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-16/ieu-a-16.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-16/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 11:33:48 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-16/ieu-a-16.vcf.gz ...
Read summary statistics for 1378794 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, 868646 SNPs remain.
After merging with regression SNP LD, 868646 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0261 (0.0042)
Lambda GC: 1.0668
Mean Chi^2: 1.0746
Intercept: 1.0009 (0.0091)
Ratio: 0.0124 (0.1214)
Analysis finished at Wed Feb  5 11:34:08 2020
Total time elapsed: 19.82s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9014,
    "inflation_factor": 1.0782,
    "mean_EFFECT": -0,
    "n": 130925,
    "n_snps": 1378794,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 109,
    "n_miss_AF_reference": 9295,
    "n_est": 130720.7071,
    "ratio_se_n": 0.9992,
    "mean_diff": 0,
    "ratio_diff": 17.1646,
    "sd_y_est1": 3.2794,
    "sd_y_est2": 3.2768,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 868646,
    "ldsc_nsnp_merge_regression_ld": 868646,
    "ldsc_observed_scale_h2_beta": 0.0261,
    "ldsc_observed_scale_h2_se": 0.0042,
    "ldsc_intercept_beta": 1.0009,
    "ldsc_intercept_se": 0.0091,
    "ldsc_lambda_gc": 1.0668,
    "ldsc_mean_chisq": 1.0746,
    "ldsc_ratio": 0.0121
}

Flags

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

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 33 0 1378794 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 8.418373e+00 5.584493e+00 1.00000e+00 4.000000e+00 7.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▁
numeric POS 0 1.0000000 NA NA NA NA NA 8.004734e+07 5.497822e+07 3.37990e+04 3.469297e+07 7.181955e+07 1.148427e+08 2.491707e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.150000e-05 1.853850e-02 -1.91700e-01 -1.130000e-02 -1.000000e-04 1.120000e-02 2.000000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.699700e-02 5.779000e-03 1.26000e-02 1.340000e-02 1.480000e-02 1.830000e-02 6.760000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.873074e-01 2.921266e-01 3.60000e-06 2.305998e-01 4.836999e-01 7.403993e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.873103e-01 2.921299e-01 3.80000e-06 2.304910e-01 4.839273e-01 7.405832e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 109 0.9999209 NA NA NA NA NA 3.853598e-01 2.555432e-01 8.00000e-03 1.670000e-01 3.330000e-01 5.760000e-01 9.920000e-01 ▇▇▅▃▂
numeric AF_reference 9295 0.9932586 NA NA NA NA NA 3.859263e-01 2.403072e-01 1.99700e-04 1.837060e-01 3.384580e-01 5.643970e-01 9.970050e-01 ▇▇▆▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.309250e+05 0.000000e+00 1.30925e+05 1.309250e+05 1.309250e+05 1.309250e+05 1.309250e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1018562 rs9442371 C T 0.0134 0.0131 0.3043000 0.3063548 0.592 0.530152 130925
1 1018704 rs9442372 A G 0.0127 0.0131 0.3309002 0.3323129 0.602 0.611022 130925
1 1040026 rs6671356 T C 0.0101 0.0195 0.6028996 0.6044940 0.075 0.282947 130925
1 1048955 rs4970405 A G 0.0117 0.0208 0.5737002 0.5737754 0.052 0.110623 130925
1 1049950 rs12726255 A G 0.0043 0.0189 0.8208001 0.8200247 0.067 0.289736 130925
1 1053452 rs4970409 G A 0.0063 0.0208 0.7614002 0.7619778 0.050 0.136182 130925
1 1097335 rs9442385 T G -0.0257 0.0263 0.3291001 0.3284769 0.942 0.834665 130925
1 1129672 rs11260554 G T -0.0034 0.0201 0.8645000 0.8656753 0.125 0.254393 130925
1 1156131 rs2887286 T C 0.0018 0.0179 0.9218000 0.9199008 0.183 0.511182 130925
1 1158277 rs3813199 G A 0.0157 0.0217 0.4681004 0.4693713 0.100 0.124201 130925
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51101938 rs6010044 A C 0.0147 0.0161 0.3597999 0.3612197 0.245 0.2390180 130925
22 51103692 rs8138460 A G 0.0149 0.0129 0.2471997 0.2480746 0.442 0.2951280 130925
22 51104680 rs9616906 G A 0.0176 0.0128 0.1695001 0.1691314 0.450 0.2689700 130925
22 51105556 rs9616812 C T 0.0093 0.0128 0.4685004 0.4674940 0.483 0.3628190 130925
22 51109992 rs9628185 T C 0.0084 0.0128 0.5117997 0.5116633 0.483 0.4053510 130925
22 51150473 rs5770820 G A -0.0471 0.0155 0.0024160 0.0023759 0.190 0.2462060 130925
22 51163138 rs715586 C T 0.0352 0.0184 0.0557096 0.0557425 0.150 0.0902556 130925
22 51175626 rs3810648 A G 0.0681 0.0280 0.0149599 0.0150098 0.067 0.1084270 130925
23 51666786 rs14115 A G 0.0735 0.0315 0.0194998 0.0196307 0.025 NA 130925
23 118495837 rs12882977 G A 0.0135 0.0128 0.2939998 0.2915683 0.509 0.2307280 130925

