Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

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}

LDSC

*********************************************************************
* 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-1160/ieu-a-1160.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-1160/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 11:36:46 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1160/ieu-a-1160.vcf.gz ...
Read summary statistics for 191057 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, 136822 SNPs remain.
After merging with regression SNP LD, 136822 SNPs remain.
WARNING: number of SNPs less than 200k; this is almost always bad.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1165 (0.0278)
Lambda GC: 1.0898
Mean Chi^2: 1.1459
Intercept: 1.0446 (0.0153)
Ratio: 0.3058 (0.1052)
Analysis finished at Wed Feb  5 11:36:56 2020
Total time elapsed: 9.95s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.403,
    "inflation_factor": 1.1474,
    "mean_EFFECT": -0.0002,
    "n": 50225,
    "n_snps": 191057,
    "n_clumped_hits": 6,
    "n_p_sig": 139,
    "n_mono": 0,
    "n_ns": 1,
    "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": 1152,
    "n_est": 50376.095,
    "ratio_se_n": 1.0015,
    "mean_diff": 0.0003,
    "ratio_diff": 2.1661,
    "sd_y_est1": 2.9706,
    "sd_y_est2": 2.975,
    "r2_sum1": 0.0522,
    "r2_sum2": 0.0059,
    "r2_sum3": 0.0059,
    "r2_sum4": 0.006,
    "ldsc_nsnp_merge_refpanel_ld": 136822,
    "ldsc_nsnp_merge_regression_ld": 136822,
    "ldsc_observed_scale_h2_beta": 0.1165,
    "ldsc_observed_scale_h2_se": 0.0278,
    "ldsc_intercept_beta": 1.0446,
    "ldsc_intercept_se": 0.0153,
    "ldsc_lambda_gc": 1.0898,
    "ldsc_mean_chisq": 1.1459,
    "ldsc_ratio": 0.3057
}

Flags

name value
af_correlation TRUE
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

Definitions

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 SNPs
  • n_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:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 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.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • 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.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • 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.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • 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.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

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 > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

