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-781/ieu-a-781.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-781/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 11:34:13 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-781/ieu-a-781.vcf.gz ...
Read summary statistics for 119270 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, 53290 SNPs remain.
After merging with regression SNP LD, 53290 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: 1.2236 (0.4191)
Lambda GC: 1.2921
Mean Chi^2: 2.4726
Intercept: 1.1351 (0.0461)
Ratio: 0.0918 (0.0313)
Analysis finished at Wed Feb  5 11:34:23 2020
Total time elapsed: 9.63s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9365,
    "inflation_factor": 1.2204,
    "mean_EFFECT": 0.0002,
    "n": 83197.6,
    "n_snps": 119270,
    "n_clumped_hits": 41,
    "n_p_sig": 1423,
    "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": 25,
    "n_miss_AF_reference": 756,
    "n_est": 80842.0017,
    "ratio_se_n": 0.9857,
    "mean_diff": -7.6506e-06,
    "ratio_diff": 3.7537,
    "sd_y_est1": 1.0679,
    "sd_y_est2": 1.0527,
    "r2_sum1": 0.0866,
    "r2_sum2": 0.0759,
    "r2_sum3": 0.0782,
    "r2_sum4": 0.0784,
    "ldsc_nsnp_merge_refpanel_ld": 53290,
    "ldsc_nsnp_merge_regression_ld": 53290,
    "ldsc_observed_scale_h2_beta": 1.2236,
    "ldsc_observed_scale_h2_se": 0.4191,
    "ldsc_intercept_beta": 1.1351,
    "ldsc_intercept_se": 0.0461,
    "ldsc_lambda_gc": 1.2921,
    "ldsc_mean_chisq": 2.4726,
    "ldsc_ratio": 0.0917
}

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 119270 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 8.655454e+00 5.544551e+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 7.376183e+07 5.532306e+07 4.0483e+04 2.795968e+07 6.162139e+07 1.108185e+08 2.491546e+08 ▇▅▃▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.918000e-04 1.921650e-02 -5.8980e-01 -6.400000e-03 0.000000e+00 6.400000e-03 3.090000e-01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.092330e-02 1.094530e-02 5.1000e-03 5.600000e-03 7.100000e-03 1.140000e-02 2.455000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.644603e-01 3.029176e-01 0.0000e+00 1.939001e-01 4.561997e-01 7.289001e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.489947e-01 3.054321e-01 0.0000e+00 1.721322e-01 4.335827e-01 7.144743e-01 1.000000e+00 ▇▆▅▅▅
numeric AF 25 0.9997904 NA NA NA NA NA 2.830127e-01 2.628648e-01 1.3190e-03 6.332000e-02 1.953000e-01 4.446000e-01 9.986810e-01 ▇▃▂▂▁
numeric AF_reference 756 0.9936614 NA NA NA NA NA 2.864424e-01 2.548989e-01 1.9970e-04 7.967250e-02 2.044730e-01 4.394970e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 7.753923e+04 1.123076e+04 2.0001e+04 7.735350e+04 8.297620e+04 8.311200e+04 8.319760e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0587 0.0257 0.0160901 0.0223688 0.04354 0.0371406 30614.1
