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/ukb-d-import/processed/ukb-d-20112_101/ukb-d-20112_101.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/ukb-d-import/processed/ukb-d-20112_101/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 14:59:02 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20112_101/ukb-d-20112_101.vcf.gz ...
Read summary statistics for 10396960 SNPs.
Dropped 8253 SNPs with duplicated rs numbers.
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, 1280170 SNPs remain.
After merging with regression SNP LD, 1280170 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.3567 (0.1575)
Lambda GC: 0.9965
Mean Chi^2: 0.995
Intercept: 1.0129 (0.0055)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 15:00:44 2019
Total time elapsed: 1.0m:42.29s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9434,
    "inflation_factor": 0.9969,
    "mean_EFFECT": 0,
    "n": 2545,
    "n_snps": 10396960,
    "n_clumped_hits": 1,
    "n_p_sig": 3,
    "n_mono": 0,
    "n_ns": 1105765,
    "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": 205037,
    "n_est": 2561.0394,
    "ratio_se_n": 1.0031,
    "mean_diff": 0.0001,
    "ratio_diff": 12.4475,
    "sd_y_est1": 0.4491,
    "sd_y_est2": 0.4506,
    "r2_sum1": 0.0031,
    "r2_sum2": 0.0155,
    "r2_sum3": 0.0154,
    "r2_sum4": 0.0153,
    "ldsc_nsnp_merge_refpanel_ld": 1280170,
    "ldsc_nsnp_merge_regression_ld": 1280170,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0129,
    "ldsc_intercept_se": 0.0055,
    "ldsc_lambda_gc": 0.9965,
    "ldsc_mean_chisq": 0.995,
    "ldsc_ratio": -2.58
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
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 94 0 10389274 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 49377 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30616 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.077151e+00 6.179228e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.878119e+07 5.605545e+07 302.0000000 3.254145e+07 6.972414e+07 1.147169e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 4.490000e-05 3.318050e-02 -0.3763450 -1.421730e-02 1.669000e-04 1.459090e-02 2.981910e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.789970e-02 1.826780e-02 0.0102628 1.397880e-02 1.954440e-02 3.655360e-02 1.037080e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.005475e-01 2.880428e-01 0.0000000 2.514997e-01 5.006555e-01 7.499408e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.004843e-01 2.880808e-01 0.0000000 2.513911e-01 5.005945e-01 7.499145e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.456762e-01 2.627257e-01 0.0064571 3.222930e-02 1.365590e-01 3.932060e-01 9.935430e-01 ▇▂▂▁▁
numeric AF_reference 205037 0.9802791 NA NA NA NA NA 2.454986e-01 2.536310e-01 0.0000000 3.414540e-02 1.531550e-01 3.897760e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.545000e+03 0.000000e+00 2545.0000000 2.545000e+03 2.545000e+03 2.545000e+03 2.545000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0181848 0.0223165 0.4152293 0.4151530 0.1121680 0.1894970 2545
1 693731 rs12238997 A G 0.0067605 0.0205053 0.7416568 0.7416295 0.1190560 0.1417730 2545
1 707522 rs371890604 G C 0.0056200 0.0229094 0.8062310 0.8062115 0.0993605 0.1293930 2545
1 717587 rs144155419 G A -0.0139067 0.0555169 0.8022250 0.8022047 0.0161231 0.0045926 2545
1 730087 rs148120343 T C -0.0164449 0.0287819 0.5678034 0.5677539 0.0575307 0.0127796 2545
1 731718 rs142557973 T C 0.0122456 0.0196381 0.5329715 0.5329144 0.1242440 0.1543530 2545
1 732032 rs61770163 A C 0.0104623 0.0209637 0.6177774 0.6177319 0.1234760 0.1555510 2545
1 734349 rs141242758 T C 0.0126130 0.0196425 0.5208480 0.5207901 0.1236160 0.1525560 2545
