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-1057/ieu-a-1057.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-1057/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 11:33:50 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1057/ieu-a-1057.vcf.gz ...
Read summary statistics for 420645 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, 409410 SNPs remain.
After merging with regression SNP LD, 409410 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 1.8872 (0.5552)
Lambda GC: 1.0164
Mean Chi^2: 0.9936
Intercept: 0.9633 (0.0082)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Wed Feb  5 11:34:02 2020
Total time elapsed: 11.18s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8526,
    "inflation_factor": 1.0155,
    "mean_EFFECT": -0.0073,
    "n": 899,
    "n_snps": 420645,
    "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": 0,
    "n_miss_AF_reference": 2356,
    "n_est": 886.2579,
    "ratio_se_n": 0.9929,
    "mean_diff": 0.0089,
    "ratio_diff": 2.8883,
    "sd_y_est1": 4.9972,
    "sd_y_est2": 4.9617,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 409410,
    "ldsc_nsnp_merge_regression_ld": 409410,
    "ldsc_observed_scale_h2_beta": 1.8872,
    "ldsc_observed_scale_h2_se": 0.5552,
    "ldsc_intercept_beta": 0.9633,
    "ldsc_intercept_se": 0.0082,
    "ldsc_lambda_gc": 1.0164,
    "ldsc_mean_chisq": 0.9936,
    "ldsc_ratio": 5.7344
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 TRUE
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 4 25 0 420645 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 8.828204e+00 5.797304e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.803069e+07 5.682980e+07 2.75640e+04 3.089996e+07 6.865614e+07 1.147939e+08 2.492107e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -7.250000e-03 3.547384e-01 -2.57702e+00 -2.070140e-01 0.000000e+00 2.037570e-01 2.525730e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.331195e-01 1.536173e-01 2.14000e-01 2.430000e-01 2.730000e-01 3.540000e-01 1.233000e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.981628e-01 2.874987e-01 3.50000e-06 2.487998e-01 4.966998e-01 7.470007e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.982747e-01 2.874994e-01 3.40000e-06 2.489412e-01 4.967128e-01 7.471114e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 4.002435e-01 2.680492e-01 1.00000e-02 1.695430e-01 3.536480e-01 6.068080e-01 9.900000e-01 ▇▆▅▃▃
numeric AF_reference 2356 0.9943991 NA NA NA NA NA 3.874917e-01 2.273489e-01 1.99700e-04 1.972840e-01 3.434500e-01 5.559110e-01 9.862220e-01 ▆▇▆▃▂
numeric N 0 1.0000000 NA NA NA NA NA 8.987715e+02 8.270134e-01 8.90000e+02 8.990000e+02 8.990000e+02 8.990000e+02 8.990000e+02 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1005806 rs3934834 C T 0.195567 0.353 0.5785994 0.5795692 0.100912 0.223442 899
1 1018704 rs9442372 A G -0.297137 0.276 0.2819000 0.2816665 0.817720 0.611022 899
1 1021415 rs3737728 A G -0.410121 0.370 0.2671001 0.2676739 0.918176 0.812700 899
1 1030565 rs6687776 C T 0.268499 0.278 0.3346000 0.3341324 0.181824 0.306709 899
1 1031540 rs9651273 A G -0.307485 0.714 0.6671001 0.6667220 0.980000 0.881989 899
1 1048955 rs4970405 A G 0.493476 0.273 0.0702393 0.0706681 0.163648 0.110623 899
1 1049950 rs12726255 A G 0.341460 0.256 0.1813001 0.1822602 0.212736 0.289736 899
1 1061166 rs11807848 T C 0.400788 0.249 0.1072001 0.1074873 0.223192 0.329673 899
1 1062638 rs9442373 C A -0.317726 0.228 0.1626002 0.1634580 0.556808 0.574281 899
