Chi^2: 1.0105
Intercept: 1.0114 (0.0066)
Ratio: 1.0854 (0.631)
Analysis finished at Mon Nov 25 17:54:16 2019
Total time elapsed: 1.0m:34.05s
{
"af_correlation": 0.9386,
"inflation_factor": 0.996,
"mean_EFFECT": 1.6662e-06,
"n": 361194,
"n_snps": 9452871,
"n_clumped_hits": 0,
"n_p_sig": 1,
"n_mono": 0,
"n_ns": 1047340,
"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": 189409,
"n_est": 361071.259,
"ratio_se_n": 0.9998,
"mean_diff": 0,
"ratio_diff": 175.393,
"sd_y_est1": 0.0552,
"sd_y_est2": 0.0552,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1272361,
"ldsc_nsnp_merge_regression_ld": 1272361,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0114,
"ldsc_intercept_se": 0.0066,
"ldsc_lambda_gc": 1.0161,
"ldsc_mean_chisq": 1.0105,
"ldsc_ratio": 1.0857
}
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 | 9446434 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 98 | 0 | 46224 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 29347 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.080866e+00 | 6.173814e+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 | 7.869893e+07 | 5.611294e+07 | 3.02000e+02 | 3.241462e+07 | 6.956373e+07 | 1.147156e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.700000e-06 | 2.773000e-04 | -2.43860e-03 | -1.368000e-04 | 0.000000e+00 | 1.367000e-04 | 3.530300e-03 | ▁▅▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.441000e-04 | 1.322000e-04 | 1.06900e-04 | 1.416000e-04 | 1.861000e-04 | 3.097000e-04 | 7.662000e-04 | ▇▂▂▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.003078e-01 | 2.886481e-01 | 0.00000e+00 | 2.502770e-01 | 5.008515e-01 | 7.502794e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.003073e-01 | 2.886484e-01 | 0.00000e+00 | 2.502755e-01 | 5.008508e-01 | 7.502789e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.677107e-01 | 2.626779e-01 | 1.13636e-02 | 4.909090e-02 | 1.681840e-01 | 4.252610e-01 | 9.886360e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 189409 | 0.9799628 | NA | NA | NA | NA | NA | 2.670415e-01 | 2.534755e-01 | 0.00000e+00 | 5.630990e-02 | 1.827080e-01 | 4.199280e-01 | 1.000000e+00 | ▇▃▂▂▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.611940e+05 | 0.000000e+00 | 3.61194e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0000446 | 0.0002277 | 0.8447500 | 0.8447501 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | -0.0001699 | 0.0002151 | 0.4296353 | 0.4296335 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | -0.0000675 | 0.0002418 | 0.7802971 | 0.7802974 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | 0.0005195 | 0.0005771 | 0.3680510 | 0.3680510 | 0.0156880 | 0.0045926 | 361194 |
1 | 730087 | rs148120343 | T | C | -0.0001723 | 0.0002997 | 0.5654042 | 0.5654023 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | -0.0000328 | 0.0002040 | 0.8723280 | 0.8723272 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | -0.0000142 | 0.0002176 | 0.9480630 | 0.9480625 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | -0.0000403 | 0.0002041 | 0.8433651 | 0.8433645 | 0.1209650 | 0.1525560 | 361194 |
1 | 749963 | rs529266287 | T | TAA | 0.0000179 | 0.0002012 | 0.9289450 | 0.9289449 | 0.8697420 | 0.7641770 | 361194 |
1 | 751343 | rs28544273 | T | A | 0.0000315 | 0.0001993 | 0.8743399 | 0.8743400 | 0.1229160 | 0.2426120 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0000475 | 0.0002357 | 0.8401919 | 0.8401917 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | 0.0001058 | 0.0002590 | 0.6828574 | 0.6828575 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | -0.0001561 | 0.0001246 | 0.2104370 | 0.2104355 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | -0.0001752 | 0.0001275 | 0.1693332 | 0.1693337 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | -0.0001213 | 0.0001172 | 0.3006312 | 0.3006310 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | -0.0001546 | 0.0001247 | 0.2150582 | 0.2150592 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | -0.0001849 | 0.0001301 | 0.1553860 | 0.1553863 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | -0.0001776 | 0.0001311 | 0.1755351 | 0.1755337 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | -0.0001599 | 0.0001247 | 0.1995281 | 0.1995268 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | -0.0002059 | 0.0004276 | 0.6301196 | 0.6301201 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID 4.45834e-05:0.000227674:0.0732718:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID -0.000169909:0.000215124:0.3669:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID -6.74579e-05:0.000241844:0.10774:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID 0.000519466:0.000577101:0.434092:0.015688:361194:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID -0.000172276:0.000299696:0.247641:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID -3.27873e-05:0.000204024:0.0593202:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID -1.41765e-05:0.000217631:0.0231628:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID -4.03352e-05:0.000204134:0.0739844:0.120965:361194:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID 1.79454e-05:0.000201244:0.03201:0.869742:361194:rs529266287
