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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-70/ieu-a-70.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-70/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 11:25:53 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-70/ieu-a-70.vcf.gz ...
Read summary statistics for 2295840 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, 1093137 SNPs remain.
After merging with regression SNP LD, 1093137 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1635 (0.0107)
Lambda GC: 1.032
Mean Chi^2: 1.0826
Intercept: 0.883 (0.0076)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 11:26:22 2020
Total time elapsed: 28.92s
{
"af_correlation": 0.9116,
"inflation_factor": 1.0475,
"mean_EFFECT": -0.0001,
"n": 109678,
"n_snps": 2295840,
"n_clumped_hits": 23,
"n_p_sig": 262,
"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": 9968,
"n_miss_AF_reference": 18219,
"n_est": 107609.6454,
"ratio_se_n": 0.9905,
"mean_diff": 0,
"ratio_diff": 4.3259,
"sd_y_est1": 1.5059,
"sd_y_est2": 1.4917,
"r2_sum1": 0.012,
"r2_sum2": 0.0053,
"r2_sum3": 0.0054,
"r2_sum4": 0.0095,
"ldsc_nsnp_merge_refpanel_ld": 1093137,
"ldsc_nsnp_merge_regression_ld": 1093137,
"ldsc_observed_scale_h2_beta": 0.1635,
"ldsc_observed_scale_h2_se": 0.0107,
"ldsc_intercept_beta": 0.883,
"ldsc_intercept_se": 0.0076,
"ldsc_lambda_gc": 1.032,
"ldsc_mean_chisq": 1.0826,
"ldsc_ratio": -1.4165
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
is_snpid_non_unique | FALSE |
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 | 42 | 0 | 2295840 | 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 | 8.539854e+00 | 5.626866e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.894087e+07 | 5.547674e+07 | 1.3034e+04 | 3.294729e+07 | 7.042867e+07 | 1.142225e+08 | 2.491808e+08 | ▇▇▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.410000e-04 | 1.024110e-02 | -1.1000e-01 | -5.900000e-03 | -1.000000e-04 | 5.700000e-03 | 1.500000e-01 | ▁▂▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.298800e-03 | 4.129200e-03 | 4.6000e-03 | 6.700000e-03 | 7.700000e-03 | 1.000000e-02 | 4.500000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.938654e-01 | 2.916507e-01 | 0.0000e+00 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.937143e-01 | 2.914415e-01 | 0.0000e+00 | 2.404299e-01 | 4.923555e-01 | 7.462943e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 9968 | 0.9956582 | NA | NA | NA | NA | NA | 3.660935e-01 | 2.691558e-01 | 8.3000e-03 | 1.333000e-01 | 3.070000e-01 | 5.667000e-01 | 9.917000e-01 | ▇▅▃▃▂ |
numeric | AF_reference | 18219 | 0.9920643 | NA | NA | NA | NA | NA | 3.682943e-01 | 2.512998e-01 | 1.9970e-04 | 1.567490e-01 | 3.095050e-01 | 5.509190e-01 | 1.000000e+00 | ▇▇▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.162393e+04 | 9.199425e+03 | 5.0000e+04 | 6.016000e+04 | 6.107400e+04 | 6.146100e+04 | 1.096780e+05 | ▇▁▁▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 785050 | rs2905062 | G | A | -0.0052 | 0.0090 | 0.5600000 | 0.5634142 | NA | 0.626997 | 64740 |
1 | 1003629 | rs4075116 | C | T | 0.0015 | 0.0080 | 0.8499999 | 0.8512686 | 0.7373 | 0.720647 | 58568 |
1 | 1017170 | rs3766193 | C | G | 0.0055 | 0.0075 | 0.4600002 | 0.4633551 | 0.5667 | 0.575479 | 59110 |
1 | 1017197 | rs3766192 | C | T | 0.0071 | 0.0072 | 0.3200000 | 0.3240786 | 0.5763 | 0.511182 | 58855 |
