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/3cf46127-6bca-41ab-8bf3-cc41d6ad52ea/call-ldsc/inputs/-261021475/ieu-b-5114.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5114/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 12 14:45:54 2023
Reading summary statistics from /data/cromwell-executions/qc/3cf46127-6bca-41ab-8bf3-cc41d6ad52ea/call-ldsc/inputs/-261021475/ieu-b-5114.vcf.gz ...
Read summary statistics for 8171001 SNPs.
Dropped 44757 SNPs with duplicated rs numbers.
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.
After merging with reference panel LD, 1185527 SNPs remain.
After merging with regression SNP LD, 1185527 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 3.81 (0.1396)
Lambda GC: 1.6793
Mean Chi^2: 1.9246
Intercept: 1.0752 (0.0121)
Ratio: 0.0813 (0.0131)
Analysis finished at Thu Oct 12 14:47:47 2023
Total time elapsed: 1.0m:53.0s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8967,
    "inflation_factor": 1.5843,
    "mean_EFFECT": 0.0008,
    "n": 11260,
    "n_snps": 8171059,
    "n_clumped_hits": 123,
    "n_p_sig": 18280,
    "n_mono": 963,
    "n_ns": 492374,
    "n_mac": 805,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 191074,
    "n_est": 11112.3009,
    "ratio_se_n": 0.9934,
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": 0.7286,
    "sd_y_est2": 0.7238,
    "r2_sum1": 0.2499,
    "r2_sum2": 0.4709,
    "r2_sum3": 0.4771,
    "r2_sum4": 0.4689,
    "ldsc_nsnp_merge_refpanel_ld": 1185527,
    "ldsc_nsnp_merge_regression_ld": 1185527,
    "ldsc_observed_scale_h2_beta": 3.81,
    "ldsc_observed_scale_h2_se": 0.1396,
    "ldsc_intercept_beta": 1.0752,
    "ldsc_intercept_se": 0.0121,
    "ldsc_lambda_gc": 1.6793,
    "ldsc_mean_chisq": 1.9246,
    "ldsc_ratio": 0.0813
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique TRUE
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 5 0.9999994 3 58 0 8170632 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 44 0 27997 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 37 0 5827 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.714998e+00 5.862673e+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 7.938528e+07 5.623654e+07 8.28000e+02 3.270995e+07 7.028263e+07 1.153246e+08 2.492223e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 8.199000e-04 2.565460e-02 -2.84427e-01 -1.262000e-02 4.701000e-04 1.399950e-02 2.640440e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.859580e-02 1.060830e-02 8.09730e-03 1.060020e-02 1.398330e-02 2.333550e-02 1.073040e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.256732e-01 3.066380e-01 0.00000e+00 1.415999e-01 3.958995e-01 6.901000e-01 1.000000e+00 ▇▅▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.256819e-01 3.066409e-01 0.00000e+00 1.415785e-01 3.958660e-01 6.901048e-01 1.000000e+00 ▇▅▅▅▅
numeric AF 0 1.0000000 NA NA NA NA NA 2.712151e-01 2.670754e-01 0.00000e+00 5.070000e-02 1.690000e-01 4.294000e-01 1.000000e+00 ▇▃▂▁▁
numeric AF_reference 191074 0.9766158 NA NA NA NA NA 2.635554e-01 2.522526e-01 1.99700e-04 5.650960e-02 1.771170e-01 4.111420e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.126000e+04 0.000000e+00 1.12600e+04 1.126000e+04 1.126000e+04 1.126000e+04 1.126000e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 1026707 rs4074137 C A 0.0014911 0.0115992 0.8975999 0.8977115 0.6014 0.6269970 11260
1 1026801 rs4562563 T A -0.0007997 0.0116552 0.9439000 0.9452989 0.5944 0.6265970 11260
1 1027070 rs11260590 G A -0.0048880 0.0175924 0.7808004 0.7811283 0.1183 0.1894970 11260
1 1027845 rs74048006 T G 0.0007203 0.0137203 0.9579001 0.9581336 0.1680 0.3089060 11260
1 1027846 rs76994018 T C 0.0006502 0.0137203 0.9620001 0.9622021 0.1680 0.3089060 11260
1 1028259 rs12077244 C T -0.0037928 0.0173874 0.8273000 0.8273240 0.1203 0.1962860 11260
1 1029805 rs6689308 A G 0.0004801 0.0134603 0.9713000 0.9715463 0.1670 0.3156950 11260
1 1030374 rs12731175 G A 0.0163428 0.0250225 0.5136000 0.5136762 0.0457 0.0740815 11260
