manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1239/ieu-a-1239_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
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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/ieu-a-import/processed/ieu-a-1239/ieu-a-1239.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/ieu-a-import/processed/ieu-a-1239/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Wed Feb 5 08:25:29 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1239/ieu-a-1239.vcf.gz ...
Read summary statistics for 10054403 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, 1276597 SNPs remain.
After merging with regression SNP LD, 1276597 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1065 (0.0026)
Lambda GC: 2.0897
Mean Chi^2: 2.6414
Intercept: 1.0251 (0.0135)
Ratio: 0.0153 (0.0082)
Analysis finished at Wed Feb 5 08:27:08 2020
Total time elapsed: 1.0m:39.78s
{
"af_correlation": 0.9535,
"inflation_factor": 1.5903,
"mean_EFFECT": -0.0001,
"n": 766345,
"n_snps": 10054403,
"n_clumped_hits": 317,
"n_p_sig": 30389,
"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": 2369,
"n_est": 758809.7657,
"ratio_se_n": 0.9951,
"mean_diff": 0,
"ratio_diff": 1.5261,
"sd_y_est1": 1.072,
"sd_y_est2": 1.0668,
"r2_sum1": 0.0226,
"r2_sum2": 0.0196,
"r2_sum3": 0.0198,
"r2_sum4": 0.0203,
"ldsc_nsnp_merge_refpanel_ld": 1276597,
"ldsc_nsnp_merge_regression_ld": 1276597,
"ldsc_observed_scale_h2_beta": 0.1065,
"ldsc_observed_scale_h2_se": 0.0026,
"ldsc_intercept_beta": 1.0251,
"ldsc_intercept_se": 0.0135,
"ldsc_lambda_gc": 2.0897,
"ldsc_mean_chisq": 2.6414,
"ldsc_ratio": 0.0153
}
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 | 47 | 0 | 10054403 | 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 | 8.643709e+00 | 5.769073e+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 | 7.915177e+07 | 5.644155e+07 | 8.28000e+02 | 3.276902e+07 | 6.988553e+07 | 1.150264e+08 | 2.492251e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.015000e-04 | 1.483220e-02 | -4.25690e-01 | -3.580000e-03 | -4.000000e-05 | 3.470000e-03 | 4.031400e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.159800e-03 | 1.237830e-02 | 1.70000e-03 | 2.040000e-03 | 3.660000e-03 | 9.310000e-03 | 1.118300e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.242246e-01 | 3.083991e-01 | 0.00000e+00 | 1.370001e-01 | 3.949999e-01 | 6.899999e-01 | 1.000000e+00 | ▇▅▅▅▅ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.242206e-01 | 3.083998e-01 | 0.00000e+00 | 1.371123e-01 | 3.954691e-01 | 6.906863e-01 | 1.000000e+00 | ▇▅▅▅▅ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.952060e-01 | 2.554429e-01 | 1.70100e-03 | 1.020000e-02 | 6.633000e-02 | 2.993000e-01 | 9.982990e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 2369 | 0.9997644 | NA | NA | NA | NA | NA | 1.968793e-01 | 2.465400e-01 | 1.99700e-04 | 9.584700e-03 | 8.506390e-02 | 3.013180e-01 | 9.996010e-01 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.663450e+05 | 0.000000e+00 | 7.66345e+05 | 7.663450e+05 | 7.663450e+05 | 7.663450e+05 | 7.663450e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 713092 | rs4565649 | G | A | -0.01119 | 0.02382 | 0.6390002 | 0.6385170 | 0.008503 | 0.0249601 | 766345 |
1 | 715205 | rs141090730 | C | G | -0.01730 | 0.02382 | 0.4680002 | 0.4676669 | 0.008503 | 0.0299521 | 766345 |
1 | 715265 | rs12184267 | C | T | 0.00226 | 0.00574 | 0.6939992 | 0.6937817 | 0.040820 | 0.0275559 | 766345 |
1 | 715367 | rs12184277 | A | G | 0.00369 | 0.00579 | 0.5239997 | 0.5239257 | 0.040820 | 0.0281550 | 766345 |
1 | 717474 | rs141784362 | C | T | -0.01391 | 0.02471 | 0.5730005 | 0.5734826 | 0.008503 | 0.0249601 | 766345 |
1 | 717587 | rs144155419 | G | A | 0.00078 | 0.00846 | 0.9269999 | 0.9265403 | 0.008503 | 0.0045926 | 766345 |
