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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-90/ieu-a-90.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-90/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 10:58:51 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-90/ieu-a-90.vcf.gz ...
Read summary statistics for 2377582 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, 1133956 SNPs remain.
After merging with regression SNP LD, 1133956 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1718 (0.0078)
Lambda GC: 1.0303
Mean Chi^2: 1.1058
Intercept: 0.7942 (0.007)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 10:59:20 2020
Total time elapsed: 28.97s
{
"af_correlation": 0.9128,
"inflation_factor": 1.0475,
"mean_EFFECT": 0.0005,
"n": 98697,
"n_snps": 2377582,
"n_clumped_hits": 17,
"n_p_sig": 569,
"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": 3593,
"n_miss_AF_reference": 19684,
"n_est": 103452.2481,
"ratio_se_n": 1.0238,
"mean_diff": -0.0003,
"ratio_diff": 134.8593,
"sd_y_est1": 2.7516,
"sd_y_est2": 2.8171,
"r2_sum1": 0.0807,
"r2_sum2": 0.0107,
"r2_sum3": 0.0102,
"r2_sum4": 0.0112,
"ldsc_nsnp_merge_refpanel_ld": 1133956,
"ldsc_nsnp_merge_regression_ld": 1133956,
"ldsc_observed_scale_h2_beta": 0.1718,
"ldsc_observed_scale_h2_se": 0.0078,
"ldsc_intercept_beta": 0.7942,
"ldsc_intercept_se": 0.007,
"ldsc_lambda_gc": 1.0303,
"ldsc_mean_chisq": 1.1058,
"ldsc_ratio": -1.9452
}
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 | 2377582 | 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 | 8.580741e+00 | 5.655387e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.884569e+07 | 5.564803e+07 | 1.15230e+04 | 3.268772e+07 | 7.027656e+07 | 1.143652e+08 | 2.492107e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.777000e-04 | 2.226800e-02 | -3.10000e-01 | -1.100000e-02 | 3.000000e-04 | 1.200000e-02 | 3.000000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.981360e-02 | 1.136600e-02 | 1.20000e-02 | 1.300000e-02 | 1.500000e-02 | 2.100000e-02 | 1.600000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.925582e-01 | 2.920187e-01 | 0.00000e+00 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.925489e-01 | 2.921009e-01 | 0.00000e+00 | 2.420769e-01 | 4.917677e-01 | 7.462943e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 3593 | 0.9984888 | NA | NA | NA | NA | NA | 3.639383e-01 | 2.710376e-01 | 8.00000e-03 | 1.270000e-01 | 3.000000e-01 | 5.670000e-01 | 9.920000e-01 | ▇▅▃▃▂ |
numeric | AF_reference | 19684 | 0.9917210 | NA | NA | NA | NA | NA | 3.667091e-01 | 2.524240e-01 | 1.99700e-04 | 1.545530e-01 | 3.077080e-01 | 5.499200e-01 | 1.000000e+00 | ▇▆▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.056408e+04 | 1.247555e+04 | 4.43076e+04 | 9.061910e+04 | 9.644060e+04 | 9.760210e+04 | 9.869700e+04 | ▁▁▁▁▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 775659 | rs2905035 | A | G | -0.0100 | 0.026 | 0.6999999 | 0.7005224 | 0.875 | 0.745008 | 48417.0 |
1 | 777122 | rs2980319 | A | T | -0.0110 | 0.026 | 0.6899999 | 0.6722391 | 0.875 | 0.747204 | 48417.0 |
1 | 779322 | rs4040617 | A | G | 0.0039 | 0.027 | 0.8800001 | 0.8851495 | 0.125 | 0.226438 | 48367.0 |
1 | 780785 | rs2977612 | T | A | -0.0049 | 0.027 | 0.8499999 | 0.8559897 | 0.866 | 0.669329 | 48417.0 |
1 | 785050 | rs2905062 | G | A | -0.0074 | 0.027 | 0.7800007 | 0.7840277 | 0.856 | 0.626997 | 48417.0 |
