Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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 /data/cromwell-executions/qc/fd05c00f-baad-45b8-b30c-9b140bf75877/call-ldsc/inputs/-261044286/ieu-b-4899.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4899/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Mar  3 17:11:33 2022
Reading summary statistics from /data/cromwell-executions/qc/fd05c00f-baad-45b8-b30c-9b140bf75877/call-ldsc/inputs/-261044286/ieu-b-4899.vcf.gz ...
Read summary statistics for 0 SNPs.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
Traceback (most recent call last):
  File "./ldsc/ldsc.py", line 647, in <module>
    sumstats.estimate_h2(args, log)
  File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
    args, log, args.h2)
  File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
    sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
  File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
    raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.

Analysis finished at Thu Mar  3 17:12:25 2022
Total time elapsed: 51.73s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.5873,
    "inflation_factor": 1.0151,
    "mean_EFFECT": 0.0005,
    "n": "-Inf",
    "n_snps": 7002835,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 58038,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 0,
    "ldsc_nsnp_merge_regression_ld": "NA",
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": "NA",
    "ldsc_intercept_se": "NA",
    "ldsc_lambda_gc": "NA",
    "ldsc_mean_chisq": "NA",
    "ldsc_ratio": "NA"
}

Flags

name value
af_correlation TRUE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq NA
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio NA
ldsc_intercept_beta NA
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 72 0.9999897 3 47 0 7000417 0 NA NA 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 NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 7002835 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.618705e+00 5.749463e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.915377e+07 5.617346e+07 2801.0000000 3.284028e+07 6.984962e+07 1.148257e+08 2.492225e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 5.146000e-04 3.133617e-01 -113.1130000 -6.909240e-02 -2.488000e-04 6.916480e-02 1.777100e+02 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.302526e-01 1.672676e-01 0.0557149 6.770930e-02 9.476200e-02 1.673130e-01 1.139880e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.977622e-01 2.890375e-01 0.0000004 2.473147e-01 4.967913e-01 7.484676e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.974535e-01 2.892217e-01 0.0000003 2.467804e-01 4.964866e-01 7.483380e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 1.660951e-01 1.470647e-01 0.0096754 3.513900e-02 1.158300e-01 2.772200e-01 5.000000e-01 ▇▃▂▂▂
numeric AF_reference 58038 0.9917122 NA NA NA NA NA NA NA 2.437210e-01 2.514234e-01 0.0000000 3.953670e-02 1.501600e-01 3.793930e-01 1.000000e+00 ▇▂▂▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 568800 rs375217967 G A -0.5581800 0.594899 0.3485403 0.3481021 0.016076 0.0778754 NA
1 569004 rs9285835 T C -0.6655050 1.670290 0.6904735 0.6903082 0.012532 NA NA
1 569624 rs6594035 T C -1.0623600 2.182780 0.6266774 0.6264706 0.011422 NA NA
1 717587 rs144155419 G A 0.3801720 0.907952 0.6755990 0.6754253 0.016514 0.0045927 NA
1 724849 rs12126395 C A 0.4031590 0.643323 0.5311437 0.5308676 0.030038 NA NA
1 731453 rs186002080 G A 0.7017430 0.653348 0.2832911 0.2827903 0.015304 0.0059904 NA
1 732989 rs369030935 C T 0.4837700 0.348493 0.1656800 0.1650831 0.021775 0.0093850 NA
1 755240 rs181660517 T G 0.0349149 0.926766 0.9699620 0.9699477 0.011824 0.0025958 NA
1 769885 rs200025137 G A 0.1401010 1.204760 0.9074680 0.9074231 0.014613 NA NA
1 770181 rs146076599 A G -0.2377960 1.076090 0.8251950 0.8251068 0.010521 0.0059904 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51198569 rs142671391 G C -0.0125921 0.145472 0.9310541 0.9310210 0.049827 0.1110220 NA
22 51198868 rs185017671 T C -0.0289812 0.303909 0.9240650 0.9240277 0.012517 0.0045927 NA
22 51198998 rs117815989 C A -0.0369882 0.303912 0.9031779 0.9031311 0.012531 0.0045927 NA
22 51208568 rs148425445 G T -0.0304442 0.131254 0.8166691 0.8165778 0.055549 0.1160140 NA
22 51212614 rs142823097 C T 0.2171730 0.277774 0.4346703 0.4343125 0.017949 0.0073882 NA
22 51217556 rs187294336 C T -0.0607304 0.367258 0.8687240 0.8686593 0.010315 0.0023962 NA
22 51220517 rs9616980 C G 0.0827797 0.406427 0.8386860 0.8386062 0.011741 0.0027955 NA
22 51222100 rs114553188 G T -0.0553128 0.133564 0.6789519 0.6787792 0.053551 0.0880591 NA
22 51223637 rs375798137 G A -0.0620132 0.134964 0.6460825 0.6458898 0.053086 0.0788738 NA
22 51232488 rs376461333 A G -0.0956401 0.269597 0.7229196 0.7227753 0.020104 NA NA

