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-780/ieu-a-780.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-780/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-780/ieu-a-780.vcf.gz ...
Read summary statistics for 119687 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, 53315 SNPs remain.
After merging with regression SNP LD, 53315 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: 1.2999 (0.4634)
Lambda GC: 1.5767
Mean Chi^2: 3.1264
Intercept: 1.2689 (0.0539)
Ratio: 0.1265 (0.0253)
Analysis finished at Wed Feb  5 11:36:55 2020
Total time elapsed: 8.89s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9366,
    "inflation_factor": 1.405,
    "mean_EFFECT": 0.0002,
    "n": 92859.8,
    "n_snps": 119687,
    "n_clumped_hits": 42,
    "n_p_sig": 1613,
    "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": 30,
    "n_miss_AF_reference": 760,
    "n_est": 90739.0116,
    "ratio_se_n": 0.9885,
    "mean_diff": -0,
    "ratio_diff": 16.3961,
    "sd_y_est1": 1.0609,
    "sd_y_est2": 1.0487,
    "r2_sum1": 0.0623,
    "r2_sum2": 0.0553,
    "r2_sum3": 0.0566,
    "r2_sum4": 0.0589,
    "ldsc_nsnp_merge_refpanel_ld": 53315,
    "ldsc_nsnp_merge_regression_ld": 53315,
    "ldsc_observed_scale_h2_beta": 1.2999,
    "ldsc_observed_scale_h2_se": 0.4634,
    "ldsc_intercept_beta": 1.2689,
    "ldsc_intercept_se": 0.0539,
    "ldsc_lambda_gc": 1.5767,
    "ldsc_mean_chisq": 3.1264,
    "ldsc_ratio": 0.1265
}
 

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 5 23 0 119687 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 8.657950e+00 5.546209e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.200000e+01 ▇▆▆▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.372507e+07 5.531398e+07 4.0483e+04 2.794585e+07 6.160932e+07 1.108098e+08 2.491546e+08 ▇▅▃▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.352000e-04 2.095100e-02 -5.3080e-01 -6.400000e-03 2.000000e-04 6.800000e-03 3.134000e-01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.053450e-02 1.153350e-02 4.8000e-03 5.300000e-03 6.700000e-03 1.080000e-02 2.333000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.419682e-01 3.086670e-01 0.0000e+00 1.574001e-01 4.240001e-01 7.121000e-01 9.999000e-01 ▇▅▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.233108e-01 3.113564e-01 0.0000e+00 1.311879e-01 3.936919e-01 6.930371e-01 1.000000e+00 ▇▅▅▅▅
numeric AF 30 0.9997493 NA NA NA NA NA 2.824370e-01 2.629376e-01 1.3190e-03 6.332000e-02 1.939000e-01 4.446000e-01 9.986810e-01 ▇▃▂▂▁