1 | 785989 | rs2980300 | T | C | -0.0094 | 0.026 | 0.7199992 | 0.7176970 | 0.873 | 0.626997 | 48343.0 |
1 | 990380 | rs3121561 | C | T | 0.0016 | 0.022 | 0.9400001 | 0.9420231 | 0.267 | 0.343450 | 73457.7 |
1 | 998501 | rs3813193 | G | C | 0.0200 | 0.022 | 0.3700002 | 0.3633021 | 0.150 | 0.206669 | 68941.3 |
1 | 1003629 | rs4075116 | C | T | 0.0140 | 0.016 | 0.4000000 | 0.3815739 | 0.737 | 0.720647 | 93793.8 |
1 | 1005806 | rs3934834 | C | T | 0.0260 | 0.022 | 0.2300001 | 0.2372779 | 0.119 | 0.223442 | 68924.0 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51216564 | rs9616970 | T | C | 0.0088 | 0.030 | 0.7700005 | 0.7692674 | 0.150 | 0.1563500 | 64010.0 |
22 | 51217134 | rs117417021 | A | G | 0.0140 | 0.023 | 0.5400003 | 0.5427262 | 0.442 | 0.2671730 | 52319.0 |
22 | 51222100 | rs114553188 | G | T | -0.0170 | 0.038 | 0.6499995 | 0.6546091 | 0.067 | 0.0880591 | 72911.3 |
22 | 51223637 | rs375798137 | G | A | -0.0140 | 0.038 | 0.7099994 | 0.7125593 | 0.067 | 0.0788738 | 72911.2 |
22 | 51229805 | rs9616985 | T | C | 0.0088 | 0.044 | 0.8400000 | 0.8414806 | 0.092 | 0.0730831 | 49183.0 |
23 | 35921591 | rs2204667 | C | G | 0.0110 | 0.017 | 0.5400003 | 0.5175939 | 0.167 | NA | 95559.8 |
23 | 51666786 | rs14115 | A | G | 0.0091 | 0.032 | 0.7700005 | 0.7761230 | 0.025 | NA | 74299.0 |
23 | 70163799 | rs1626496 | A | C | -0.0520 | 0.026 | 0.0449997 | 0.0455003 | 0.075 | NA | 78957.7 |
23 | 91415872 | rs6562597 | G | A | 0.0600 | 0.062 | 0.3400001 | 0.3331733 | 0.008 | 0.0021192 | 47524.9 |
23 | 118495837 | rs12882977 | G | A | 0.0084 | 0.012 | 0.5000000 | 0.4839273 | 0.509 | 0.2307280 | 98668.7 |
1 775659 rs2905035 A G . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.01:0.026:0.154902:0.875:48417:rs2905035
1 777122 rs2980319 A T . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.011:0.026:0.161151:0.875:48417:rs2980319
1 779322 rs4040617 A G . PASS AF=0.125 ES:SE:LP:AF:SS:ID 0.0039:0.027:0.0555173:0.125:48367:rs4040617
1 780785 rs2977612 T A . PASS AF=0.866 ES:SE:LP:AF:SS:ID -0.0049:0.027:0.0705811:0.866:48417:rs2977612
1 785050 rs2905062 G A . PASS AF=0.856 ES:SE:LP:AF:SS:ID -0.0074:0.027:0.107905:0.856:48417:rs2905062
1 785989 rs2980300 T C . PASS AF=0.873 ES:SE:LP:AF:SS:ID -0.0094:0.026:0.142668:0.873:48343:rs2980300
1 990380 rs3121561 C T . PASS AF=0.267 ES:SE:LP:AF:SS:ID 0.0016:0.022:0.0268721:0.267:73457.7:rs3121561
1 998501 rs3813193 G C . PASS AF=0.15 ES:SE:LP:AF:SS:ID 0.02:0.022:0.431798:0.15:68941.3:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.737 ES:SE:LP:AF:SS:ID 0.014:0.016:0.39794:0.737:93793.8:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.119 ES:SE:LP:AF:SS:ID 0.026:0.022:0.638272:0.119:68924:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.569 ES:SE:LP:AF:SS:ID 0.0021:0.016:0.05061:0.569:94953.8:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.576 ES:SE:LP:AF:SS:ID 0.0026:0.015:0.0655015:0.576:95551.8:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.096 ES:SE:LP:AF:SS:ID 0.021:0.023:0.443698:0.096:68645.4:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.592 ES:SE:LP:AF:SS:ID 0.0035:0.015:0.091515:0.592:95671.7:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.602 ES:SE:LP:AF:SS:ID 0.0033:0.015:0.0861861:0.602:95671.2:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.127 ES:SE:LP:AF:SS:ID 0.017:0.023:0.327902:0.127:68519.4:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.717 ES:SE:LP:AF:SS:ID 0.0064:0.015:0.167491:0.717:95634:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.113 