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 22 0 191057 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 2 0 5 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.863763e+00 5.775966e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▆▅▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.855534e+07 5.659384e+07 5.0814e+04 3.160562e+07 6.887478e+07 1.160604e+08 2.491747e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.208000e-04 3.559110e-02 -1.8357e+00 -1.770000e-02 -2.000000e-04 1.770000e-02 5.713000e-01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.840830e-02 1.753530e-02 1.8600e-02 1.960000e-02 2.260000e-02 3.030000e-02 1.063700e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.777936e-01 2.938254e-01 0.0000e+00 2.200002e-01 4.700002e-01 7.300002e-01 1.000000e+00 ▇▇▇▆▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.826570e-01 2.939977e-01 0.0000e+00 2.240651e-01 4.776811e-01 7.370669e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.330795e-01 1.425261e-01 1.0000e-04 1.073000e-01 2.207000e-01 3.533000e-01 5.473000e-01 ▇▇▆▆▃
numeric AF_reference 1152 0.9939704 NA NA NA NA NA 3.488452e-01 2.521501e-01 1.9970e-04 1.393770e-01 2.885380e-01 5.265580e-01 9.996010e-01 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 5.022500e+04 0.000000e+00 5.0225e+04 5.022500e+04 5.022500e+04 5.022500e+04 5.022500e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1018704 rs9442372 A G -0.0139 0.0189 0.4600002 0.4620656 0.4424 0.611022 50225
1 1062638 rs9442373 C A 0.0129 0.0188 0.4899999 0.4926058 0.4584 0.574281 50225
1 1094738 rs4970362 A G -0.0136 0.0198 0.4899999 0.4921655 0.3705 0.604034 50225
1 1099342 rs9660710 A C 0.0591 0.0355 0.0899995 0.0959549 0.0725 0.829872 50225
1 1106473 rs4970420 G A -0.0211 0.0240 0.3700002 0.3793109 0.1909 0.550319 50225
1 1110019 rs11260542 A G -0.0340 0.0325 0.2900000 0.2954900 0.0942 0.144569 50225
1 1119858 rs1320565 C T -0.0800 0.0358 0.0200000 0.0254412 0.0773 0.318690 50225
1 1135242 rs9729550 A C -0.0443 0.0218 0.0400000 0.0421425 0.2561 0.551917 50225
1 1138913 rs3819001 T C -0.0723 0.0413 0.0700003 0.0800139 0.0575 0.198482 50225
1 1156131 rs2887286 T C -0.0244 0.0257 0.3400001 0.3424089 0.1615 0.511182 50225
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50960682 rs140524 C T 0.0000 0.0250 0.9900000 1.0000000 0.1734 0.2302320 50225
22 50966914 rs470119 T C 0.0023 0.0192 0.9000000 0.9046482 0.3935 0.5547120 50225
22 50971266 rs140522 T C 0.0159 0.0200 0.4199997 0.4266135 0.3274 0.6190100 50225
22 50988062 rs140519 G T -0.0011 0.0187 0.9500000 0.9530927 0.5023 0.4051520 50225
22 50989326 rs131778 A G -0.0085 0.0188 0.6499995 0.6511770 0.4776 0.4984030 50225
22 51080760 rs134774 A G 0.0013 0.0337 0.9599999 0.9692287 0.0861 0.9536740 50225
22 51123505 rs9616816 G A 0.0157 0.0226 0.4799997 0.4872494 0.2273 0.3783950 50225
22 51151350 rs6009951 C T -0.0181 0.0191 0.3400001 0.3433107 0.4165 0.5559110 50225
22 51151724 rs6010061 C T -0.0148 0.0191 0.4400003 0.4384170 0.4126 0.6098240 50225
22 51178090 rs2285395 G A 0.0862 0.0405 0.0299999 0.0333043 0.0534 0.0666933 50225