numeric AF_reference 760 0.9936501 NA NA NA NA NA 2.859455e-01 2.549693e-01 1.9970e-04 7.887380e-02 2.038740e-01 4.388980e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 8.646054e+04 1.282965e+04 2.0004e+04 8.610630e+04 9.260690e+04 9.275910e+04 9.285980e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C 0.0472 0.0250 0.0739997 0.0590260 0.04354 0.0371406 33029.6
1 1140435 rs1815606 G T 0.0080 0.0053 0.1627002 0.1311879 0.31270 0.7120610 84436.0
1 1706136 rs6603811 T C 0.0120 0.0101 0.2099999 0.2347866 0.93668 0.7466050 92098.8
1 1706160 rs7531583 A G -0.0169 0.0059 0.0064840 0.0041779 0.75730 0.5832670 86770.1
1 1708801 rs12044597 A G -0.0203 0.0049 0.0000899 0.0000343 0.51060 0.3602240 86751.0
1 1723031 rs9660180 G A -0.0194 0.0050 0.0002388 0.0001045 0.51320 0.3580270 83925.1
1 1812688 rs6603803 A G -0.0184 0.0049 0.0003863 0.0001733 0.50790 0.3606230 86371.0
1 1823922 rs6688000 A G 0.0170 0.0107 0.1315001 0.1121089 0.94195 0.7651760 92103.3
1 1874326 rs2803328 C G -0.0216 0.0052 0.0000730 0.0000327 0.50000 0.3835860 78906.9
1 2035379 rs10910029 A G 0.0020 0.0050 0.6782003 0.6891565 0.62270 0.5315500 92088.0
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50661869 rs5771242 T C 0.0141 0.0056 0.0168000 0.0118071 0.76780 0.8512380 92100.0
22 50672097 rs17248301 T C -0.0004 0.0180 0.7781996 0.9822707 0.01583 0.0517173 80022.2
22 50858813 rs7410608 G C 0.0000 0.0050 0.9967000 1.0000000 0.34960 0.4916130 91949.1
22 50873497 rs1134848 C T 0.0247 0.0099 0.0134899 0.0125975 0.13980 0.0529153 52898.6
22 50873694 rs2273259 T C 0.0009 0.0053 0.8877000 0.8651585 0.33910 0.4802320 80371.0
22 50878927 rs12171249 G A 0.0062 0.0058 0.2880998 0.2850852 0.28760 0.2062700 82984.0
22 51062832 rs8142033 G A 0.0020 0.0096 0.9425999 0.8349687 0.08575 0.1773160 92091.2
22 51163138 rs715586 C T 0.0041 0.0071 0.7161995 0.5636255 0.12140 0.0902556 89822.0
22 51165664 rs8137951 G A 0.0062 0.0052 0.2704002 0.2331406 0.28100 0.4063500 92112.0
22 51178090 rs2285395 G A -0.0081 0.0109 0.5535999 0.4574095 0.05145 0.0666933 85455.4

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.04354  ES:SE:LP:AF:SS:ID   0.0472:0.025:1.13077:0.04354:33029.6:rs12565286
1   1140435 rs1815606   G   T   .   PASS    AF=0.3127   ES:SE:LP:AF:SS:ID   0.008:0.0053:0.788612:0.3127:84436:rs1815606
1   1706136 rs6603811   T   C   .   PASS    AF=0.93668  ES:SE:LP:AF:SS:ID   0.012:0.0101:0.677781:0.93668:92098.8:rs6603811
1   1706160 rs7531583   A   G   .   PASS    AF=0.7573   ES:SE:LP:AF:SS:ID   -0.0169:0.0059:2.18816:0.7573:86770.1:rs7531583
1   1708801 rs12044597  A   G   .   PASS    AF=0.5106   ES:SE:LP:AF:SS:ID   -0.0203:0.0049:4.04648:0.5106:86751:rs12044597
1   1723031 rs9660180   G   A   .   PASS    AF=0.5132   ES:SE:LP:AF:SS:ID   -0.0194:0.005:3.62197:0.5132:83925.1:rs9660180