ES:SE:LP:AF:SS:ID 0.016:0.023:0.30103:0.113:68577:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID 0.0085:0.016:0.229148:0.725:95032.9:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.567 ES:SE:LP:AF:SS:ID 0.0065:0.016:0.167491:0.567:86873.5:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.6 ES:SE:LP:AF:SS:ID -0.0079:0.017:0.19382:0.6:71500.9:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.083 ES:SE:LP:AF:SS:ID 0.021:0.021:0.508638:0.083:70498:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.086 ES:SE:LP:AF:SS:ID 0.018:0.022:0.387216:0.086:59409.7:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.658 ES:SE:LP:AF:SS:ID 0.01:0.017:0.251812:0.658:69542:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.056:0.025:1.5376:0.05:74962.6:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.075 ES:SE:LP:AF:SS:ID 0.035:0.022:0.920819:0.075:75032.7:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.067 ES:SE:LP:AF:SS:ID 0.037:0.022:1.03152:0.067:80898.1:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.052 ES:SE:LP:AF:SS:ID 0.053:0.025:1.4437:0.052:74942:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.067 ES:SE:LP:AF:SS:ID 0.034:0.021:0.958607:0.067:80574:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.054:0.025:1.49485:0.05:76952.5:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.398 ES:SE:LP:AF:SS:ID -0.018:0.022:0.376751:0.398:54281.9:rs7548798
1 1060608 rs17160824 G A . PASS AF=0.058 ES:SE:LP:AF:SS:ID 0.055:0.025:1.5376:0.058:77745.2:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.055 ES:SE:LP:AF:SS:ID 0.055:0.025:1.5376:0.055:76924.3:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.056:0.025:1.56864:0.05:76924.2:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.412 ES:SE:LP:AF:SS:ID 0.0023:0.018:0.0457575:0.412:67843.1:rs11807848
1 1062638 rs9442373 C A . PASS AF=0.552 ES:SE:LP:AF:SS:ID 0.0018:0.018:0.0362122:0.552:67234:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.754 ES:SE:LP:AF:SS:ID -0.031:0.024:0.721246:0.754:64592.3:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.083 ES:SE:LP:AF:SS:ID 0.026:0.022:0.619789:0.083:69945:rs2298217
1 1066403 rs10907182 T C . PASS AF=0.675 ES:SE:LP:AF:SS:ID 0.0068:0.019:0.136677:0.675:64387:rs10907182
1 1071118 rs10907183 G C . PASS AF=0.683 ES:SE:LP:AF:SS:ID 0.016:0.021:0.346787:0.683:62053.9:rs10907183
1 1077064 rs4970357 C A . PASS AF=0.924 ES:SE:LP:AF:SS:ID 0.011:0.03:0.136677:0.924:78952.9:rs4970357
1 1087683 rs9442380 T C . PASS AF=0.912 ES:SE:LP:AF:SS:ID -0.0098:0.027:0.142668:0.912:88325.8:rs9442380
1 1089262 rs4970358 A G . PASS AF=0.966 ES:SE:LP:AF:SS:ID -0.028:0.04:0.318759:0.966:69596.8:rs4970358
1 1097335 rs9442385 T G . PASS AF=0.942 ES:SE:LP:AF:SS:ID -0.022:0.026:0.387216:0.942:84363.9:rs9442385
1 1099342 rs9660710 A C . PASS AF=0.941 ES:SE:LP:AF:SS:ID -0.024:0.026:0.443698:0.941:84194:rs9660710
1 1100217 rs1891905 C T . PASS AF=0.958 ES:SE:LP:AF:SS:ID -0.013:0.043:0.119186:0.958:66831.9:rs1891905
1 1106473 rs4970420 G A . PASS AF=0.144 ES:SE:LP:AF:SS:ID -0.02:0.023:0.408935:0.144:62467:rs4970420
1 1119858 rs1320565 C T . PASS AF=0.092 ES:SE:LP:AF:SS:ID -0.039:0.028:0.769551:0.092:63655:rs1320565
1 1120431 rs1320571 G A . PASS AF=0.042 ES:SE:LP:AF:SS:ID -0.033:0.045:0.327902:0.042:59017.6:rs1320571
1 1121014 rs3813204 G A . PASS AF=0.112 ES:SE:LP:AF:SS:ID 0.0086:0.027:0.124939:0.112:59206.7:rs3813204