1 1140435 rs1815606 G T -0.0148 0.0057 0.0135500 0.0094181 0.31270 0.7120610 75333.0
1 1706136 rs6603811 T C -0.0011 0.0108 0.9809000 0.9188743 0.93668 0.7466050 82531.1
1 1706160 rs7531583 A G -0.0008 0.0062 0.9394001 0.8973321 0.75730 0.5832670 77222.0
1 1708801 rs12044597 A G 0.0061 0.0053 0.2737001 0.2497555 0.51060 0.3602240 77205.1
1 1723031 rs9660180 G A 0.0053 0.0054 0.3595001 0.3263554 0.51320 0.3580270 74405.9
1 1812688 rs6603803 A G 0.0053 0.0053 0.3297000 0.3173105 0.50790 0.3606230 76869.0
1 1823922 rs6688000 A G -0.0081 0.0114 0.5748996 0.4773778 0.94195 0.7651760 82524.6
1 1874326 rs2803328 C G 0.0083 0.0055 0.1650000 0.1312756 0.50000 0.3835860 70716.0
1 2035379 rs10910029 A G -0.0029 0.0053 0.5976006 0.5842621 0.62270 0.5315500 82513.1
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 50661869 rs5771242 T C 0.0071 0.0059 0.2247000 0.2288255 0.76780 0.8512380 82509.0
22 50672097 rs17248301 T C -0.0046 0.0197 0.8232001 0.8153712 0.01583 0.0517173 71802.5
22 50858813 rs7410608 G C 0.0122 0.0053 0.0281501 0.0213416 0.34960 0.4916130 82394.1
22 50873497 rs1134848 C T -0.0135 0.0100 0.1605000 0.1770160 0.13980 0.0529153 51716.0
22 50873694 rs2273259 T C 0.0100 0.0057 0.0882592 0.0793644 0.33910 0.4802320 72178.1
22 50878927 rs12171249 G A -0.0089 0.0062 0.1737001 0.1511493 0.28760 0.2062700 73882.0
22 51062832 rs8142033 G A 0.0016 0.0101 0.8372000 0.8741291 0.08575 0.1773160 82502.5
22 51163138 rs715586 C T -0.0089 0.0075 0.2391002 0.2353591 0.12140 0.0902556 80673.9
22 51165664 rs8137951 G A 0.0053 0.0055 0.3577997 0.3352283 0.28100 0.4063500 82520.0
22 51178090 rs2285395 G A 0.0161 0.0116 0.1647002 0.1651580 0.05145 0.0666933 77204.8

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.04354  ES:SE:LP:AF:SS:ID   -0.0587:0.0257:1.79344:0.04354:30614.1:rs12565286
1   1140435 rs1815606   G   T   .   PASS    AF=0.3127   ES:SE:LP:AF:SS:ID   -0.0148:0.0057:1.86806:0.3127:75333:rs1815606
1   1706136 rs6603811   T   C   .   PASS    AF=0.93668  ES:SE:LP:AF:SS:ID   -0.0011:0.0108:0.00837527:0.93668:82531.1:rs6603811
1   1706160 rs7531583   A   G   .   PASS    AF=0.7573   ES:SE:LP:AF:SS:ID   -0.0008:0.0062:0.0271494:0.7573:77222:rs7531583
1   1708801 rs12044597  A   G   .   PASS    AF=0.5106   ES:SE:LP:AF:SS:ID   0.0061:0.0053:0.562725:0.5106:77205.1:rs12044597
1   1723031 rs9660180   G   A   .   PASS    AF=0.5132   ES:SE:LP:AF:SS:ID   0.0053:0.0054:0.444301:0.5132:74405.9:rs9660180
1   1812688 rs6603803   A   G   .   PASS    AF=0.5079   ES:SE:LP:AF:SS:ID   0.0053:0.0053:0.481881:0.5079:76869:rs6603803