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID 3.15199e-05:0.000199306:0.0583197:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID 0.000107335:0.000197003:0.232204:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID 3.52338e-05:0.000199028:0.0657612:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID -3.7494e-05:0.000193946:0.0722668:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID -7.94634e-06:0.00019716:0.0141915:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID 4.478e-05:0.000194433:0.0873263:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID -0.000294308:0.000352745:0.393519:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID -4.78252e-05:0.000193745:0.0941896:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID -4.93606e-05:0.000193833:0.0974592:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID -4.71617e-05:0.000193738:0.092765:0.870481:361194:rs3131967
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID -3.51987e-05:0.000193397:0.0677389:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID 2.85997e-05:0.000197335:0.0531711:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID -3.88762e-05:0.000192931:0.0755631:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID -6.1834e-05:0.000192755:0.125884:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID -4.80479e-05:0.000193097:0.0950174:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID -4.81102e-05:0.000193111:0.0951449:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID -4.84996e-05:0.000193117:0.0959854:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID -3.95125e-05:0.000193609:0.0766068:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID -8.34773e-05:0.000224985:0.148367:0.0988442:361194:rs10157329
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID -1.22805e-05:0.000196494:0.0222005:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID -3.67348e-05:0.000192692:0.0711911:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID -3.70876e-05:0.000194562:0.0711829:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID -6.3034e-05:0.000194602:0.127259:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -8.36475e-05:0.000232975:0.14293:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID -3.3917e-05:0.000196819:0.0638976:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID -3.39156e-05:0.000196819:0.0638951:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID -3.38357e-05:0.000196823:0.0637331:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID -4.01322e-05:0.000196935:0.0764855:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID 2.34462e-05:0.00019709:0.0432046:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID -9.34263e-05:0.00021456:0.178323:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID -5.82297e-05:0.000192619:0.117806:0.855376:361194:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID -0.000223564:0.000189764:0.622053:0.838358:361194:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763351 ES:SE:LP:AF:SS:ID -0.000133504:0.000152725:0.417893:0.763351:361194:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105921 ES:SE:LP:AF:SS:ID 0.000195946:0.000210418:0.453781:0.105921:361194:rs12562034
1 769138 rs59306077 CAT C . PASS AF=0.128938 ES:SE:LP:AF:SS:ID 5.19169e-05:0.000194333:0.10273:0.128938:361194:rs762168062
1 769223 rs60320384 C G . PASS AF=0.128608 ES:SE:LP:AF:SS:ID 5.89949e-05:0.000194154:0.11848:0.128608:361194:rs60320384
1 769963 rs7518545 G A . PASS AF=0.105213 ES:SE:LP:AF:SS:ID 0.000197035:0.000212007:0.452602:0.105213:361194:rs7518545
1 770886 rs371458725 G A . PASS AF=0.104268 ES:SE:LP:AF:SS:ID 0.000202928:0.000213701:0.465564:0.104268:361194:rs371458725
1 771410 rs2519006 C T . PASS AF=0.830106 ES:SE:LP:AF:SS:ID -0.000207271:0.00018918:0.563456:0.830106:361194:rs2519006
1 771823 rs2977605 T C . PASS AF=0.87012 ES:SE:LP:AF:SS:ID -6.40918e-05:0.000193284:0.130653:0.87012:361194:rs2977605
1 771967 rs59066358 G A . PASS AF=0.128668 ES:SE:LP:AF:SS:ID 5.75993e-05:0.000194063:0.115423:0.128668:361194:rs59066358