1 | 1018562 | rs9442371 | C | T | 0.0058 | 0.0071 | 0.4100001 | 0.4139848 | 0.5917 | 0.530152 | 59436 |
1 | 1018704 | rs9442372 | A | G | 0.0053 | 0.0072 | 0.4600002 | 0.4616631 | 0.6017 | 0.611022 | 58906 |
1 | 1021415 | rs3737728 | A | G | 0.0076 | 0.0077 | 0.3200000 | 0.3236363 | 0.7167 | 0.812700 | 58766 |
1 | 1021695 | rs9442398 | A | G | 0.0082 | 0.0079 | 0.2999998 | 0.2992818 | 0.7250 | 0.727236 | 59056 |
1 | 1022037 | rs6701114 | C | T | 0.0090 | 0.0079 | 0.2500000 | 0.2546029 | 0.5667 | 0.586661 | 53280 |
1 | 1036959 | rs11579015 | T | C | 0.0024 | 0.0130 | 0.8499999 | 0.8535307 | 0.0500 | 0.156949 | 50183 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51163138 | rs715586 | C | T | -0.0033 | 0.0072 | 0.6499995 | 0.6467130 | 0.1500 | 0.0902556 | 100068 |
22 | 51165664 | rs8137951 | G | A | 0.0048 | 0.0053 | 0.3599996 | 0.3651156 | 0.2750 | 0.4063500 | 106714 |
22 | 51175626 | rs3810648 | A | G | -0.0073 | 0.0150 | 0.6200004 | 0.6264946 | 0.0667 | 0.1084270 | 51179 |
22 | 51178090 | rs2285395 | G | A | 0.0140 | 0.0100 | 0.1700000 | 0.1615133 | 0.0667 | 0.0666933 | 102051 |
22 | 51196164 | rs8136603 | A | T | -0.0047 | 0.0180 | 0.8000000 | 0.7940068 | 0.0750 | 0.1427720 | 50214 |
23 | 35921591 | rs2204667 | C | G | 0.0130 | 0.0087 | 0.1499999 | 0.1351095 | 0.1667 | NA | 61429 |
23 | 51666786 | rs14115 | A | G | -0.0058 | 0.0150 | 0.6899999 | 0.6990030 | 0.0250 | NA | 55140 |
23 | 70163799 | rs1626496 | A | C | -0.0002 | 0.0130 | 0.9900000 | 0.9877253 | 0.0750 | NA | 61441 |
23 | 91415872 | rs6562597 | G | A | -0.0240 | 0.0250 | 0.3300000 | 0.3370552 | 0.0083 | 0.0021192 | 52407 |
23 | 118495837 | rs12882977 | G | A | 0.0043 | 0.0063 | 0.4899999 | 0.4948978 | 0.5167 | 0.2307280 | 61362 |
1 785050 rs2905062 G A . PASS . ES:SE:LP:SS:ID -0.0052:0.009:0.251812:64740:rs2905062
1 1003629 rs4075116 C T . PASS AF=0.7373 ES:SE:LP:AF:SS:ID 0.0015:0.008:0.0705811:0.7373:58568:rs4075116
1 1017170 rs3766193 C G . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.0055:0.0075:0.337242:0.5667:59110:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.5763 ES:SE:LP:AF:SS:ID 0.0071:0.0072:0.49485:0.5763:58855:rs3766192
1 1018562 rs9442371 C T . PASS AF=0.5917 ES:SE:LP:AF:SS:ID 0.0058:0.0071:0.387216:0.5917:59436:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.6017 ES:SE:LP:AF:SS:ID 0.0053:0.0072:0.337242:0.6017:58906:rs9442372
1 1021415 rs3737728 A G . PASS AF=0.7167 ES:SE:LP:AF:SS:ID 0.0076:0.0077:0.49485:0.7167:58766:rs3737728
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID 0.0082:0.0079:0.522879:0.725:59056:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.009:0.0079:0.60206:0.5667:53280:rs6701114
1 1036959 rs11579015 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0024:0.013:0.0705811:0.05:50183:rs11579015
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0053:0.013:0.161151:0.05:50706:rs4970409
1 1060608 rs17160824 G A . PASS AF=0.0583 ES:SE:LP:AF:SS:ID 0.0045:0.013:0.130768:0.0583:50671:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.0546 ES:SE:LP:AF:SS:ID 0.0077:0.013:0.251812:0.0546:50675:rs17160826
1 1061152 rs12748370 T C . PASS . ES:SE:LP:SS:ID 0.0074:0.013:0.236572:50673:rs12748370
1 1077064 rs4970357 C A . PASS AF=0.9237 ES:SE:LP:AF:SS:ID -0.01:0.015:0.29243:0.9237:51038:rs4970357
1 1087683 rs9442380 T C . PASS AF=0.9123 ES:SE:LP:AF:SS:ID -0.0083:0.013:0.267606:0.9123:53234:rs9442380
1 1089262 rs4970358 A G . PASS AF=0.9661 ES:SE:LP:AF:SS:ID -0.018:0.017:0.508638:0.9661:54732:rs4970358