1   1812688 rs6603803   A   G   .   PASS    AF=0.5079   ES:SE:LP:AF:SS:ID   -0.0184:0.0049:3.41308:0.5079:86371:rs6603803
1   1823922 rs6688000   A   G   .   PASS    AF=0.94195  ES:SE:LP:AF:SS:ID   0.017:0.0107:0.881074:0.94195:92103.3:rs6688000
1   1874326 rs2803328   C   G   .   PASS    AF=0.5  ES:SE:LP:AF:SS:ID   -0.0216:0.0052:4.13668:0.5:78906.9:rs2803328
1   2035379 rs10910029  A   G   .   PASS    AF=0.6227   ES:SE:LP:AF:SS:ID   0.002:0.005:0.168642:0.6227:92088:rs10910029
1   2069172 rs425277    C   T   .   PASS    AF=0.2836   ES:SE:LP:AF:SS:ID   0.0038:0.0054:0.269864:0.2836:92169:rs425277
1   2119833 rs2460002   A   G   .   PASS    AF=0.6755   ES:SE:LP:AF:SS:ID   -0.0045:0.0051:0.391367:0.6755:92145.9:rs2460002
1   2142518 rs380190    A   C   .   PASS    AF=0.2863   ES:SE:LP:AF:SS:ID   0.0051:0.0057:0.333576:0.2863:78909.9:rs380190
1   2182342 rs10797416  T   C   .   PASS    AF=0.3654   ES:SE:LP:AF:SS:ID   0.004:0.005:0.30557:0.3654:92162:rs10797416
1   2184855 rs12385717  G   C   .   PASS    AF=0.06464  ES:SE:LP:AF:SS:ID   0.0129:0.0102:0.581367:0.06464:92030.1:rs12385717
1   2204755 rs7553178   G   A   .   PASS    AF=0.6596   ES:SE:LP:AF:SS:ID   -0.0071:0.0052:0.700711:0.6596:92105.1:rs7553178
1   2251357 rs12080256  C   A   .   PASS    AF=0.2177   ES:SE:LP:AF:SS:ID   -0.0207:0.0069:2.32486:0.2177:72384.9:rs12080256
1   2280661 rs2055204   G   A   .   PASS    AF=0.5158   ES:SE:LP:AF:SS:ID   0.011:0.0049:1.46559:0.5158:92054:rs2055204
1   2390331 rs10910077  G   A   .   PASS    AF=0.2916   ES:SE:LP:AF:SS:ID   0.0001:0.0053:0.00489154:0.2916:89083:rs10910077
1   2409383 rs12742193  G   A   .   PASS    AF=0.1253   ES:SE:LP:AF:SS:ID   -0.0063:0.0103:0.25516:0.1253:46460.7:rs12742193
1   2420913 rs6668720   A   G   .   PASS    AF=0.6359   ES:SE:LP:AF:SS:ID   0.0028:0.005:0.214741:0.6359:91968:rs6668720
1   2541727 rs11589185  C   T   .   PASS    AF=0.07916  ES:SE:LP:AF:SS:ID   0.0196:0.0089:1.44382:0.07916:79918.3:rs11589185
1   2723345 rs4648360   C   T   .   PASS    AF=0.4288   ES:SE:LP:AF:SS:ID   0.0091:0.0049:1.11031:0.4288:92118.9:rs4648360
1   2725952 rs7538063   C   T   .   PASS    AF=0.1715   ES:SE:LP:AF:SS:ID   -0.0164:0.0066:1.77832:0.1715:87102:rs7538063
1   2727804 rs10909880  C   T   .   PASS    AF=0.4274   ES:SE:LP:AF:SS:ID   0.0094:0.006:0.837436:0.4274:62155.9:rs10909880
1   2829551 rs1869970   A   G   .   PASS    AF=0.2322   ES:SE:LP:AF:SS:ID   -0.0043:0.0057:0.315514:0.2322:92081.9:rs1869970
1   2839757 rs4648432   A   C   .   PASS    AF=0.2691   ES:SE:LP:AF:SS:ID   0.0075:0.0054:0.67469:0.2691:92023:rs4648432
1   2842270 rs2045331   G   A   .   PASS    AF=0.2691   ES:SE:LP:AF:SS:ID   0.0075:0.0054:0.681937:0.2691:92078.9:rs2045331