bcf preview

1   568800  rs375217967 G   A   .   PASS    AF=0.016076 ES:SE:LP:AF:ID  -0.55818:0.594899:0.457747:0.016076:rs375217967
1   569004  rs9285835   T   C   .   PASS    AF=0.012532 ES:SE:LP:AF:ID  -0.665505:1.67029:0.160853:0.012532:rs9285835
1   569624  rs6594035   T   C   .   PASS    AF=0.011422 ES:SE:LP:AF:ID  -1.06236:2.18278:0.202956:0.011422:rs6594035
1   717587  rs144155419 G   A   .   PASS    AF=0.016514 ES:SE:LP:AF:ID  0.380172:0.907952:0.170311:0.016514:rs144155419
1   724849  rs12126395  C   A   .   PASS    AF=0.030038 ES:SE:LP:AF:ID  0.403159:0.643323:0.274788:0.030038:rs12126395
1   731453  rs186002080 G   A   .   PASS    AF=0.015304 ES:SE:LP:AF:ID  0.701743:0.653348:0.547767:0.015304:rs186002080
1   732989  rs369030935 C   T   .   PASS    AF=0.021775 ES:SE:LP:AF:ID  0.48377:0.348493:0.78073:0.021775:rs369030935
1   755240  rs181660517 T   G   .   PASS    AF=0.011824 ES:SE:LP:AF:ID  0.0349149:0.926766:0.0132453:0.011824:rs181660517
1   769885  rs200025137 G   A   .   PASS    AF=0.014613 ES:SE:LP:AF:ID  0.140101:1.20476:0.0421687:0.014613:rs200025137
1   770181  rs146076599 A   G   .   PASS    AF=0.010521 ES:SE:LP:AF:ID  -0.237796:1.07609:0.0834434:0.010521:rs146076599
1   772927  rs116390263 C   T   .   PASS    AF=0.016549 ES:SE:LP:AF:ID  2.07833:1.19669:1.08077:0.016549:rs116390263
1   773124  rs142049927 T   C   .   PASS    AF=0.013657 ES:SE:LP:AF:ID  1.88318:1.24438:0.883389:0.013657:rs142049927
1   773136  rs146709693 G   T   .   PASS    AF=0.013816 ES:SE:LP:AF:ID  1.59696:1.24248:0.700573:0.013816:rs146709693
1   774760  rs1387547637    C   T   .   PASS    AF=0.012828 ES:SE:LP:AF:ID  -0.413324:0.715673:0.24885:0.012828:rs1387547637
1   775125  rs147281566 C   T   .   PASS    AF=0.012821 ES:SE:LP:AF:ID  0.543384:1.24287:0.179046:0.012821:rs147281566
1   776556  rs151160018 C   T   .   PASS    AF=0.010383 ES:SE:LP:AF:ID  -0.0877346:1.48775:0.020908:0.010383:rs151160018
1   782721  rs185280546 G   A   .   PASS    AF=0.012589 ES:SE:LP:AF:ID  -0.182712:0.791466:0.0875011:0.012589:rs185280546
1   783071  rs142849724 C   T   .   PASS    AF=0.017654 ES:SE:LP:AF:ID  0.560877:0.822125:0.305044:0.017654:rs142849724
1   783193  rs145767270 G   C   .   PASS    AF=0.012227 ES:SE:LP:AF:ID  -0.232549:0.801589:0.112468:0.012227:rs145767270
1   783194  rs138555831 G   T   .   PASS    AF=0.01225  ES:SE:LP:AF:ID  -0.229464:0.802705:0.110644:0.01225:rs138555831
1   787173  rs115093905 G   T   .   PASS    AF=0.030501 ES:SE:LP:AF:ID  -0.071685:0.995408:0.0256647:0.030501:rs115093905
1   793947  rs2519031   A   G   .   PASS    AF=0.020591 ES:SE:LP:AF:ID  0.0279886:0.900312:0.010901:0.020591:rs2519031
1   799879  rs149363311 C   T   .   PASS    AF=0.012097 ES:SE:LP:AF:ID  -0.28462:0.737129:0.155171:0.012097:rs149363311
1   801536  rs79373928  T   G   .   PASS    AF=0.013709 ES:SE:LP:AF:ID  -0.582269:1.09348:0.225766:0.013709:rs79373928
1   807994  rs192742681 C   T   .   PASS    AF=0.016807 ES:SE:LP:AF:ID  0.142732:0.56512:0.0965291:0.016807:rs192742681