1 1064979 rs2298217 C T 0.258511 0.236 0.2729003 0.2733477 0.402280 0.164736 899
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51105556 rs9616812 C T -0.0682788 0.344 0.8431000 0.8426657 0.1395440 0.3628190 899
22 51109992 rs9628185 T C 0.1248690 0.273 0.6478001 0.6473867 0.1818240 0.4053510 899
22 51123505 rs9616816 G A 0.6465800 0.248 0.0091540 0.0091292 0.3668410 0.3783950 899
22 51146139 rs5770992 A G 0.8729660 0.272 0.0013460 0.0013300 0.1868410 0.1136180 899
22 51147015 rs2040487 A G 0.6792440 0.278 0.0144800 0.0145527 0.6350220 0.4556710 898
22 51150473 rs5770820 G A 0.0411419 0.235 0.8599001 0.8610231 0.4108920 0.2462060 897
22 51151724 rs6010061 C T 0.2984060 0.338 0.3758997 0.3773130 0.8318240 0.6098240 899
22 51163138 rs715586 C T 0.2911760 0.413 0.4801003 0.4807937 0.0709131 0.0902556 898
22 51165664 rs8137951 G A 0.1195590 0.247 0.6268000 0.6283543 0.3922800 0.4063500 899
23 51666786 rs14115 A G -0.1554850 0.526 0.7679996 0.7675364 0.0595439 NA 899

bcf preview

1   1005806 rs3934834   C   T   .   PASS    AF=0.100912 ES:SE:LP:AF:SS:ID   0.195567:0.353:0.237622:0.100912:899:rs3934834
1   1018704 rs9442372   A   G   .   PASS    AF=0.81772  ES:SE:LP:AF:SS:ID   -0.297137:0.276:0.549905:0.81772:899:rs9442372
1   1021415 rs3737728   A   G   .   PASS    AF=0.918176 ES:SE:LP:AF:SS:ID   -0.410121:0.37:0.573326:0.918176:899:rs3737728
1   1030565 rs6687776   C   T   .   PASS    AF=0.181824 ES:SE:LP:AF:SS:ID   0.268499:0.278:0.475474:0.181824:899:rs6687776
1   1031540 rs9651273   A   G   .   PASS    AF=0.98 ES:SE:LP:AF:SS:ID   -0.307485:0.714:0.175809:0.98:899:rs9651273
1   1048955 rs4970405   A   G   .   PASS    AF=0.163648 ES:SE:LP:AF:SS:ID   0.493476:0.273:1.15342:0.163648:899:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.212736 ES:SE:LP:AF:SS:ID   0.34146:0.256:0.741602:0.212736:899:rs12726255
1   1061166 rs11807848  T   C   .   PASS    AF=0.223192 ES:SE:LP:AF:SS:ID   0.400788:0.249:0.969805:0.223192:899:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.556808 ES:SE:LP:AF:SS:ID   -0.317726:0.228:0.788879:0.556808:899:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.40228  ES:SE:LP:AF:SS:ID   0.258511:0.236:0.563996:0.40228:899:rs2298217
1   1087683 rs9442380   T   C   .   PASS    AF=0.600912 ES:SE:LP:AF:SS:ID   0.0932124:0.246:0.150949:0.600912:899:rs9442380
1   1099342 rs9660710   A   C   .   PASS    AF=0.598176 ES:SE:LP:AF:SS:ID   -0.187309:0.24:0.362811:0.598176:899:rs9660710
1   1106473 rs4970420   G   A   .   PASS    AF=0.8  ES:SE:LP:AF:SS:ID   -0.0168571:0.294:0.0204516:0.8:899:rs4970420
1   1119858 rs1320565   C   T   .   PASS    AF=0.216808 ES:SE:LP:AF:SS:ID   -0.482886:0.327:0.856985:0.216808:899:rs1320565
1   1121794 rs11260549  G   A   .   PASS    AF=0.562736 ES:SE:LP:AF:SS:ID   0.306525:0.239:0.698536:0.562736:899:rs11260549
1   1135242 rs9729550   A   C   .   PASS    AF=0.878176 ES:SE:LP:AF:SS:ID   -0.281412:0.318:0.424928:0.878176:899:rs9729550
1   1152631 rs11721 C   A   .   PASS    AF=0.276352 ES:SE:LP:AF:SS:ID   -0.474815:0.289:1.00244:0.276352:899:rs11721
1   1156131 rs2887286   T   C   .   PASS    AF=0.841368 ES:SE:LP:AF:SS:ID   0.221894:0.331:0.297742:0.841368:899:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.168174 ES:SE:LP:AF:SS:ID   -0.339677:0.328:0.522879:0.168174:898:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.168176 ES:SE:LP:AF:SS:ID   -0.34249:0.329:0.526513:0.168176:899:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.188172 ES:SE:LP:AF:SS:ID   -0.400478:0.32:0.678609:0.188172:897:rs7515488