1   2890345 rs4648445   G   A   .   PASS    AF=0.7111   ES:SE:LP:AF:SS:ID   0.0077:0.0051:0.84649:0.7111:90893:rs4648445
1   2904056 rs10797373  G   A   .   PASS    AF=0.7058   ES:SE:LP:AF:SS:ID   0.0144:0.0064:1.46623:0.7058:63106:rs10797373
1   2996196 rs7525173   C   G   .   PASS    AF=0.4974   ES:SE:LP:AF:SS:ID   -0.0067:0.0052:0.612966:0.4974:77372.9:rs7525173
1   3089849 rs17390062  T   C   .   PASS    AF=0.1135   ES:SE:LP:AF:SS:ID   0.0065:0.0083:0.22614:0.1135:92332.3:rs17390062
1   3103826 rs4233024   C   T   .   PASS    AF=0.8522   ES:SE:LP:AF:SS:ID   0.0032:0.0085:0.215454:0.8522:63236.1:rs4233024
1   3105276 rs2817138   T   G   .   PASS    AF=0.8588   ES:SE:LP:AF:SS:ID   0.002:0.0072:0.148925:0.8588:92228.9:rs2817138
1   3117678 rs12095716  G   C   .   PASS    AF=0.2256   ES:SE:LP:AF:SS:ID   -0.0041:0.006:0.282662:0.2256:92087:rs12095716
1   3138136 rs2817148   A   G   .   PASS    AF=0.02375  ES:SE:LP:AF:SS:ID   -0.0291:0.016:1.32331:0.02375:77046.1:rs2817148
1   3144068 rs10158583  G   A   .   PASS    AF=0.08971  ES:SE:LP:AF:SS:ID   0.0046:0.0095:0.291749:0.08971:79866.5:rs10158583
1   3209631 rs4648376   G   A   .   PASS    AF=0.562    ES:SE:LP:AF:SS:ID   -0.0074:0.0049:0.791559:0.562:92298:rs4648376
1   3214170 rs7553849   T   C   .   PASS    AF=0.7625   ES:SE:LP:AF:SS:ID   0.0022:0.0058:0.128427:0.7625:92307:rs7553849
1   3229185 rs12743017  G   A   .   PASS    AF=0.07652  ES:SE:LP:AF:SS:ID   0.0111:0.0089:0.590913:0.07652:92303.3:rs12743017
1   3264190 rs2483289   A   C   .   PASS    AF=0.7098   ES:SE:LP:AF:SS:ID   -0.0018:0.0052:0.159455:0.7098:92298:rs2483289
1   3491107 rs4431782   T   C   .   PASS    AF=0.0752   ES:SE:LP:AF:SS:ID   0.005:0.0086:0.323489:0.0752:85727.2:rs4431782
1   3564818 rs3765690   A   T   .   PASS    AF=0.04222  ES:SE:LP:AF:SS:ID   -0.0004:0.0114:0.0571985:0.04222:88619:rs3765690
1   3654747 rs7515164   C   A   .   PASS    AF=0.06464  ES:SE:LP:AF:SS:ID   0.0101:0.0101:0.459045:0.06464:92265.1:rs7515164
1   3793324 rs6668103   A   G   .   PASS    AF=0.2876   ES:SE:LP:AF:SS:ID   0.0043:0.0063:0.304343:0.2876:69498:rs6668103
1   3812610 rs12757243  G   A   .   PASS    AF=0.009235 ES:SE:LP:AF:SS:ID   0.0053:0.023:0.00353211:0.009235:84514.8:rs12757243
1   4010342 rs12046333  A   G   .   PASS    AF=0.06992  ES:SE:LP:AF:SS:ID   0.0222:0.0104:1.36241:0.06992:79406.3:rs12046333
1   4039896 rs11587331  C   T   .   PASS    AF=0.5897   ES:SE:LP:AF:SS:ID   0.0034:0.0049:0.269622:0.5897:92307:rs11587331
1   4080885 rs4378174   C   T   .   PASS    AF=0.1583   ES:SE:LP:AF:SS:ID   -0.0038:0.007:0.264321:0.1583:92253.3:rs4378174
1   4085543 rs12026862  T   C   .   PASS    AF=0.01451  ES:SE:LP:AF:SS:ID   0.0151:0.0166:0.203564:0.01451:72381.7:rs12026862