1 1097335 rs9442385 T G . PASS AF=0.9417 ES:SE:LP:AF:SS:ID -0.012:0.013:0.431798:0.9417:56034:rs9442385
1 1099342 rs9660710 A C . PASS AF=0.9407 ES:SE:LP:AF:SS:ID -0.0063:0.013:0.207608:0.9407:58303:rs9660710
1 1100217 rs1891905 C T . PASS AF=0.9583 ES:SE:LP:AF:SS:ID 0.011:0.018:0.275724:0.9583:58482:rs1891905
1 1124663 rs6684820 G A . PASS AF=0.2667 ES:SE:LP:AF:SS:ID -0.001:0.0083:0.0457575:0.2667:58800:rs6684820
1 1125553 rs10907174 A T . PASS AF=0.225 ES:SE:LP:AF:SS:ID 0.0032:0.0087:0.148742:0.225:58697:rs10907174
1 1130727 rs10907175 A C . PASS AF=0.1 ES:SE:LP:AF:SS:ID 0.0004:0.012:0.0132283:0.1:59277:rs10907175
1 1135242 rs9729550 A C . PASS AF=0.275 ES:SE:LP:AF:SS:ID 0.0011:0.008:0.05061:0.275:58324:rs9729550
1 1138913 rs3819001 T C . PASS AF=0.0431 ES:SE:LP:AF:SS:ID -0.017:0.018:0.468521:0.0431:54432:rs3819001
1 1140435 rs1815606 G T . PASS AF=0.3103 ES:SE:LP:AF:SS:ID -0.013:0.0059:1.5376:0.3103:87406:rs1815606
1 1143657 rs3753348 C G . PASS AF=0.0333 ES:SE:LP:AF:SS:ID -0.017:0.02:0.408935:0.0333:55900:rs3753348
1 1152631 rs11721 C A . PASS AF=0.0833 ES:SE:LP:AF:SS:ID 0.011:0.013:0.420216:0.0833:57598:rs11721
1 1158277 rs3813199 G A . PASS AF=0.1 ES:SE:LP:AF:SS:ID 0.0026:0.012:0.0861861:0.1:58770:rs3813199
1 1162435 rs3766186 C A . PASS AF=0.1 ES:SE:LP:AF:SS:ID 0.004:0.012:0.136677:0.1:59298:rs3766186
1 1163804 rs7515488 C T . PASS AF=0.15 ES:SE:LP:AF:SS:ID -0.005:0.01:0.207608:0.15:58725:rs7515488
1 1165310 rs11260562 G A . PASS AF=0.0517 ES:SE:LP:AF:SS:ID -0.015:0.016:0.468521:0.0517:54065:rs11260562
1 1176597 rs6675798 T C . PASS AF=0.1083 ES:SE:LP:AF:SS:ID 0.0023:0.013:0.0705811:0.1083:56002:rs6675798
1 1181751 rs6603783 T C . PASS AF=0.1 ES:SE:LP:AF:SS:ID 0.0025:0.012:0.0757207:0.1:58026:rs6603783
1 1192515 rs7524470 A G . PASS AF=0.0583 ES:SE:LP:AF:SS:ID -0.014:0.019:0.337242:0.0583:54576:rs7524470
1 1194804 rs11804831 T C . PASS AF=0.2083 ES:SE:LP:AF:SS:ID -0.0087:0.0091:0.468521:0.2083:59187:rs11804831
1 1198618 rs12563338 T A . PASS AF=0.0417 ES:SE:LP:AF:SS:ID -0.024:0.019:0.721246:0.0417:58256:rs12563338
1 1206343 rs6667923 C A . PASS AF=0.0583 ES:SE:LP:AF:SS:ID -0.017:0.018:0.468521:0.0583:59416:rs6667923
1 1206619 rs6668223 C A . PASS AF=0.0339 ES:SE:LP:AF:SS:ID -0.012:0.021:0.251812:0.0339:59203:rs6668223
1 1211292 rs6685064 C T . PASS AF=0.1 ES:SE:LP:AF:SS:ID -0.016:0.013:0.69897:0.1:57319:rs6685064
1 1232319 rs604618 G A . PASS AF=0.0917 ES:SE:LP:AF:SS:ID -0.019:0.016:0.638272:0.0917:50414:rs604618
1 1474304 rs1571150 C A . PASS AF=0.3 ES:SE:LP:AF:SS:ID 0.0081:0.007:0.60206:0.3:61254:rs1571150
1 1478153 rs3766180 T C . PASS AF=0.2417 ES:SE:LP:AF:SS:ID 0.0097:0.0072:0.744727:0.2417:60823:rs3766180
1 1478180 rs3766178 T C . PASS AF=0.2667 ES:SE:LP:AF:SS:ID 0.0095:0.0072:0.721246:0.2667:60821:rs3766178
1 1481348 rs3766177 T C . PASS . ES:SE:LP:SS:ID 0.012:0.0077:0.886057:60578:rs3766177
1 1483010 rs7517401 G A . PASS AF=0.2833 ES:SE:LP:AF:SS:ID 0.0076:0.0072:0.537602:0.2833:60803:rs7517401
1 1486834 rs3128342 C A . PASS AF=0.3333 ES:SE:LP:AF:SS:ID 0.0043:0.0074:0.251812:0.3333:55339:rs3128342
1 1489670 rs7531530 C T . PASS AF=0.25 ES:SE:LP:AF:SS:ID 0.012:0.0075:0.920819:0.25:60322:rs7531530
1 1489928 rs7366884 T C . PASS AF=0.25 ES:SE:LP:AF:SS:ID 0.011:0.0076:0.79588:0.25:60855:rs7366884
1 1497201 rs3766169 A C . PASS AF=0.2458 ES:SE:LP:AF:SS:ID 0.0096:0.0072:0.744727:0.2458:61404:rs3766169