1 | 720381 | rs116801199 | G | T | 0.00400 | 0.00574 | 0.4850003 | 0.4858878 | 0.040820 | 0.0359425 | 766345 |
1 | 721290 | rs12565286 | G | C | 0.00329 | 0.00570 | 0.5639999 | 0.5638091 | 0.042520 | 0.0371406 | 766345 |
1 | 722559 | rs150361918 | T | C | -0.01471 | 0.02409 | 0.5419996 | 0.5414467 | 0.008503 | 0.0373403 | 766345 |
1 | 722603 | rs138029171 | T | C | 0.00191 | 0.02613 | 0.9420000 | 0.9417297 | 0.008503 | 0.0177716 | 766345 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51213613 | rs34726907 | C | T | -0.00459 | 0.00281 | 0.1029999 | 0.1023740 | 0.165000 | 0.1727240 | 766345 |
22 | 51217556 | rs187294336 | C | T | 0.02341 | 0.01031 | 0.0232001 | 0.0231705 | 0.005102 | 0.0023962 | 766345 |
22 | 51217954 | rs9616974 | G | A | -0.00511 | 0.00378 | 0.1769999 | 0.1764227 | 0.093540 | 0.0621006 | 766345 |
22 | 51218224 | rs9616975 | C | A | -0.00520 | 0.00377 | 0.1679999 | 0.1677991 | 0.091840 | 0.0619010 | 766345 |
22 | 51219006 | rs28729663 | G | A | -0.00347 | 0.00277 | 0.2099999 | 0.2103121 | 0.176900 | 0.2052720 | 766345 |
22 | 51219387 | rs9616832 | T | C | -0.00507 | 0.00376 | 0.1780000 | 0.1775284 | 0.090140 | 0.0654952 | 766345 |
22 | 51219704 | rs147475742 | G | A | -0.01050 | 0.00504 | 0.0371997 | 0.0372209 | 0.044220 | 0.0473243 | 766345 |
22 | 51221731 | rs115055839 | T | C | -0.00528 | 0.00377 | 0.1610000 | 0.1613545 | 0.091840 | 0.0625000 | 766345 |
22 | 51229805 | rs9616985 | T | C | -0.00522 | 0.00378 | 0.1669998 | 0.1672936 | 0.091840 | 0.0730831 | 766345 |
22 | 51237063 | rs3896457 | T | C | -0.00285 | 0.00216 | 0.1880001 | 0.1870206 | 0.226200 | 0.2050720 | 766345 |
1 713092 rs4565649 G A . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.01119:0.02382:0.194499:0.008503:766345:rs4565649
1 715205 rs141090730 C G . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.0173:0.02382:0.329754:0.008503:766345:rs141090730
1 715265 rs12184267 C T . PASS AF=0.04082 ES:SE:LP:AF:SS:ID 0.00226:0.00574:0.158641:0.04082:766345:rs12184267
1 715367 rs12184277 A G . PASS AF=0.04082 ES:SE:LP:AF:SS:ID 0.00369:0.00579:0.280669:0.04082:766345:rs12184277
1 717474 rs141784362 C T . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.01391:0.02471:0.241845:0.008503:766345:rs141784362
1 717587 rs144155419 G A . PASS AF=0.008503 ES:SE:LP:AF:SS:ID 0.00078:0.00846:0.0329203:0.008503:766345:rs144155419
1 720381 rs116801199 G T . PASS AF=0.04082 ES:SE:LP:AF:SS:ID 0.004:0.00574:0.314258:0.04082:766345:rs116801199
1 721290 rs12565286 G C . PASS AF=0.04252 ES:SE:LP:AF:SS:ID 0.00329:0.0057:0.248721:0.04252:766345:rs12565286
1 722559 rs150361918 T C . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.01471:0.02409:0.266001:0.008503:766345:rs150361918
1 722603 rs138029171 T C . PASS AF=0.008503 ES:SE:LP:AF:SS:ID 0.00191:0.02613:0.0259491:0.008503:766345:rs138029171
1 722980 rs114222710 C T . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.00777:0.02409:0.126679:0.008503:766345:rs114222710
1 723891 rs2977670 G C . PASS AF=0.95238 ES:SE:LP:AF:SS:ID -0.00485:0.00555:0.417937:0.95238:766345:rs2977670
1 723918 rs144434834 G A . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.00624:0.02447:0.0974532:0.008503:766345:rs144434834
1 726794 rs28454925 C G . PASS AF=0.04082 ES:SE:LP:AF:SS:ID 0.00581:0.00579:0.501689:0.04082:766345:rs28454925
1 729632 rs116720794 C T . PASS AF=0.001701 ES:SE:LP:AF:SS:ID 0.0036:0.00573:0.275724:0.001701:766345:rs116720794
1 729679 rs4951859 C G . PASS AF=0.8554 ES:SE:LP:AF:SS:ID -0.00148:0.00292:0.213249:0.8554:766345:rs4951859
1 730087 rs148120343 T C . PASS AF=0.05272 ES:SE:LP:AF:SS:ID 0.0014:0.0045:0.120904:0.05272:766345:rs148120343
