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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-30750_raw/ukb-d-30750_raw.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-30750_raw/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 14:50:47 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30750_raw/ukb-d-30750_raw.vcf.gz ...
Read summary statistics for 13586179 SNPs.
Dropped 12713 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.108 (0.0069)
Lambda GC: 1.4423
Mean Chi^2: 1.8538
Intercept: 1.0998 (0.0134)
Ratio: 0.1169 (0.0157)
Analysis finished at Mon Nov 25 14:53:07 2019
Total time elapsed: 2.0m:19.93s
{
"af_correlation": 0.9521,
"inflation_factor": 1.2833,
"mean_EFFECT": 0.0006,
"n": 344182,
"n_snps": 13586179,
"n_clumped_hits": 190,
"n_p_sig": 41329,
"n_mono": 0,
"n_ns": 1251783,
"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": 569193,
"n_est": 345486.7655,
"ratio_se_n": 1.0019,
"mean_diff": -0.0005,
"ratio_diff": 1354.4167,
"sd_y_est1": 6.3852,
"sd_y_est2": 6.3973,
"r2_sum1": 2.1018,
"r2_sum2": 0.0516,
"r2_sum3": 0.0514,
"r2_sum4": 0.051,
"ldsc_nsnp_merge_refpanel_ld": 1283504,
"ldsc_nsnp_merge_regression_ld": 1283504,
"ldsc_observed_scale_h2_beta": 0.108,
"ldsc_observed_scale_h2_se": 0.0069,
"ldsc_intercept_beta": 1.0998,
"ldsc_intercept_se": 0.0134,
"ldsc_lambda_gc": 1.4423,
"ldsc_mean_chisq": 1.8538,
"ldsc_ratio": 0.1169
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | TRUE |
n | FALSE |
is_snpid_non_unique | TRUE |
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 | TRUE |
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 | 1.000000 | 3 | 94 | 0 | 13574130 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.000000 | 1 | 100 | 0 | 57081 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.000000 | 1 | 342 | 0 | 33337 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | 9.051361e+00 | 6.184991e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.902488e+07 | 5.591481e+07 | 3.02000e+02 | 3.293102e+07 | 7.013812e+07 | 1.148586e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | 6.456000e-04 | 9.395850e-02 | -2.23360e+00 | -2.818300e-02 | -8.780000e-05 | 2.813900e-02 | 1.505500e+00 | ▁▁▇▅▁ |
numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | 6.467110e-02 | 6.238360e-02 | 1.26520e-02 | 1.841200e-02 | 3.393000e-02 | 9.293600e-02 | 3.156600e-01 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.581021e-01 | 3.015233e-01 | 0.00000e+00 | 1.863902e-01 | 4.448197e-01 | 7.197307e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.581017e-01 | 3.015236e-01 | 0.00000e+00 | 1.863895e-01 | 4.448198e-01 | 7.197312e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | 1.908070e-01 | 2.544038e-01 | 1.00000e-03 | 7.430800e-03 | 6.004000e-02 | 2.953300e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 569193 | 0.958105 | NA | NA | NA | NA | NA | 1.963368e-01 | 2.471017e-01 | 0.00000e+00 | 5.591000e-03 | 8.426520e-02 | 3.081070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.441820e+05 | 0.000000e+00 | 3.44182e+05 | 3.441820e+05 | 3.441820e+05 | 3.441820e+05 | 3.441820e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0191390 | 0.026974 | 0.4780001 | 0.4779925 | 0.1104400 | 0.1894970 | 344182 |
1 | 693731 | rs12238997 | A | G | -0.0080255 | 0.025483 | 0.7528093 | 0.7528107 | 0.1156900 | 0.1417730 | 344182 |
1 | 707522 | rs371890604 | G | C | -0.0280540 | 0.028653 | 0.3275397 | 0.3275332 | 0.0971900 | 0.1293930 | 344182 |
1 | 717587 | rs144155419 | G | A | 0.0722420 | 0.068373 | 0.2907000 | 0.2907003 | 0.0156590 | 0.0045926 | 344182 |
1 | 723329 | rs189787166 | A | T | 0.0012502 | 0.202170 | 0.9950700 | 0.9950660 | 0.0017229 | 0.0003994 | 344182 |