1   1823922 rs6688000   A   G   .   PASS    AF=0.94195  ES:SE:LP:AF:SS:ID   -0.0081:0.0114:0.240408:0.94195:82524.6:rs6688000
1   1874326 rs2803328   C   G   .   PASS    AF=0.5  ES:SE:LP:AF:SS:ID   0.0083:0.0055:0.782516:0.5:70716:rs2803328
1   2035379 rs10910029  A   G   .   PASS    AF=0.6227   ES:SE:LP:AF:SS:ID   -0.0029:0.0053:0.223589:0.6227:82513.1:rs10910029
1   2069172 rs425277    C   T   .   PASS    AF=0.2836   ES:SE:LP:AF:SS:ID   0.0024:0.0057:0.162096:0.2836:82592.1:rs425277
1   2119833 rs2460002   A   G   .   PASS    AF=0.6755   ES:SE:LP:AF:SS:ID   -0.0028:0.0054:0.213249:0.6755:82574:rs2460002
1   2142518 rs380190    A   C   .   PASS    AF=0.2863   ES:SE:LP:AF:SS:ID   -0.0005:0.0061:0.0290955:0.2863:71146.9:rs380190
1   2182342 rs10797416  T   C   .   PASS    AF=0.3654   ES:SE:LP:AF:SS:ID   -0.0033:0.0053:0.238373:0.3654:82586:rs10797416
1   2184855 rs12385717  G   C   .   PASS    AF=0.06464  ES:SE:LP:AF:SS:ID   -0.0134:0.0107:0.65189:0.06464:82485.1:rs12385717
1   2204755 rs7553178   G   A   .   PASS    AF=0.6596   ES:SE:LP:AF:SS:ID   -0.0127:0.0055:1.54577:0.6596:82530:rs7553178
1   2251357 rs12080256  C   A   .   PASS    AF=0.2177   ES:SE:LP:AF:SS:ID   0.0021:0.0073:0.0587371:0.2177:64649:rs12080256
1   2280661 rs2055204   G   A   .   PASS    AF=0.5158   ES:SE:LP:AF:SS:ID   -0.013:0.0051:1.75895:0.5158:82513:rs2055204
1   2390331 rs10910077  G   A   .   PASS    AF=0.2916   ES:SE:LP:AF:SS:ID   -0.0111:0.0056:1.17659:0.2916:79950.9:rs10910077
1   2409383 rs12742193  G   A   .   PASS    AF=0.1253   ES:SE:LP:AF:SS:ID   -0.0032:0.0111:0.114695:0.1253:39179:rs12742193
1   2420913 rs6668720   A   G   .   PASS    AF=0.6359   ES:SE:LP:AF:SS:ID   0.0019:0.0053:0.121651:0.6359:82428:rs6668720
1   2541727 rs11589185  C   T   .   PASS    AF=0.07916  ES:SE:LP:AF:SS:ID   0.0043:0.0094:0.144481:0.07916:71723.8:rs11589185
1   2723345 rs4648360   C   T   .   PASS    AF=0.4288   ES:SE:LP:AF:SS:ID   0.0035:0.0051:0.301986:0.4288:82544.1:rs4648360
1   2725952 rs7538063   C   T   .   PASS    AF=0.1715   ES:SE:LP:AF:SS:ID   -0.0073:0.0071:0.488117:0.1715:78043:rs7538063
1   2727804 rs10909880  C   T   .   PASS    AF=0.4274   ES:SE:LP:AF:SS:ID   -0.0018:0.0063:0.0987052:0.4274:54836:rs10909880
1   2829551 rs1869970   A   G   .   PASS    AF=0.2322   ES:SE:LP:AF:SS:ID   -0.0023:0.0061:0.158703:0.2322:82519:rs1869970
1   2839757 rs4648432   A   C   .   PASS    AF=0.2691   ES:SE:LP:AF:SS:ID   0.0028:0.0057:0.217384:0.2691:82451:rs4648432
1   2842270 rs2045331   G   A   .   PASS    AF=0.2691   ES:SE:LP:AF:SS:ID   0.0027:0.0057:0.21056:0.2691:82501:rs2045331