1 749963 rs529266287 T TAA -0.0118551 0.0193186 0.5394932 0.5394384 0.8687000 0.7641770 2545
1 751343 rs28544273 T A 0.0139427 0.0190777 0.4649465 0.4648784 0.1257360 0.2426120 2545
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0076881 0.0221723 0.7288128 0.7287847 0.0592288 0.0309934 2545
23 154923374 rs111332691 T A -0.0018926 0.0252240 0.9401960 0.9401898 0.0440079 0.0116556 2545
23 154925045 rs509981 C T 0.0068446 0.0121225 0.5723820 0.5723320 0.2465290 0.3634440 2545
23 154925895 rs538470 C T 0.0068708 0.0124103 0.5798745 0.5798257 0.2425990 0.3634440 2545
23 154927581 rs644138 G A 0.0032512 0.0113491 0.7745403 0.7745152 0.3063260 0.4635760 2545
23 154929412 rs557132 C T 0.0065346 0.0121325 0.5902065 0.5901586 0.2461910 0.3568210 2545
23 154929637 rs35185538 CT C 0.0061385 0.0126467 0.6274469 0.6274043 0.2311270 0.3011920 2545
23 154929952 rs4012982 CAA C 0.0061828 0.0127068 0.6266009 0.6265596 0.2408100 0.3165560 2545
23 154930230 rs781880 A G 0.0059030 0.0121308 0.6265735 0.6265311 0.2462840 0.3618540 2545
23 154930487 rs781879 T A -0.0260335 0.0377596 0.4906005 0.4905377 0.0241242 0.1263580 2545

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112168 ES:SE:LP:AF:SS:ID   0.0181848:0.0223165:0.381712:0.112168:2545:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.119056 ES:SE:LP:AF:SS:ID   0.00676052:0.0205053:0.129797:0.119056:2545:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0993605    ES:SE:LP:AF:SS:ID   0.00562005:0.0229094:0.0935405:0.0993605:2545:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0161231    ES:SE:LP:AF:SS:ID   -0.0139067:0.0555169:0.0957038:0.0161231:2545:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0575307    ES:SE:LP:AF:SS:ID   -0.0164449:0.0287819:0.245802:0.0575307:2545:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.124244 ES:SE:LP:AF:SS:ID   0.0122456:0.0196381:0.273296:0.124244:2545:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.123476 ES:SE:LP:AF:SS:ID   0.0104623:0.0209637:0.209168:0.123476:2545:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.123616 ES:SE:LP:AF:SS:ID   0.012613:0.0196425:0.283289:0.123616:2545:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.8687   ES:SE:LP:AF:SS:ID   -0.0118551:0.0193186:0.268014:0.8687:2545:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.125736 ES:SE:LP:AF:SS:ID   0.0139427:0.0190777:0.332597:0.125736:2545:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.147326 ES:SE:LP:AF:SS:ID   0.0254532:0.018917:0.748167:0.147326:2545:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.125841 ES:SE:LP:AF:SS:ID   0.0136784:0.0190491:0.325334:0.125841:2545:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869394 ES:SE:LP:AF:SS:ID   -0.015662:0.0185926:0.398311:0.869394:2545:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.872965 ES:SE:LP:AF:SS:ID   -0.0125391:0.0188382:0.296095:0.872965:2545:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.130403 ES:SE:LP:AF:SS:ID   0.0155825:0.0186571:0.393961:0.130403:2545:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0337917    ES:SE:LP:AF:SS:ID   0.0230578:0.0353447:0.288848:0.0337917:2545:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869067 ES:SE:LP:AF:SS:ID   -0.0157848:0.0185855:0.402534:0.869067:2545:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.86927  ES:SE:LP:AF:SS:ID   -0.0153671:0.0186264:0.387809:0.86927:2545:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869254 ES:SE:LP:AF:SS:ID   -0.0153242:0.0185921:0.387337:0.869254:2545:rs3131967