bcf preview

1   1018704 rs9442372   A   G   .   PASS    AF=0.4424   ES:SE:LP:AF:SS:ID   -0.0139:0.0189:0.337242:0.4424:50225:rs9442372
1   1062638 rs9442373   C   A   .   PASS    AF=0.4584   ES:SE:LP:AF:SS:ID   0.0129:0.0188:0.309804:0.4584:50225:rs9442373
1   1094738 rs4970362   A   G   .   PASS    AF=0.3705   ES:SE:LP:AF:SS:ID   -0.0136:0.0198:0.309804:0.3705:50225:rs4970362
1   1099342 rs9660710   A   C   .   PASS    AF=0.0725   ES:SE:LP:AF:SS:ID   0.0591:0.0355:1.04576:0.0725:50225:rs9660710
1   1106473 rs4970420   G   A   .   PASS    AF=0.1909   ES:SE:LP:AF:SS:ID   -0.0211:0.024:0.431798:0.1909:50225:rs4970420
1   1110019 rs11260542  A   G   .   PASS    AF=0.0942   ES:SE:LP:AF:SS:ID   -0.034:0.0325:0.537602:0.0942:50225:rs11260542
1   1119858 rs1320565   C   T   .   PASS    AF=0.0773   ES:SE:LP:AF:SS:ID   -0.08:0.0358:1.69897:0.0773:50225:rs1320565
1   1135242 rs9729550   A   C   .   PASS    AF=0.2561   ES:SE:LP:AF:SS:ID   -0.0443:0.0218:1.39794:0.2561:50225:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.0575   ES:SE:LP:AF:SS:ID   -0.0723:0.0413:1.1549:0.0575:50225:rs3819001
1   1156131 rs2887286   T   C   .   PASS    AF=0.1615   ES:SE:LP:AF:SS:ID   -0.0244:0.0257:0.468521:0.1615:50225:rs2887286
1   1162435 rs3766186   C   A   .   PASS    AF=0.0921   ES:SE:LP:AF:SS:ID   -0.0149:0.0327:0.19382:0.0921:50225:rs3766186
1   1211292 rs6685064   C   T   .   PASS    AF=0.0682   ES:SE:LP:AF:SS:ID   -0.1:0.0383:2.04139:0.0682:50225:rs6685064
1   1239953 rs10399878  A   G   .   PASS    AF=0.0476   ES:SE:LP:AF:SS:ID   -0.1391:0.0458:2.62269:0.0476:50225:rs10399878
1   1775175 rs11260622  A   G   .   PASS    AF=0.0402   ES:SE:LP:AF:SS:ID   -0.011:0.0474:0.091515:0.0402:50225:rs11260622
1   1978857 rs3121825   A   G   .   PASS    AF=0.3503   ES:SE:LP:AF:SS:ID   -0.0029:0.0197:0.0555173:0.3503:50225:rs3121825
1   1980639 rs6683042   G   A   .   PASS    AF=0.2348   ES:SE:LP:AF:SS:ID   -0.0219:0.0223:0.49485:0.2348:50225:rs6683042
1   1981118 rs3795277   A   C   .   PASS    AF=0.0839   ES:SE:LP:AF:SS:ID   0.0376:0.0334:0.585027:0.0839:50225:rs3795277
1   1983160 rs28703783  C   A   .   PASS    AF=0.2581   ES:SE:LP:AF:SS:ID   0.0313:0.0216:0.853872:0.2581:50225:rs28703783
1   1983421 rs4648795   T   C   .   PASS    AF=0.405    ES:SE:LP:AF:SS:ID   -0.0129:0.0192:0.30103:0.405:50225:rs4648795
1   1983701 rs28671574  G   A   .   PASS    AF=0.0825   ES:SE:LP:AF:SS:ID   0.043:0.0336:0.69897:0.0825:50225:rs28671574
1   1984227 rs3128319   C   T   .   PASS    AF=0.2385   ES:SE:LP:AF:SS:ID   -0.0251:0.0223:0.585027:0.2385:50225:rs3128319
1   1985170 rs35020387  G   A   .   PASS    AF=0.3816   ES:SE:LP:AF:SS:ID   0.0048:0.0193:0.09691:0.3816:50225:rs35020387
1   1985553 rs13302968  T   C   .   PASS    AF=0.1459   ES:SE:LP:AF:SS:ID   -0.035:0.0268:0.721246:0.1459:50225:rs13302968
1   1992977 rs17777295  G   T   .   PASS    AF=0.2472   ES:SE:LP:AF:SS:ID   -0.0051:0.0217:0.091515:0.2472:50225:rs17777295
1   1993722 rs13303346  C   T   .   PASS    AF=0.1339   ES:SE:LP:AF:SS:ID   -0.0302:0.0278:0.568636:0.1339:50225:rs13303346