1 1030565 rs6687776 C T 0.0006202 0.0133873 0.9628000 0.9630497 0.1660 0.3067090 11260
1 1030633 rs6678318 G A 0.0006502 0.0133873 0.9614000 0.9612626 0.1660 0.3065100 11260
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154918383 rs641588 G T -0.0305004 0.0095049 0.0013120 0.0013323 0.13690 0.3565560 11260
23 154923374 rs111332691 T A -0.0601004 0.0333001 0.0711902 0.0711042 0.02688 0.0116556 11260
23 154925045 rs509981 C T -0.0324003 0.0095049 0.0006203 0.0006525 0.13690 0.3634440 11260
23 154925895 rs538470 C T -0.0311997 0.0098020 0.0014110 0.0014576 0.14590 0.3634440 11260
23 154927185 rs185685661 T C -0.0439020 0.0156965 0.0051839 0.0051591 0.08060 0.1796030 11260
23 154927199 rs645904 C T -0.0312998 0.0095049 0.0009285 0.0009912 0.13840 0.3674170 11260
23 154927581 rs644138 G A -0.0271996 0.0091978 0.0031180 0.0031045 0.18570 0.4635760 11260
23 154929412 rs557132 C T -0.0304004 0.0095049 0.0013260 0.0013819 0.13690 0.3568210 11260
23 154929952 rs4012982 CAA C -0.0305971 0.0096039 0.0014880 0.0014431 0.10640 0.3165560 11260
23 154930230 rs781880 A G -0.0312952 0.0095049 0.0010430 0.0009929 0.13690 0.3618540 11260

bcf preview

1   1026707 rs4074137   C   A   .   PASS    AF=0.6014   ES:SE:LP:AF:SS:ID   0.00149111:0.0115992:0.0469172:0.6014:11260:rs4074137
1   1026801 rs566418987 T   A   .   PASS    AF=0.5944   ES:SE:LP:AF:SS:ID   -0.00079968:0.0116552:0.025074:0.5944:11260:rs566418987
1   1027070 rs1478830411    G   A   .   PASS    AF=0.1183   ES:SE:LP:AF:SS:ID   -0.00488803:0.0175924:0.10746:0.1183:11260:rs1478830411
1   1027845 rs71576594  T   G   .   PASS    AF=0.168    ES:SE:LP:AF:SS:ID   0.000720259:0.0137203:0.0186798:0.168:11260:rs71576594
1   1027846 rs71576594  T   C   .   PASS    AF=0.168    ES:SE:LP:AF:SS:ID   0.000650211:0.0137203:0.0168249:0.168:11260:rs71576594
1   1028259 rs12077244  C   T   .   PASS    AF=0.1203   ES:SE:LP:AF:SS:ID   -0.0037928:0.0173874:0.082337:0.1203:11260:rs12077244
1   1029805 rs891281851 A   G   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   0.000480115:0.0134603:0.0126466:0.167:11260:rs891281851
1   1030374 rs12731175  G   A   .   PASS    AF=0.0457   ES:SE:LP:AF:SS:ID   0.0163428:0.0250225:0.289375:0.0457:11260:rs12731175
1   1030565 rs6687776   C   T   .   PASS    AF=0.166    ES:SE:LP:AF:SS:ID   0.000620192:0.0133873:0.0164639:0.166:11260:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.166    ES:SE:LP:AF:SS:ID   0.000650211:0.0133873:0.0170959:0.166:11260:rs6678318
1   1031060 rs7545952   A   G   .   PASS    AF=0.0467   ES:SE:LP:AF:SS:ID   0.0159465:0.0245295:0.287771:0.0467:11260:rs7545952
1   1031540 rs776599533 A   G   .   PASS    AF=0.7276   ES:SE:LP:AF:SS:ID   -0.00637961:0.0124663:0.217456:0.7276:11260:rs776599533
1   1031973 rs9651270   C   T   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   -9.9995e-05:0.0134073:0.00318198:0.167:11260:rs9651270
1   1031977 rs9651271   A   T   .   PASS    AF=0.1203   ES:SE:LP:AF:SS:ID   -0.0131136:0.0175374:0.342657:0.1203:11260:rs9651271
1   1032184 rs9651272   A   G   .   PASS    AF=0.7276   ES:SE:LP:AF:SS:ID   -0.00697561:0.0124463:0.238749:0.7276:11260:rs9651272
1   1032388 rs71628929  G   C   .   PASS    AF=0.0457   ES:SE:LP:AF:SS:ID   0.0153066:0.0250225:0.266963:0.0457:11260:rs71628929
1   1032954 rs6699750   A   G   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   5.00013e-05:0.0134603:0.00130484:0.167:11260:rs6699750
1   1033596 rs6604964   T   C   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   0.00249311:0.0136603:0.0679831:0.167:11260:rs6604964
1   1033626 rs6604965   C   G   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   -0.00039992:0.0135583:0.00908425:0.167:11260:rs6604965
1   1033670 rs1370950991    T   C   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   -0.00149888:0.0135003:0.039672:0.167:11260:rs1370950991
1   1033680 rs1370950991    T   A   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   0.000570162:0.0134463:0.0150678:0.167:11260:rs1370950991
