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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-IX_CIRCULATORY/ukb-d-IX_CIRCULATORY.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-IX_CIRCULATORY/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 15:35:12 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-IX_CIRCULATORY/ukb-d-IX_CIRCULATORY.vcf.gz ...
Read summary statistics for 13586588 SNPs.
Dropped 12710 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: 0.0265 (0.0018)
Lambda GC: 1.1731
Mean Chi^2: 1.2091
Intercept: 1.0248 (0.008)
Ratio: 0.1184 (0.0381)
Analysis finished at Mon Nov 25 15:37:33 2019
Total time elapsed: 2.0m:20.89s
{
"af_correlation": 0.9521,
"inflation_factor": 1.1053,
"mean_EFFECT": 5.021e-06,
"n": 361194,
"n_snps": 13586588,
"n_clumped_hits": 11,
"n_p_sig": 517,
"n_mono": 0,
"n_ns": 1251809,
"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": 569299,
"n_est": 362577.6936,
"ratio_se_n": 1.0019,
"mean_diff": 8.3862e-06,
"ratio_diff": 37.4929,
"sd_y_est1": 0.3677,
"sd_y_est2": 0.3684,
"r2_sum1": 0.0002,
"r2_sum2": 0.0016,
"r2_sum3": 0.0016,
"r2_sum4": 0.0016,
"ldsc_nsnp_merge_refpanel_ld": 1283504,
"ldsc_nsnp_merge_regression_ld": 1283504,
"ldsc_observed_scale_h2_beta": 0.0265,
"ldsc_observed_scale_h2_se": 0.0018,
"ldsc_intercept_beta": 1.0248,
"ldsc_intercept_se": 0.008,
"ldsc_lambda_gc": 1.1731,
"ldsc_mean_chisq": 1.2091,
"ldsc_ratio": 0.1186
}
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 | 13574542 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57083 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33337 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051333e+00 | 6.184971e+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 | 7.902505e+07 | 5.591478e+07 | 3.02000e+02 | 3.293100e+07 | 7.013845e+07 | 1.148590e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.000000e-06 | 5.092400e-03 | -5.67022e-02 | -1.425700e-03 | 6.000000e-07 | 1.421000e-03 | 6.480010e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.635300e-03 | 3.506700e-03 | 7.11300e-04 | 1.034900e-03 | 1.907200e-03 | 5.224200e-03 | 1.764200e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.834395e-01 | 2.934473e-01 | 0.00000e+00 | 2.252071e-01 | 4.782500e-01 | 7.377292e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.834391e-01 | 2.934475e-01 | 0.00000e+00 | 2.252062e-01 | 4.782501e-01 | 7.377299e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.908016e-01 | 2.544020e-01 | 1.00000e-03 | 7.429000e-03 | 6.002940e-02 | 2.953060e-01 | 9.989990e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 569299 | 0.9580985 | NA | NA | NA | NA | NA | 1.963330e-01 | 2.471005e-01 | 0.00000e+00 | 5.591000e-03 | 8.426520e-02 | 3.081070e-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 | 0.0005642 | 0.0015149 | 0.7095582 | 0.7095570 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | -0.0004218 | 0.0014314 | 0.7682631 | 0.7682644 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | 0.0000164 | 0.0016092 | 0.9918470 | 0.9918468 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | 0.0027291 | 0.0038400 | 0.4772720 | 0.4772717 | 0.0156880 | 0.0045926 | 361194 |
1 | 723329 | rs189787166 | A | T | -0.0038113 | 0.0113296 | 0.7365649 | 0.7365651 | 0.0017336 | 0.0003994 | 361194 |
1 | 730087 | rs148120343 | T | C | -0.0016465 | 0.0019942 | 0.4090016 | 0.4090012 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | -0.0001333 | 0.0013576 | 0.9217940 | 0.9217942 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | -0.0000911 | 0.0014481 | 0.9498191 | 0.9498186 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | -0.0000056 | 0.0013583 | 0.9967380 | 0.9967377 | 0.1209650 | 0.1525560 | 361194 |
1 | 740284 | rs61770167 | C | T | -0.0060712 | 0.0062143 | 0.3285829 | 0.3285828 | 0.0057851 | 0.0023962 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0027883 | 0.0015684 | 0.0754345 | 0.0754334 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | 0.0014259 | 0.0017237 | 0.4081013 | 0.4080979 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | 0.0009753 | 0.0008293 | 0.2396012 | 0.2396002 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | 0.0009358 | 0.0008484 | 0.2700238 | 0.2700229 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | 0.0015951 | 0.0007799 | 0.0408442 | 0.0408431 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | 0.0009768 | 0.0008296 | 0.2390380 | 0.2390371 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | 0.0008066 | 0.0008658 | 0.3515540 | 0.3515537 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | 0.0009162 | 0.0008725 | 0.2936811 | 0.2936799 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | 0.0009362 | 0.0008295 | 0.2590341 | 0.2590329 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | 0.0002610 | 0.0028455 | 0.9269139 | 0.9269136 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID 