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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I63/ukb-d-I63_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T17:04:29.592281",
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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-I63/ukb-d-I63.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I63/ukb-d-I63_data.vcf.gz; Date=Mon Nov 25 17:18:53 2019",
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}
*********************************************************************
* 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-I63/ukb-d-I63.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-I63/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 17:43:27 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I63/ukb-d-I63.vcf.gz ...
Read summary statistics for 10889322 SNPs.
Dropped 8903 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, 1281701 SNPs remain.
After merging with regression SNP LD, 1281701 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0015 (0.0011)
Lambda GC: 1.0142
Mean Chi^2: 1.0171
Intercept: 1.0062 (0.0059)
Ratio: 0.3646 (0.3441)
Analysis finished at Mon Nov 25 17:45:18 2019
Total time elapsed: 1.0m:51.47s
{
"af_correlation": 0.9455,
"inflation_factor": 1.0268,
"mean_EFFECT": -4.5764e-07,
"n": 361194,
"n_snps": 10889322,
"n_clumped_hits": 1,
"n_p_sig": 6,
"n_mono": 0,
"n_ns": 1132472,
"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": 216572,
"n_est": 361722.6106,
"ratio_se_n": 1.0007,
"mean_diff": -4.63e-06,
"ratio_diff": 13.8847,
"sd_y_est1": 0.0844,
"sd_y_est2": 0.0844,
"r2_sum1": 5.8963e-07,
"r2_sum2": 0.0001,
"r2_sum3": 0.0001,
"r2_sum4": 0.0001,
"ldsc_nsnp_merge_refpanel_ld": 1281701,
"ldsc_nsnp_merge_regression_ld": 1281701,
"ldsc_observed_scale_h2_beta": 0.0015,
"ldsc_observed_scale_h2_se": 0.0011,
"ldsc_intercept_beta": 1.0062,
"ldsc_intercept_se": 0.0059,
"ldsc_lambda_gc": 1.0142,
"ldsc_mean_chisq": 1.0171,
"ldsc_ratio": 0.3626
}
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 | 10881002 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 50784 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 31199 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.075029e+00 | 6.180106e+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 | 7.880849e+07 | 5.603288e+07 | 3.02000e+02 | 3.258471e+07 | 6.977317e+07 | 1.147444e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -5.000000e-07 | 5.961000e-04 | -8.02600e-03 | -2.449000e-04 | -3.800000e-06 | 2.377000e-04 | 8.408800e-03 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.825000e-04 | 3.431000e-04 | 1.63400e-04 | 2.227000e-04 | 3.226000e-04 | 6.429000e-04 | 2.025100e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.959967e-01 | 2.890422e-01 | 0.00000e+00 | 2.452082e-01 | 4.943118e-01 | 7.456688e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.959962e-01 | 2.890425e-01 | 0.00000e+00 | 2.452076e-01 | 4.943119e-01 | 7.456677e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.353031e-01 | 2.620224e-01 | 4.83750e-03 | 2.564610e-02 | 1.218340e-01 | 3.765880e-01 | 9.951620e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 216572 | 0.9801115 | NA | NA | NA | NA | NA | 2.354195e-01 | 2.530840e-01 | 0.00000e+00 | 2.496010e-02 | 1.391770e-01 | 3.748000e-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 | -0.0005462 | 0.0003480 | 0.1164729 | 0.1164724 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | -0.0006243 | 0.0003288 | 0.0576036 | 0.0576030 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | -0.0003826 | 0.0003696 | 0.3005910 | 0.3005900 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | -0.0010441 | 0.0008820 | 0.2365130 | 0.2365133 | 0.0156880 | 0.0045926 | 361194 |
1 | 730087 | rs148120343 | T | C | -0.0007279 | 0.0004580 | 0.1119951 | 0.1119943 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | -0.0004906 | 0.0003118 | 0.1156099 | 0.1156093 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | -0.0006027 | 0.0003326 | 0.0699761 | 0.0699752 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | -0.0005067 | 0.0003120 | 0.1043780 | 0.1043770 | 0.1209650 | 0.1525560 | 361194 |
1 | 740284 | rs61770167 | C | T | -0.0007731 | 0.0014273 | 0.5880564 | 0.5880564 | 0.0057851 | 0.0023962 | 361194 |
1 | 749963 | rs529266287 | T | TAA | 0.0005022 | 0.0003076 | 0.1025010 | 0.1025009 | 0.8697420 | 0.7641770 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0000426 | 0.0003602 | 0.9058790 | 0.9058789 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | 0.0000236 | 0.0003959 | 0.9524910 | 0.9524912 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | -0.0001875 | 0.0001905 | 0.3248389 | 0.3248373 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | -0.0002265 | 0.0001949 | 0.2450039 | 0.2450024 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | -0.0001630 | 0.0001791 | 0.3627689 | 0.3627678 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | -0.0001918 | 0.0001905 | 0.3141442 | 0.3141437 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | -0.0002349 | 0.0001989 | 0.2374729 | 0.2374737 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | -0.0002279 | 0.0002004 | 0.2553630 | 0.2553605 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | -0.0002256 | 0.0001905 | 0.2363442 | 0.2363432 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | 0.0009054 | 0.0006536 | 0.1659411 | 0.1659396 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID -0.00054621:0.000347959:0.933775:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID -0.000624253:0.000328778:1.23955:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID -0.000382614:0.000369615:0.522024:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID -0.00104406:0.000881996:0.626145:0.015688:361194:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID -0.000727947:0.000458032:0.950801:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID -0.000490631:0.000311814:0.937005:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID -0.000602713:0.00033261:1.15505:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID -0.000506657:0.000311982:0.981391:0.120965:361194:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00578512 ES:SE:LP:AF:SS:ID -0.00077312:0.00142733:0.230581:0.00578512:361194:rs61770167
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID 0.000502207:0.000307565:0.989272:0.869742:361194:rs529266287
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID -0.000409921:0.000304603:0.748649:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID -0.000524817:0.000301083:1.08982:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID -0.000404801:0.000304179:0.736942:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID 0.000337948:0.000296412:0.594766:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID 0.000398888:0.000301324:0.731481:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID -0.000371292:0.000297156:0.674714:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID 1.67168e-05:0.00053911:0.0108783:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID 0.000352535:0.000296104:0.631118:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID 0.000378547:0.000296239:0.696143:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID 0.00036033:0.000296093:0.65048:0.870481:361194:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00504367 ES:SE:LP:AF:SS:ID 0.00240757:0.00152009:0.946031:0.00504367:361194:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00501064 ES:SE:LP:AF:SS:ID 0.0023723:0.00152416:0.922272:0.00501064:361194:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00558665 ES:SE:LP:AF:SS:ID 0.00205067:0.00147224:0.786071:0.00558665:361194:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID 0.00035085:0.000295572:0.628526:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID -0.000438616:0.000301592:0.836085:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID 0.000358813:0.000294861:0.650437:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID 0.000385285:0.000294592:0.719146:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID 0.000359524:0.000295114:0.651446:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID 0.000359241:0.000295135:0.65067:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID 0.000358855:0.000295145:0.649678:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID 0.000348909:0.000295896:0.622812:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID -0.000356409:0.00034385:0.52294:0.0988442:361194:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00647588 ES:SE:LP:AF:SS:ID 0.00176267:0.00133003:0.732648:0.00647588:361194:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID 0.000420987:0.000300306:0.793287:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID 0.000407892:0.000294494:0.7798:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID 0.000363198:0.000297354:0.653798:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID 0.000342684:0.000297414:0.603389:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -0.000443008:0.00035606:0.670747:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000417782:0.000300802:0.782869:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000417786:0.000300802:0.782877:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID 0.000417768:0.000300808:0.782808:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID 0.000405734:0.00030098:0.750447:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID -0.000439235:0.000301217:0.839273:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID -0.000376942:0.000327916:0.601458:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID 0.000379658:0.000294384:0.705168:0.855376:361194:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID 0.000758924:0.000290019:2.05178:0.838358:361194:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763351 ES:SE:LP:AF:SS:ID 0.000628673:0.000233411:2.15041:0.763351:361194:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105921 ES:SE:LP:AF:SS:ID -0.000753203:0.000321584:1.71731:0.105921:361194:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00768395 ES:SE:LP:AF:SS:ID -4.12019e-07:0.00119484:0.000119447:0.00768395:361194:rs12562811
1 769138 rs59306077 CAT C . PASS AF=0.128938 ES:SE:LP:AF:SS:ID -0.000354193:0.000297004:0.632562:0.128938:361194:rs762168062