bcf preview

1   1018562 rs9442371   C   T   .   PASS    AF=0.592    ES:SE:LP:AF:SS:ID   0.0134:0.0131:0.516698:0.592:130925:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.602    ES:SE:LP:AF:SS:ID   0.0127:0.0131:0.480303:0.602:130925:rs9442372
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0101:0.0195:0.219755:0.075:130925:rs6671356
1   1048955 rs4970405   A   G   .   PASS    AF=0.052    ES:SE:LP:AF:SS:ID   0.0117:0.0208:0.241315:0.052:130925:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.0043:0.0189:0.0857626:0.067:130925:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0063:0.0208:0.118387:0.05:130925:rs4970409
1   1097335 rs9442385   T   G   .   PASS    AF=0.942    ES:SE:LP:AF:SS:ID   -0.0257:0.0263:0.482672:0.942:130925:rs9442385
1   1129672 rs11260554  G   T   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   -0.0034:0.0201:0.063235:0.125:130925:rs11260554
1   1156131 rs2887286   T   C   .   PASS    AF=0.183    ES:SE:LP:AF:SS:ID   0.0018:0.0179:0.0353633:0.183:130925:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0157:0.0217:0.329661:0.1:130925:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0157:0.022:0.322941:0.1:130925:rs3766186
1   1165310 rs11260562  G   A   .   PASS    AF=0.052    ES:SE:LP:AF:SS:ID   -0.0654:0.0295:1.57988:0.052:130925:rs11260562
1   1211292 rs6685064   C   T   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.0539:0.0254:1.4675:0.1:130925:rs6685064
1   1462766 rs9439462   C   T   .   PASS    AF=0.042    ES:SE:LP:AF:SS:ID   -0.0364:0.0357:0.511873:0.042:130925:rs9439462
1   1477244 rs7290  T   C   .   PASS    AF=0.25 ES:SE:LP:AF:SS:ID   0.0067:0.0142:0.195111:0.25:130925:rs7290
1   1478153 rs3766180   T   C   .   PASS    AF=0.242    ES:SE:LP:AF:SS:ID   0.007:0.0142:0.208309:0.242:130925:rs3766180
1   1478180 rs3766178   T   C   .   PASS    AF=0.267    ES:SE:LP:AF:SS:ID   0.0081:0.0142:0.244735:0.267:130925:rs3766178
1   1479333 rs7533  A   G   .   PASS    AF=0.246    ES:SE:LP:AF:SS:ID   0.0069:0.0142:0.203495:0.246:130925:rs7533
1   1497201 rs3766169   A   C   .   PASS    AF=0.246    ES:SE:LP:AF:SS:ID   0.0056:0.0142:0.158015:0.246:130925:rs3766169
1   1499298 rs9439468   A   G   .   PASS    AF=0.31 ES:SE:LP:AF:SS:ID   -0.0119:0.0136:0.417709:0.31:130925:rs9439468
1   1500941 rs6603791   A   G   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   -0.0125:0.0136:0.445996:0.3:130925:rs6603791
1   1505255 rs6603793   C   T   .   PASS    AF=0.3  ES:SE:LP:AF:SS:ID   -0.0116:0.0136:0.405166:0.3:130925:rs6603793
1   1509034 rs7520996   T   C   .   PASS    AF=0.28 ES:SE:LP:AF:SS:ID   -0.0152:0.0141:0.549905:0.28:130925:rs7520996
1   1510801 rs7519837   C   T   .   PASS    AF=0.292    ES:SE:LP:AF:SS:ID   -0.0137:0.0141:0.479385:0.292:130925:rs7519837
1   1706160 rs7531583   A   G   .   PASS    AF=0.783    ES:SE:LP:AF:SS:ID   0.0073:0.0156:0.193413:0.783:130925:rs7531583
1   1708801 rs12044597  A   G   .   PASS    AF=0.517    ES:SE:LP:AF:SS:ID   -0.0005:0.0129:0.0146634:0.517:130925:rs12044597