1 | 730087 | rs148120343 | T | C | -0.0131150 | 0.035516 | 0.7119295 | 0.7119263 | 0.0563600 | 0.0127796 | 344182 |
1 | 731718 | rs142557973 | T | C | -0.0106740 | 0.024166 | 0.6586899 | 0.6587100 | 0.1216100 | 0.1543530 | 344182 |
1 | 732032 | rs61770163 | A | C | -0.0019570 | 0.025779 | 0.9394901 | 0.9394871 | 0.1210600 | 0.1555510 | 344182 |
1 | 734349 | rs141242758 | T | C | -0.0096491 | 0.024179 | 0.6898505 | 0.6898420 | 0.1208300 | 0.1525560 | 344182 |
1 | 740284 | rs61770167 | C | T | -0.0108930 | 0.110940 | 0.9217800 | 0.9217828 | 0.0057445 | 0.0023962 | 344182 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0118080 | 0.027895 | 0.6720893 | 0.6720752 | 0.056197 | 0.0309934 | 344182 |
23 | 154923374 | rs111332691 | T | A | 0.0591460 | 0.030631 | 0.0534958 | 0.0534930 | 0.044889 | 0.0116556 | 344182 |
23 | 154925045 | rs509981 | C | T | -0.0460480 | 0.014757 | 0.0018060 | 0.0018059 | 0.245480 | 0.3634440 | 344182 |
23 | 154925895 | rs538470 | C | T | -0.0493460 | 0.015096 | 0.0010800 | 0.0010800 | 0.241790 | 0.3634440 | 344182 |
23 | 154927581 | rs644138 | G | A | -0.0426440 | 0.013877 | 0.0021192 | 0.0021192 | 0.302060 | 0.4635760 | 344182 |
23 | 154929412 | rs557132 | C | T | -0.0455780 | 0.014761 | 0.0020178 | 0.0020169 | 0.245330 | 0.3568210 | 344182 |
23 | 154929637 | rs35185538 | CT | C | -0.0353650 | 0.015408 | 0.0217240 | 0.0217196 | 0.229580 | 0.3011920 | 344182 |
23 | 154929952 | rs4012982 | CAA | C | -0.0451760 | 0.015525 | 0.0036159 | 0.0036156 | 0.239300 | 0.3165560 | 344182 |
23 | 154930230 | rs781880 | A | G | -0.0452330 | 0.014759 | 0.0021786 | 0.0021783 | 0.245720 | 0.3618540 | 344182 |
23 | 154930487 | rs781879 | T | A | 0.0049815 | 0.050584 | 0.9215500 | 0.9215513 | 0.019594 | 0.1263580 | 344182 |
1 692794 rs530212009 CA C . PASS AF=0.11044 ES:SE:LP:AF:SS:ID -0.019139:0.026974:0.320572:0.11044:344182:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11569 ES:SE:LP:AF:SS:ID -0.0080255:0.025483:0.123315:0.11569:344182:rs12238997
1 707522 rs371890604 G C . PASS AF=0.09719 ES:SE:LP:AF:SS:ID -0.028054:0.028653:0.484736:0.09719:344182:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015659 ES:SE:LP:AF:SS:ID 0.072242:0.068373:0.536555:0.015659:344182:rs144155419
1 723329 rs189787166 A T . PASS AF=0.0017229 ES:SE:LP:AF:SS:ID 0.0012502:0.20217:0.00214637:0.0017229:344182:rs189787166
1 730087 rs148120343 T C . PASS AF=0.05636 ES:SE:LP:AF:SS:ID -0.013115:0.035516:0.147563:0.05636:344182:rs148120343
1 731718 rs58276399 T C . PASS AF=0.12161 ES:SE:LP:AF:SS:ID -0.010674:0.024166:0.181319:0.12161:344182:rs58276399
1 732032 rs61770163 A C . PASS AF=0.12106 ES:SE:LP:AF:SS:ID -0.001957:0.025779:0.0271078:0.12106:344182:rs61770163
1 734349 rs141242758 T C . PASS AF=0.12083 ES:SE:LP:AF:SS:ID -0.0096491:0.024179:0.161245:0.12083:344182:rs141242758
1 740284 rs61770167 C T . PASS AF=0.0057445 ES:SE:LP:AF:SS:ID -0.010893:0.11094:0.0353727:0.0057445:344182:rs61770167
1 742813 rs112573343 C T . PASS AF=0.001891 ES:SE:LP:AF:SS:ID -0.14547:0.20798:0.314912:0.001891:344182:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.86988 ES:SE:LP:AF:SS:ID 0.018604:0.023837:0.361401:0.86988:344182:rs529266287
1 750230 rs190826124 G C . PASS AF=0.0015301 ES:SE:LP:AF:SS:ID 0.018481:0.21577:0.0307053:0.0015301:344182:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12278 ES:SE:LP:AF:SS:ID -0.015952:0.023608:0.301717:0.12278:344182:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.14261 ES:SE:LP:AF:SS:ID -0.0092031:0.023331:0.159116:0.14261:344182:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12289 ES:SE:LP:AF:SS:ID -0.015986:0.023575:0.303024:0.12289:344182:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87101 ES:SE:LP:AF:SS:ID 0.014338:0.022968:0.273721:0.87101:344182:rs3115860