1   1033994 rs6698368   C   T   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   -0.0009995:0.0134463:0.0252121:0.167:11260:rs6698368
1   1033999 rs747150202 C   T   .   PASS    AF=0.5567   ES:SE:LP:AF:SS:ID   -0.00409162:0.0108032:0.151626:0.5567:11260:rs747150202
1   1034200 rs77977351  T   C   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   -0.00119928:0.0134073:0.0317973:0.167:11260:rs77977351
1   1034243 rs1471240371    C   T   .   PASS    AF=0.1372   ES:SE:LP:AF:SS:ID   -0.00975229:0.0149083:0.291239:0.1372:11260:rs1471240371
1   1036817 rs61766341  T   C   .   PASS    AF=0.2614   ES:SE:LP:AF:SS:ID   0.00490199:0.0123693:0.160145:0.2614:11260:rs61766341
1   1036860 rs11579922  A   C   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.00955421:0.0149363:0.281415:0.1342:11260:rs11579922
1   1036876 rs1553125882    T   A   .   PASS    AF=0.1322   ES:SE:LP:AF:SS:ID   -0.00518653:0.0149213:0.137272:0.1322:11260:rs1553125882
1   1036877 rs1553125882    T   A   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.00767051:0.0150693:0.214385:0.1342:11260:rs1553125882
1   1036959 rs1162868282    T   C   .   PASS    AF=0.1054   ES:SE:LP:AF:SS:ID   -0.0219572:0.0157753:0.786748:0.1054:11260:rs1162868282
1   1037047 rs1461003396    C   T   .   PASS    AF=0.2624   ES:SE:LP:AF:SS:ID   0.00528394:0.0125233:0.17192:0.2624:11260:rs1461003396
1   1037303 rs11260592  T   C   .   PASS    AF=0.1332   ES:SE:LP:AF:SS:ID   -0.0125213:0.0141853:0.424235:0.1332:11260:rs11260592
1   1037313 rs11260593  A   G   .   PASS    AF=0.1332   ES:SE:LP:AF:SS:ID   -0.0115332:0.0141853:0.380907:0.1332:11260:rs11260593
1   1037367 rs11260594  G   A   .   PASS    AF=0.1272   ES:SE:LP:AF:SS:ID   -0.0116321:0.0144463:0.377372:0.1272:11260:rs11260594
1   1038088 rs66622470  G   C   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0112366:0.0141503:0.369267:0.1342:11260:rs66622470
1   1038997 rs199678666 ACTC    A   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.00729958:0.0146003:0.21056:0.1342:11260:rs199678666
1   1039268 rs9329410   T   C   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0115332:0.0141323:0.38258:0.1342:11260:rs9329410
1   1039373 rs34796184  CT  C   .   PASS    AF=0.8648   ES:SE:LP:AF:SS:ID   0.0124998:0.0144003:0.413188:0.8648:11260:rs34796184
1   1039817 rs1205065516    A   G   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0115332:0.0141323:0.38258:0.1342:11260:rs1205065516
1   1040026 rs6671356   T   C   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0116321:0.0141323:0.385525:0.1342:11260:rs6671356
1   1040472 rs6664124   C   T   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0115332:0.0141323:0.38279:0.1342:11260:rs6664124
1   1040794 rs6687681   G   A   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0117309:0.0141673:0.389766:0.1342:11260:rs6687681
1   1040824 rs6656379   T   C   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0113355:0.0141103:0.374585:0.1342:11260:rs6656379
1   1040940 rs6702072   A   C   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.0117309:0.0141503:0.392009:0.1342:11260:rs6702072
1   1040985 rs6697379   C   G   .   PASS    AF=0.1342   ES:SE:LP:AF:SS:ID   -0.00905884:0.0140963:0.285419:0.1342:11260:rs6697379
1   1041700 rs6604968   A   G   .   PASS    AF=0.1352   ES:SE:LP:AF:SS:ID   -0.0106432:0.0140933:0.34592:0.1352:11260:rs6604968
1   1041786 rs6604969   T   C   .   PASS    AF=0.1352   ES:SE:LP:AF:SS:ID   -0.0112366:0.0141503:0.37059:0.1352:11260:rs6604969
1   1042378 rs1465575261    A   C   .   PASS    AF=0.1362   ES:SE:LP:AF:SS:ID   -0.0124225:0.0140933:0.420559:0.1362:11260:rs1465575261
1   1042483 rs12733365  C   T   .   PASS    AF=0.1352   ES:SE:LP:AF:SS:ID   -0.0111377:0.0141503:0.366633:0.1352:11260:rs12733365
1   1042527 rs1486993720    G   C   .   PASS    AF=0.1054   ES:SE:LP:AF:SS:ID   -0.0207825:0.0158983:0.717831:0.1054:11260:rs1486993720