1   1721479 rs2272908   C   T   .   PASS    AF=0.517    ES:SE:LP:AF:SS:ID   -0.0002:0.0129:0.00607904:0.517:130925:rs2272908
1   1722932 rs3737628   C   T   .   PASS    AF=0.508    ES:SE:LP:AF:SS:ID   -0.0008:0.0132:0.022505:0.508:130925:rs3737628
1   1723031 rs9660180   G   A   .   PASS    AF=0.5  ES:SE:LP:AF:SS:ID   -0.0012:0.0129:0.0334828:0.5:130925:rs9660180
1   1748734 rs2180311   T   C   .   PASS    AF=0.517    ES:SE:LP:AF:SS:ID   0.0007:0.0129:0.0180003:0.517:130925:rs2180311
1   1759054 rs10907187  G   A   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.0074:0.0143:0.219467:0.275:130925:rs10907187
1   1776269 rs4648727   C   A   .   PASS    AF=0.458    ES:SE:LP:AF:SS:ID   -0.0028:0.0129:0.0818123:0.458:130925:rs4648727
1   1778090 rs12126768  T   G   .   PASS    AF=0.186    ES:SE:LP:AF:SS:ID   -0.0151:0.0171:0.423659:0.186:130925:rs12126768
1   1778469 rs6687065   A   G   .   PASS    AF=0.517    ES:SE:LP:AF:SS:ID   0.0005:0.0129:0.0142144:0.517:130925:rs6687065
1   1783201 rs12402876  G   A   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.0077:0.0143:0.227752:0.275:130925:rs12402876
1   1787378 rs12125422  G   A   .   PASS    AF=0.192    ES:SE:LP:AF:SS:ID   -0.0162:0.0171:0.46382:0.192:130925:rs12125422
1   1797947 rs9660106   A   G   .   PASS    AF=0.517    ES:SE:LP:AF:SS:ID   0.0004:0.0129:0.0116194:0.517:130925:rs9660106
1   1801034 rs4648592   G   A   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.008:0.0143:0.237772:0.275:130925:rs4648592
1   1805391 rs10907193  G   A   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.0077:0.0143:0.230106:0.275:130925:rs10907193
1   1810090 rs7525092   C   T   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   0.0077:0.0143:0.229074:0.275:130925:rs7525092
1   1812688 rs6603803   A   G   .   PASS    AF=0.517    ES:SE:LP:AF:SS:ID   0.0008:0.0129:0.0229627:0.517:130925:rs6603803
1   1818129 rs16824526  A   C   .   PASS    AF=0.192    ES:SE:LP:AF:SS:ID   -0.0168:0.0171:0.485187:0.192:130925:rs16824526
1   1888193 rs3820011   C   A   .   PASS    AF=0.292    ES:SE:LP:AF:SS:ID   -0.0042:0.0143:0.113622:0.292:130925:rs3820011
1   2024064 rs2459994   C   T   .   PASS    AF=0.116    ES:SE:LP:AF:SS:ID   0.0302:0.0194:0.922996:0.116:130925:rs2459994
1   2027901 rs7513222   G   A   .   PASS    AF=0.292    ES:SE:LP:AF:SS:ID   0.0156:0.0143:0.559878:0.292:130925:rs7513222
1   2033256 rs908742    G   A   .   PASS    AF=0.339    ES:SE:LP:AF:SS:ID   0.0029:0.0139:0.0771189:0.339:130925:rs908742
1   2039719 rs1878752   G   A   .   PASS    AF=0.911    ES:SE:LP:AF:SS:ID   0.0003:0.0197:0.00572685:0.911:130925:rs1878752
1   2040763 rs4648805   G   A   .   PASS    AF=0.89 ES:SE:LP:AF:SS:ID   0.0003:0.0197:0.00572685:0.89:130925:rs4648805
1   2040898 rs4648807   T   C   .   PASS    AF=0.625    ES:SE:LP:AF:SS:ID   0.0015:0.0133:0.039672:0.625:130925:rs4648807
1   2040936 rs4648808   T   C   .   PASS    AF=0.89 ES:SE:LP:AF:SS:ID   0.0005:0.0196:0.008641:0.89:130925:rs4648808