1 753425 rs3131970 T C . PASS AF=0.8756 ES:SE:LP:AF:SS:ID 0.013498:0.023352:0.249291:0.8756:344182:rs3131970
1 753541 rs2073813 G A . PASS AF=0.1285 ES:SE:LP:AF:SS:ID -0.014783:0.023027:0.283271:0.1285:344182:rs2073813
1 754105 rs12184325 C T . PASS AF=0.036395 ES:SE:LP:AF:SS:ID -0.044333:0.041744:0.540276:0.036395:344182:rs12184325
1 754182 rs3131969 A G . PASS AF=0.8706 ES:SE:LP:AF:SS:ID 0.014228:0.022944:0.2715:0.8706:344182:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8707 ES:SE:LP:AF:SS:ID 0.01493:0.022954:0.287839:0.8707:344182:rs3131968
1 754334 rs3131967 T C . PASS AF=0.8706 ES:SE:LP:AF:SS:ID 0.014101:0.022943:0.268556:0.8706:344182:rs3131967
1 754433 rs150578204 G A . PASS AF=0.0050345 ES:SE:LP:AF:SS:ID 0.0072577:0.11783:0.0218697:0.0050345:344182:rs150578204
1 754458 rs142682604 G T . PASS AF=0.0050014 ES:SE:LP:AF:SS:ID 0.0047949:0.11815:0.0142907:0.0050014:344182:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0056138 ES:SE:LP:AF:SS:ID -0.092931:0.11373:0.383157:0.0056138:344182:rs184270342
1 755890 rs3115858 A T . PASS AF=0.87067 ES:SE:LP:AF:SS:ID 0.01469:0.022903:0.282962:0.87067:344182:rs3115858
1 756434 rs61768170 G C . PASS AF=0.12585 ES:SE:LP:AF:SS:ID -0.013643:0.023372:0.25227:0.12585:344182:rs61768170
1 756604 rs3131962 A G . PASS AF=0.87024 ES:SE:LP:AF:SS:ID 0.014283:0.022847:0.274203:0.87024:344182:rs3131962
1 757640 rs3115853 G A . PASS AF=0.86953 ES:SE:LP:AF:SS:ID 0.012184:0.022827:0.226565:0.86953:344182:rs3115853
1 757734 rs4951929 C T . PASS AF=0.87039 ES:SE:LP:AF:SS:ID 0.014434:0.022867:0.277448:0.87039:344182:rs4951929
1 757936 rs4951862 C A . PASS AF=0.8704 ES:SE:LP:AF:SS:ID 0.014472:0.022868:0.278313:0.8704:344182:rs4951862
1 758144 rs3131956 A G . PASS AF=0.8704 ES:SE:LP:AF:SS:ID 0.014451:0.022869:0.277802:0.8704:344182:rs3131956
1 758626 rs3131954 C T . PASS AF=0.87085 ES:SE:LP:AF:SS:ID 0.014255:0.022928:0.272361:0.87085:344182:rs3131954
1 759293 rs10157329 T A . PASS AF=0.098736 ES:SE:LP:AF:SS:ID -0.037243:0.026651:0.789735:0.098736:344182:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.0065064 ES:SE:LP:AF:SS:ID -0.044481:0.10274:0.177152:0.0065064:344182:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.87476 ES:SE:LP:AF:SS:ID 0.015741:0.023272:0.302065:0.87476:344182:rs3115851
1 761732 rs2286139 C T . PASS AF=0.86414 ES:SE:LP:AF:SS:ID 0.021651:0.022818:0.465086:0.86414:344182:rs2286139
1 761752 rs1057213 C T . PASS AF=0.86955 ES:SE:LP:AF:SS:ID 0.016057:0.023042:0.313462:0.86955:344182:rs1057213
1 762273 rs3115849 G A . PASS AF=0.86649 ES:SE:LP:AF:SS:ID 0.01791:0.023046:0.359429:0.86649:344182:rs3115849
1 762485 rs12095200 C A . PASS AF=0.098689 ES:SE:LP:AF:SS:ID -0.016215:0.027589:0.254371:0.098689:344182:rs12095200
1 762589 rs3115848 G C . PASS AF=0.87168 ES:SE:LP:AF:SS:ID 0.018124:0.023311:0.359628:0.87168:344182:rs3115848
1 762592 rs3131950 C G . PASS AF=0.87168 ES:SE:LP:AF:SS:ID 0.018125:0.023311:0.359668:0.87168:344182:rs3131950
1 762601 rs3131949 T C . PASS AF=0.87168 ES:SE:LP:AF:SS:ID 0.018116:0.023312:0.359439:0.87168:344182:rs3131949
1 762632 rs3131948 T A . PASS AF=0.87206 ES:SE:LP:AF:SS:ID 0.019479:0.023325:0.393974:0.87206:344182:rs3131948
1 764191 rs7515915 T G . PASS AF=0.12543 ES:SE:LP:AF:SS:ID -0.016079:0.023344:0.308954:0.12543:344182:rs7515915
1 766007 rs61768174 A C . PASS AF=0.10533 ES:SE:LP:AF:SS:ID -0.026608:0.025419:0.529884:0.10533:344182:rs61768174
1 766105 rs2519015 T A . PASS AF=0.85548 ES:SE:LP:AF:SS:ID 0.021945:0.02281:0.473648:0.85548:344182:rs2519015
1 767393 rs538667473 A C . PASS AF=0.0016444 ES:SE:LP:AF:SS:ID -0.066413:0.2026:0.128976:0.0016444:344182:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.83838 ES:SE:LP:AF:SS:ID -0.014574:0.022463:0.286963:0.83838:344182:rs376645387