1   2890345 rs4648445   G   A   .   PASS    AF=0.7111   ES:SE:LP:AF:SS:ID   0.0005:0.0055:0.0307705:0.7111:81320:rs4648445
1   2904056 rs10797373  G   A   .   PASS    AF=0.7058   ES:SE:LP:AF:SS:ID   0.0145:0.0069:1.37304:0.7058:54424:rs10797373
1   2996196 rs7525173   C   G   .   PASS    AF=0.4974   ES:SE:LP:AF:SS:ID   0.0084:0.0056:0.823909:0.4974:69184:rs7525173
1   3089849 rs17390062  T   C   .   PASS    AF=0.1135   ES:SE:LP:AF:SS:ID   -0.0054:0.0088:0.287266:0.1135:82743.4:rs17390062
1   3103826 rs4233024   C   T   .   PASS    AF=0.8522   ES:SE:LP:AF:SS:ID   0.0073:0.0092:0.317674:0.8522:54546:rs4233024
1   3105276 rs2817138   T   G   .   PASS    AF=0.8588   ES:SE:LP:AF:SS:ID   0.0054:0.0077:0.268814:0.8588:82640:rs2817138
1   3117678 rs12095716  G   C   .   PASS    AF=0.2256   ES:SE:LP:AF:SS:ID   0.003:0.0064:0.192871:0.2256:82516:rs12095716
1   3138136 rs2817148   A   G   .   PASS    AF=0.02375  ES:SE:LP:AF:SS:ID   -0.0237:0.0178:0.500313:0.02375:68844.8:rs2817148
1   3144068 rs10158583  G   A   .   PASS    AF=0.08971  ES:SE:LP:AF:SS:ID   -0.0098:0.0101:0.434034:0.08971:72857.4:rs10158583
1   3209631 rs4648376   G   A   .   PASS    AF=0.562    ES:SE:LP:AF:SS:ID   0.0035:0.0052:0.276134:0.562:82713.1:rs4648376
1   3214170 rs7553849   T   C   .   PASS    AF=0.7625   ES:SE:LP:AF:SS:ID   -0.0021:0.0062:0.117589:0.7625:82727:rs7553849
1   3229185 rs12743017  G   A   .   PASS    AF=0.07652  ES:SE:LP:AF:SS:ID   -0.0164:0.0095:1.14521:0.07652:82716.2:rs12743017
1   3264190 rs2483289   A   C   .   PASS    AF=0.7098   ES:SE:LP:AF:SS:ID   0.0026:0.0056:0.216239:0.7098:82715:rs2483289
1   3491107 rs4431782   T   C   .   PASS    AF=0.0752   ES:SE:LP:AF:SS:ID   0.0046:0.009:0.185153:0.0752:77490.8:rs4431782
1   3564818 rs3765690   A   T   .   PASS    AF=0.04222  ES:SE:LP:AF:SS:ID   -0.0027:0.012:0.103143:0.04222:81276.9:rs3765690
1   3654747 rs7515164   C   A   .   PASS    AF=0.06464  ES:SE:LP:AF:SS:ID   0.0035:0.0108:0.208731:0.06464:82681.5:rs7515164
1   3793324 rs6668103   A   G   .   PASS    AF=0.2876   ES:SE:LP:AF:SS:ID   0.0012:0.0068:0.0464819:0.2876:61672.1:rs6668103
1   3812610 rs12757243  G   A   .   PASS    AF=0.009235 ES:SE:LP:AF:SS:ID   0.0253:0.0239:0.422049:0.009235:76286.9:rs12757243
1   4010342 rs12046333  A   G   .   PASS    AF=0.06992  ES:SE:LP:AF:SS:ID   0.0056:0.0113:0.0879374:0.06992:71169:rs12046333
1   4039896 rs11587331  C   T   .   PASS    AF=0.5897   ES:SE:LP:AF:SS:ID   0.0093:0.0052:0.930702:0.5897:82723:rs11587331
1   4080885 rs4378174   C   T   .   PASS    AF=0.1583   ES:SE:LP:AF:SS:ID   0.0078:0.0074:0.521145:0.1583:82668:rs4378174
1   4085543 rs12026862  T   C   .   PASS    AF=0.01451  ES:SE:LP:AF:SS:ID   0.0298:0.0189:0.406936:0.01451:64620.7:rs12026862