1   810777  rs143204076 C   G   .   PASS    AF=0.022274 ES:SE:LP:AF:ID  -0.232832:0.969446:0.0913579:0.022274:rs143204076
1   812670  rs4970340   A   C   .   PASS    AF=0.011804 ES:SE:LP:AF:ID  0.126018:0.638203:0.0738907:0.011804:rs4970340
1   814870  rs149628520 T   G   .   PASS    AF=0.012136 ES:SE:LP:AF:ID  0.0966342:1.35966:0.0253189:0.012136:rs149628520
1   821452  rs138748533 G   A   .   PASS    AF=0.012585 ES:SE:LP:AF:ID  0.499941:1.33924:0.149307:0.012585:rs138748533
1   828539  rs149168804 A   T   .   PASS    AF=0.019671 ES:SE:LP:AF:ID  -0.100971:0.595898:0.0627259:0.019671:rs149168804
1   832359  rs9697294   C   T   .   PASS    AF=0.020904 ES:SE:LP:AF:ID  0.229852:0.286989:0.373094:0.020904:rs9697294
1   834056  rs28482280  A   C   .   PASS    AF=0.02293  ES:SE:LP:AF:ID  0.145945:0.283451:0.216918:0.02293:rs28482280
1   834263  rs143031236 C   T   .   PASS    AF=0.019725 ES:SE:LP:AF:ID  0.327851:0.30122:0.557644:0.019725:rs143031236
1   834956  rs7518581   G   A   .   PASS    AF=0.022651 ES:SE:LP:AF:ID  0.243227:0.2948:0.387513:0.022651:rs7518581
1   836684  rs74460547  G   A   .   PASS    AF=0.021134 ES:SE:LP:AF:ID  -0.30376:0.398344:0.350592:0.021134:rs74460547
1   837214  rs72631888  G   C   .   PASS    AF=0.016147 ES:SE:LP:AF:ID  -0.679943:0.493808:0.771787:0.016147:rs72631888
1   837657  rs149737509 G   C   .   PASS    AF=0.018657 ES:SE:LP:AF:ID  0.0972699:0.383621:0.0969437:0.018657:rs149737509
1   838665  rs28678693  T   C   .   PASS    AF=0.022006 ES:SE:LP:AF:ID  0.121056:0.285337:0.172918:0.022006:rs28678693
1   838732  rs952157075 G   A   .   PASS    AF=0.021909 ES:SE:LP:AF:ID  0.126647:0.285411:0.182158:0.021909:rs952157075
1   838890  rs28437697  A   G   .   PASS    AF=0.022031 ES:SE:LP:AF:ID  0.124107:0.285281:0.178014:0.022031:rs28437697
1   838916  rs28539852  A   T   .   PASS    AF=0.0222   ES:SE:LP:AF:ID  0.124519:0.285421:0.1786:0.0222:rs28539852
1   839461  rs78238606  T   C   .   PASS    AF=0.021873 ES:SE:LP:AF:ID  0.125855:0.285442:0.180811:0.021873:rs78238606
1   839495  rs113341842 G   T   .   PASS    AF=0.021822 ES:SE:LP:AF:ID  0.126026:0.285416:0.181115:0.021822:rs113341842
1   839528  rs115928763 A   G   .   PASS    AF=0.021885 ES:SE:LP:AF:ID  0.127633:0.285213:0.183957:0.021885:rs115928763
1   839529  rs386627407 T   G   .   PASS    AF=0.021873 ES:SE:LP:AF:ID  0.12606:0.285387:0.181194:0.021873:rs386627407
1   846236  rs138796872 G   A   .   PASS    AF=0.011191 ES:SE:LP:AF:ID  -0.0782944:1.41955:0.0195253:0.011191:rs138796872
1   846465  rs60454217  C   T   .   PASS    AF=0.019727 ES:SE:LP:AF:ID  -0.640932:0.485671:0.726941:0.019727:rs60454217
1   846543  rs79396034  G   T   .   PASS    AF=0.017995 ES:SE:LP:AF:ID  -0.381767:0.527877:0.328015:0.017995:rs79396034
1   848223  rs4246504   G   A   .   PASS    AF=0.013842 ES:SE:LP:AF:ID  -0.181271:0.37066:0.20411:0.013842:rs4246504
1   853394  rs142336952 G   A   .   PASS    AF=0.013512 ES:SE:LP:AF:ID  0.195234:0.451742:0.176662:0.013512:rs142336952