1 732120 rs114572157 T C . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.0078:0.02351:0.130768:0.008503:766345:rs114572157
1 732801 rs144022023 A G . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.00263:0.02409:0.0395292:0.008503:766345:rs144022023
1 734349 rs141242758 T C . PASS AF=0.1054 ES:SE:LP:AF:SS:ID 0.00176:0.00306:0.247184:0.1054:766345:rs141242758
1 736186 rs147133636 G A . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.01116:0.02693:0.16877:0.008503:766345:rs147133636
1 736289 rs79010578 T A . PASS AF=0.1241 ES:SE:LP:AF:SS:ID 0.00162:0.00312:0.218963:0.1241:766345:rs79010578
1 736689 rs181876450 T C . PASS AF=0.008503 ES:SE:LP:AF:SS:ID 0.00089:0.00994:0.0319843:0.008503:766345:rs181876450
1 738539 rs147999235 T C . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.00049:0.02459:0.0070049:0.008503:766345:rs147999235
1 739608 rs145267859 T C . PASS AF=0.001701 ES:SE:LP:AF:SS:ID 0.01903:0.07908:0.091515:0.001701:766345:rs145267859
1 741833 rs148581628 C T . PASS AF=0.008503 ES:SE:LP:AF:SS:ID -0.00656:0.02447:0.102923:0.008503:766345:rs148581628
1 746189 rs139221807 A G . PASS AF=0.001701 ES:SE:LP:AF:SS:ID 0.05698:0.03886:0.844664:0.001701:766345:rs139221807
1 748445 rs183774475 T C . PASS AF=0.001701 ES:SE:LP:AF:SS:ID 0.03414:0.07908:0.176526:0.001701:766345:rs183774475
1 748446 rs188307914 G A . PASS AF=0.001701 ES:SE:LP:AF:SS:ID 0.02098:0.07908:0.101824:0.001701:766345:rs188307914
1 752478 rs146277091 G A . PASS AF=0.03912 ES:SE:LP:AF:SS:ID 0.00286:0.00575:0.208309:0.03912:766345:rs146277091
1 752566 rs3094315 G A . PASS AF=0.8486 ES:SE:LP:AF:SS:ID 0.00034:0.00264:0.0462403:0.8486:766345:rs3094315
1 752721 rs3131972 A G . PASS AF=0.8486 ES:SE:LP:AF:SS:ID 0.00041:0.00264:0.0570004:0.8486:766345:rs3131972
1 753541 rs2073813 G A . PASS AF=0.1156 ES:SE:LP:AF:SS:ID 0.00046:0.00274:0.0624821:0.1156:766345:rs2073813
1 754063 rs12184312 G T . PASS AF=0.03061 ES:SE:LP:AF:SS:ID 0.00246:0.0057:0.176526:0.03061:766345:rs12184312
1 754105 rs12184325 C T . PASS AF=0.03741 ES:SE:LP:AF:SS:ID 0.00095:0.00571:0.0614803:0.03741:766345:rs12184325
1 754182 rs3131969 A G . PASS AF=0.8759 ES:SE:LP:AF:SS:ID -0.00088:0.00275:0.124939:0.8759:766345:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8759 ES:SE:LP:AF:SS:ID -0.00098:0.00275:0.142065:0.8759:766345:rs3131968
1 754211 rs12184313 G A . PASS AF=0.04082 ES:SE:LP:AF:SS:ID 0.00175:0.00571:0.119758:0.04082:766345:rs12184313
1 754334 rs3131967 T C . PASS AF=0.8759 ES:SE:LP:AF:SS:ID -0.00166:0.00277:0.260428:0.8759:766345:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005102 ES:SE:LP:AF:SS:ID -0.00052:0.01513:0.0118872:0.005102:766345:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005102 ES:SE:LP:AF:SS:ID -0.00045:0.01513:0.0105502:0.005102:766345:rs142682604
1 754503 rs3115859 G A . PASS AF=0.8486 ES:SE:LP:AF:SS:ID 0.00072:0.00264:0.105684:0.8486:766345:rs3115859
1 754629 rs10454459 A G . PASS AF=0.04082 ES:SE:LP:AF:SS:ID 0.00193:0.0057:0.133713:0.04082:766345:rs10454459
1 754964 rs3131966 C T . PASS AF=0.8469 ES:SE:LP:AF:SS:ID -0.00035:0.0027:0.0467237:0.8469:766345:rs3131966
1 755240 rs181660517 T G . PASS AF=0.0119 ES:SE:LP:AF:SS:ID -0.0062:0.00911:0.303644:0.0119:766345:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005102 ES:SE:LP:AF:SS:ID -0.00664:0.01442:0.19044:0.005102:766345:rs184270342
1 755890 rs3115858 A T . PASS AF=0.8759 ES:SE:LP:AF:SS:ID -0.00119:0.00276:0.175874:0.8759:766345:rs3115858
1 756604 rs3131962 A G . PASS AF=0.8724 ES:SE:LP:AF:SS:ID -0.00068:0.00275:0.0942041:0.8724:766345:rs3131962
1 756838 rs77239421 C G . PASS AF=0.001701 ES:SE:LP:AF:SS:ID 0.02399:0.07908:0.118045:0.001701:766345:rs77239421
1 757640 rs3115853 G A . PASS AF=0.8759 ES:SE:LP:AF:SS:ID 6e-05:0.00286:0.00744648:0.8759:766345:rs3115853