1   755435  rs184270342 T   G   .   PASS    AF=0.00648869   ES:SE:LP:AF:SS:ID   0.156466:0.0868489:1.1443:0.00648869:2545:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.868882 ES:SE:LP:AF:SS:ID   -0.0156838:0.0185292:0.400783:0.868882:2545:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.128188 ES:SE:LP:AF:SS:ID   0.0162163:0.0188976:0.407921:0.128188:2545:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868566 ES:SE:LP:AF:SS:ID   -0.0159118:0.0184746:0.409865:0.868566:2545:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867859 ES:SE:LP:AF:SS:ID   -0.0169903:0.018457:0.446867:0.867859:2545:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868693 ES:SE:LP:AF:SS:ID   -0.015659:0.0185063:0.400606:0.868693:2545:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868724 ES:SE:LP:AF:SS:ID   -0.0155821:0.018512:0.397918:0.868724:2545:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868732 ES:SE:LP:AF:SS:ID   -0.0155791:0.0185116:0.397831:0.868732:2545:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.868988 ES:SE:LP:AF:SS:ID   -0.0154811:0.0185494:0.393586:0.868988:2545:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100571 ES:SE:LP:AF:SS:ID   0.0173103:0.0213815:0.378565:0.100571:2545:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00772141   ES:SE:LP:AF:SS:ID   0.0402328:0.0769722:0.220956:0.00772141:2545:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87268  ES:SE:LP:AF:SS:ID   -0.0130344:0.0188143:0.311132:0.87268:2545:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862694 ES:SE:LP:AF:SS:ID   -0.0161717:0.0184821:0.418321:0.862694:2545:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.866953 ES:SE:LP:AF:SS:ID   -0.016374:0.0186585:0.419915:0.866953:2545:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86411  ES:SE:LP:AF:SS:ID   -0.014998:0.0186019:0.376575:0.86411:2545:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.101355 ES:SE:LP:AF:SS:ID   0.015807:0.0224297:0.317818:0.101355:2545:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.86985  ES:SE:LP:AF:SS:ID   -0.0109797:0.0188886:0.25096:0.86985:2545:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.869849 ES:SE:LP:AF:SS:ID   -0.010983:0.0188884:0.251053:0.869849:2545:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.869846 ES:SE:LP:AF:SS:ID   -0.0109833:0.0188886:0.25106:0.869846:2545:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870318 ES:SE:LP:AF:SS:ID   -0.0105537:0.018893:0.239213:0.870318:2545:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12806  ES:SE:LP:AF:SS:ID   0.013919:0.018893:0.335961:0.12806:2545:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.107649 ES:SE:LP:AF:SS:ID   0.0144911:0.0204691:0.319627:0.107649:2545:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.852429 ES:SE:LP:AF:SS:ID   -0.0218429:0.0185087:0.623325:0.852429:2545:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.832701 ES:SE:LP:AF:SS:ID   -0.00505494:0.0182522:0.106881:0.832701:2545:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.75441  ES:SE:LP:AF:SS:ID   -0.00800115:0.0146111:0.23358:0.75441:2545:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.112574 ES:SE:LP:AF:SS:ID   -0.00304316:0.0199195:0.0562137:0.112574:2545:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.131564 ES:SE:LP:AF:SS:ID   0.0167724:0.0186309:0.434061:0.131564:2545:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.130822 ES:SE:LP:AF:SS:ID   0.016728:0.0186289:0.43263:0.130822:2545:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.111982 ES:SE:LP:AF:SS:ID   -0.00418015:0.0200495:0.0783853:0.111982:2545:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00792326   ES:SE:LP:AF:SS:ID   0.00336193:0.0802407:0.0147608:0.00792326:2545:rs146076599
1   770886  rs371458725 G   A   .   PASS    AF=0.111361 ES:SE:LP:AF:SS:ID   -0.00333555:0.0201687:0.0611522:0.111361:2545:rs371458725