1   1176597 rs6675798   T   C   .   PASS    AF=0.178632 ES:SE:LP:AF:SS:ID   -0.329894:0.32:0.519849:0.178632:899:rs6675798
1   1211292 rs6685064   C   T   .   PASS    AF=0.647264 ES:SE:LP:AF:SS:ID   -0.219938:0.241:0.442854:0.647264:899:rs6685064
1   1310924 rs2765033   T   C   .   PASS    AF=0.866808 ES:SE:LP:AF:SS:ID   -0.510426:0.306:1.02241:0.866808:899:rs2765033
1   1314015 rs2649588   C   T   .   PASS    AF=0.83772  ES:SE:LP:AF:SS:ID   -0.261595:0.289:0.435926:0.83772:899:rs2649588
1   1425700 rs819980    T   C   .   PASS    AF=0.62 ES:SE:LP:AF:SS:ID   -0.0363319:0.234:0.0570499:0.62:898:rs819980
1   1462766 rs9439462   C   T   .   PASS    AF=0.292736 ES:SE:LP:AF:SS:ID   0.273076:0.241:0.589898:0.292736:899:rs9439462
1   1478180 rs3766178   T   C   .   PASS    AF=0.841824 ES:SE:LP:AF:SS:ID   0.36097:0.348:0.524038:0.841824:899:rs3766178
1   1485984 rs2031709   C   A   .   PASS    AF=0.231826 ES:SE:LP:AF:SS:ID   0.246079:0.261:0.460422:0.231826:898:rs2031709
1   1497824 rs2296716   C   T   .   PASS    AF=0.371824 ES:SE:LP:AF:SS:ID   0.183987:0.229:0.373454:0.371824:899:rs2296716
1   1505255 rs6603793   C   T   .   PASS    AF=0.84228  ES:SE:LP:AF:SS:ID   0.446287:0.362:0.66274:0.84228:899:rs6603793
1   1706136 rs6603811   T   C   .   PASS    AF=0.919087 ES:SE:LP:AF:SS:ID   -0.244514:0.398:0.26825:0.919087:898:rs6603811
1   1706160 rs7531583   A   G   .   PASS    AF=0.698176 ES:SE:LP:AF:SS:ID   -0.215918:0.24:0.43427:0.698176:899:rs7531583
1   1745726 rs16825336  G   A   .   PASS    AF=0.276808 ES:SE:LP:AF:SS:ID   -0.430783:0.286:0.878112:0.276808:899:rs16825336
1   1748734 rs2180311   T   C   .   PASS    AF=0.504527 ES:SE:LP:AF:SS:ID   -0.426574:0.24:1.12546:0.504527:899:rs2180311
1   1781220 rs6681938   T   C   .   PASS    AF=0.16772  ES:SE:LP:AF:SS:ID   -0.189951:0.347:0.233885:0.16772:899:rs6681938
1   1793111 rs10907192  A   G   .   PASS    AF=0.909543 ES:SE:LP:AF:SS:ID   -0.195567:0.401:0.20301:0.909543:898:rs10907192
1   1801034 rs4648592   G   A   .   PASS    AF=0.100456 ES:SE:LP:AF:SS:ID   0.00796817:0.376:0.00753485:0.100456:899:rs4648592
1   1810090 rs7525092   C   T   .   PASS    AF=0.17228  ES:SE:LP:AF:SS:ID   0.170586:0.282:0.263683:0.17228:899:rs7525092
1   1844046 rs2474460   C   T   .   PASS    AF=0.324978 ES:SE:LP:AF:SS:ID   -0.534436:0.278:1.26289:0.324978:898:rs2474460
1   1873625 rs12758705  G   A   .   PASS    AF=0.212283 ES:SE:LP:AF:SS:ID   0.120446:0.269:0.183692:0.212283:898:rs12758705
1   1874581 rs2803329   A   G   .   PASS    AF=0.821368 ES:SE:LP:AF:SS:ID   0.211956:0.323:0.291664:0.821368:899:rs2803329
1   1888193 rs3820011   C   A   .   PASS    AF=0.301824 ES:SE:LP:AF:SS:ID   0.111541:0.24:0.192397:0.301824:899:rs3820011
1   1892325 rs2803291   T   C   .   PASS    AF=0.855434 ES:SE:LP:AF:SS:ID   -0.755652:0.289:2.05429:0.855434:898:rs2803291
1   2024064 rs2459994   C   T   .   PASS    AF=0.545895 ES:SE:LP:AF:SS:ID   -0.432432:0.238:1.16191:0.545895:899:rs2459994
1   2026361 rs12755035  G   A   .   PASS    AF=0.170456 ES:SE:LP:AF:SS:ID   0.20945:0.315:0.295935:0.170456:899:rs12755035
1   2026749 rs884080    A   G   .   PASS    AF=0.93772  ES:SE:LP:AF:SS:ID   -0.797057:0.374:1.47821:0.93772:899:rs884080
1   2033256 rs908742    G   A   .   PASS    AF=0.545895 ES:SE:LP:AF:SS:ID   -0.447247:0.237:1.22952:0.545895:899:rs908742
1   2040936 rs4648808   T   C   .   PASS    AF=0.77 ES:SE:LP:AF:SS:ID   -0.129272:0.284:0.187153:0.77:899:rs4648808
1   2043080 rs6603813   T   G   .   PASS    AF=0.200914 ES:SE:LP:AF:SS:ID   0.211071:0.286:0.335922:0.200914:897:rs6603813