0.000564241:0.00151494:0.149012:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID -0.000421768:0.00143144:0.11449:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID 1.64442e-05:0.00160923:0.00355532:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID 0.0027291:0.00384003:0.321234:0.015688:361194:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00173363 ES:SE:LP:AF:SS:ID -0.00381134:0.0113296:0.132789:0.00173363:361194:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID -0.0016465:0.00199418:0.388275:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID -0.000133279:0.00135758:0.0353661:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID -9.11368e-05:0.00144812:0.0223591:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID -5.55369e-06:0.00135831:0.00141898:0.120965:361194:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00578512 ES:SE:LP:AF:SS:ID -0.00607117:0.00621427:0.483355:0.00578512:361194:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00187787 ES:SE:LP:AF:SS:ID -0.00135934:0.0117363:0.0420136:0.00187787:361194:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID -0.000542702:0.00133907:0.164138:0.869742:361194:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00153021 ES:SE:LP:AF:SS:ID -0.00432433:0.0121226:0.141882:0.00153021:361194:rs190826124
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID 0.000537594:0.00132618:0.164179:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID 0.000448127:0.00131085:0.135217:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID 0.000548353:0.00132433:0.168239:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID -0.000248642:0.00129052:0.0720043:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID -0.000514164:0.0013119:0.157943:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID 0.000404875:0.00129375:0.122443:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID 9.98923e-05:0.00234717:0.014999:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID -0.000246724:0.00128918:0.0714879:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID -0.000253387:0.00128976:0.0735289:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID -0.0002315:0.00128913:0.0667745:0.870481:361194:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00504367 ES:SE:LP:AF:SS:ID 0.00724241:0.00661815:0.562546:0.00504367:361194:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00501064 ES:SE:LP:AF:SS:ID 0.00717896:0.00663587:0.553893:0.00501064:361194:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00558665 ES:SE:LP:AF:SS:ID -0.00121879:0.00640985:0.0709921:0.00558665:361194:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID -0.000308732:0.00128686:0.0913011:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID 0.0004602:0.00131307:0.139075:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID -0.000224417:0.00128376:0.0648819:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID -0.000268635:0.00128259:0.0787819:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID -0.000289793:0.00128487:0.0853623:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID -0.000288009:0.00128496:0.0847849:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID -0.000288061:0.001285:0.0847986:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID -0.000354361:0.00128827:0.106091:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID 0.000332317:0.00149705:0.0838999:0.0988442:361194:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00647588 ES:SE:LP:AF:SS:ID -0.000669136:0.00579067:0.0419113:0.00647588:361194:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID -0.000389939:0.00130747:0.116043:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID -0.000218632:0.00128217:0.0631828:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID -0.000453466:0.00129462:0.138982:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID -0.000452352:0.00129488:0.138564:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -0.000459116:0.00155021:0.115145:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID -0.000468913:0.00130963:0.142483:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID -0.000468883:0.00130963:0.142473:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID -0.000471631:0.00130966:0.143417:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID -0.000471506:0.0013104:0.143281:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID 0.000521587:0.00131144:0.160625:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID -0.000344107:0.00142768:0.0917638:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID -8.78278e-05:0.00128169:0.0243991:0.855376:361194:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00165444 ES:SE:LP:AF:SS:ID -0.00513126:0.0113539:0.18621:0.00165444:361194:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID -0.00092514:0.00126269:0.333708:0.838358:361194:rs376645387