1   1997150 rs2803294   G   A   .   PASS    AF=0.1879   ES:SE:LP:AF:SS:ID   -0.0031:0.024:0.05061:0.1879:50225:rs2803294
1   1997187 rs75227206  A   G   .   PASS    AF=0.1855   ES:SE:LP:AF:SS:ID   -0.0208:0.0247:0.39794:0.1855:50225:rs75227206
1   1999345 rs28523801  T   C   .   PASS    AF=0.1387   ES:SE:LP:AF:SS:ID   -0.0373:0.0273:0.769551:0.1387:50225:rs28523801
1   1999680 rs28479788  G   A   .   PASS    AF=0.2332   ES:SE:LP:AF:SS:ID   0.0188:0.0222:0.408935:0.2332:50225:rs28479788
1   1999840 rs13303005  C   T   .   PASS    AF=0.1354   ES:SE:LP:AF:SS:ID   -0.0371:0.0276:0.769551:0.1354:50225:rs13303005
1   2000592 rs2678939   C   A   .   PASS    AF=0.1754   ES:SE:LP:AF:SS:ID   -0.0245:0.0246:0.508638:0.1754:50225:rs2678939
1   2001568 rs13303084  T   C   .   PASS    AF=0.1358   ES:SE:LP:AF:SS:ID   -0.0371:0.0276:0.769551:0.1358:50225:rs13303084
1   2002502 rs13302898  C   T   .   PASS    AF=0.3012   ES:SE:LP:AF:SS:ID   -0.0268:0.0205:0.721246:0.3012:50225:rs13302898
1   2004947 rs2678942   T   C   .   PASS    AF=0.3136   ES:SE:LP:AF:SS:ID   -0.026:0.0203:0.721246:0.3136:50225:rs2678942
1   2005740 rs2459986   T   C   .   PASS    AF=0.1524   ES:SE:LP:AF:SS:ID   0.0114:0.0263:0.180456:0.1524:50225:rs2459986
1   2006108 rs2254669   A   G   .   PASS    AF=0.3133   ES:SE:LP:AF:SS:ID   -0.0249:0.0203:0.677781:0.3133:50225:rs2254669
1   2006127 rs16824697  G   A   .   PASS    AF=0.1706   ES:SE:LP:AF:SS:ID   -0.0158:0.0249:0.283997:0.1706:50225:rs16824697
1   2006728 rs2678943   T   C   .   PASS    AF=0.3814   ES:SE:LP:AF:SS:ID   0.0202:0.0193:0.537602:0.3814:50225:rs2678943
1   2009551 rs72636371  C   T   .   PASS    AF=0.0496   ES:SE:LP:AF:SS:ID   0.0775:0.0423:1.22185:0.0496:50225:rs72636371
1   2011300 rs13303213  C   T   .   PASS    AF=0.1274   ES:SE:LP:AF:SS:ID   -0.0293:0.0284:0.522879:0.1274:50225:rs13303213
1   2014196 rs28436686  G   A   .   PASS    AF=0.2915   ES:SE:LP:AF:SS:ID   0.0039:0.0206:0.0757207:0.2915:50225:rs28436686
1   2024507 rs9729600   T   C   .   PASS    AF=0.0943   ES:SE:LP:AF:SS:ID   0.0195:0.0322:0.267606:0.0943:50225:rs9729600
1   2025607 rs61775405  G   A   .   PASS    AF=0.118    ES:SE:LP:AF:SS:ID   0.0116:0.029:0.167491:0.118:50225:rs61775405
1   2031342 rs2376802   T   C   .   PASS    AF=0.5123   ES:SE:LP:AF:SS:ID   0.0201:0.0188:0.552842:0.5123:50225:rs2376802
1   2037383 rs4648619   T   G   .   PASS    AF=0.2879   ES:SE:LP:AF:SS:ID   -0.0016:0.0207:0.031517:0.2879:50225:rs4648619
1   2038824 rs908743    G   A   .   PASS    AF=0.4922   ES:SE:LP:AF:SS:ID   0.0184:0.0187:0.49485:0.4922:50225:rs908743
1   2040096 rs6666117   T   C   .   PASS    AF=0.114    ES:SE:LP:AF:SS:ID   0.026:0.0294:0.431798:0.114:50225:rs6666117
1   2045380 rs3107144   C   A   .   PASS    AF=0.3966   ES:SE:LP:AF:SS:ID   -0.0041:0.0192:0.0809219:0.3966:50225:rs3107144
1   2047547 rs3107145   G   A   .   PASS    AF=0.399    ES:SE:LP:AF:SS:ID   -0.0051:0.0192:0.107905:0.399:50225:rs3107145
1   2048729 rs3107147   G   A   .   PASS    AF=0.4019   ES:SE:LP:AF:SS:ID   -0.0031:0.0191:0.0604807:0.4019:50225:rs3107147