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-1105/ieu-a-1105.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-1105/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 19:34:54 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1105/ieu-a-1105.vcf.gz ...
Read summary statistics for 2195871 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, 1070673 SNPs remain.
After merging with regression SNP LD, 1070673 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0936 (0.0074)
Lambda GC: 1.1822
Mean Chi^2: 1.2862
Intercept: 1.0237 (0.0098)
Ratio: 0.0827 (0.0342)
Analysis finished at Tue Feb  4 19:35:22 2020
Total time elapsed: 28.0s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9013,
    "inflation_factor": 1.1474,
    "mean_EFFECT": -9.9228e-06,
    "n": 133814,
    "n_snps": 2195871,
    "n_clumped_hits": 47,
    "n_p_sig": 1720,
    "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": 662,
    "n_miss_AF_reference": 18515,
    "n_est": 146258.8639,
    "ratio_se_n": 1.0455,
    "mean_diff": -0,
    "ratio_diff": 8.2689,
    "sd_y_est1": 0.2206,
    "sd_y_est2": 0.2307,
    "r2_sum1": 0.0012,
    "r2_sum2": 0.0253,
    "r2_sum3": 0.0231,
    "r2_sum4": 0.0221,
    "ldsc_nsnp_merge_refpanel_ld": 1070673,
    "ldsc_nsnp_merge_regression_ld": 1070673,
    "ldsc_observed_scale_h2_beta": 0.0936,
    "ldsc_observed_scale_h2_se": 0.0074,
    "ldsc_intercept_beta": 1.0237,
    "ldsc_intercept_se": 0.0098,
    "ldsc_lambda_gc": 1.1822,
    "ldsc_mean_chisq": 1.2862,
    "ldsc_ratio": 0.0828
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
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 3 42 0 2195871 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 8.602390e+00 5.663784e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.873193e+07 5.574131e+07 1.1523e+04 3.243214e+07 7.008990e+07 1.143748e+08 2.492107e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -9.900000e-06 1.356400e-03 -5.1000e-02 -8.000000e-04 0.000000e+00 8.000000e-04 3.300000e-02 ▁▁▃▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.170600e-03 3.542000e-04 9.2000e-04 9.200000e-04 1.000000e-03 1.300000e-03 2.500000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.767111e-01 2.962010e-01 0.0000e+00 2.099999e-01 4.700002e-01 7.300002e-01 1.000000e+00 ▇▇▇▆▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.747603e-01 2.974502e-01 0.0000e+00 2.112995e-01 4.670589e-01 7.443586e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 662 0.9996985 NA NA NA NA NA 3.804063e-01 2.569274e-01 4.0000e-03 1.590000e-01 3.230000e-01 5.730000e-01 9.960000e-01 ▇▆▅▃▂
numeric AF_reference 18515 0.9915683 NA NA NA NA NA 3.802959e-01 2.429126e-01 1.9970e-04 1.769170e-01 3.286740e-01 5.591050e-01 1.000000e+00 ▇▇▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.326359e+05 3.644975e+03 4.2388e+04 1.336030e+05 1.337130e+05 1.337220e+05 1.338140e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0045 0.0035 0.2000000 0.1985428 0.032 0.0371406 105444
1 723819 rs11804171 T A -0.0039 0.0035 0.2599998 0.2651566 0.034 0.1345850 103157
1 723891 rs2977670 G C 0.0037 0.0036 0.2900000 0.3040544 0.934 0.7799520 99915
1 750235 rs12138618 G A 0.0072 0.0048 0.1400000 0.1336144 0.062 NA 89781
1 752566 rs3094315 G A 0.0013 0.0015 0.3800004 0.3861247 0.835 0.7182510 114684
1 754192 rs3131968 A G 0.0013 0.0019 0.5000000 0.4938422 0.885 0.6785140 102660
1 768448 rs12562034 G A 0.0014 0.0023 0.5500004 0.5427262 0.102 0.1918930 106355
1 775659 rs2905035 A G 0.0022 0.0019 0.2399999 0.2469070 0.885 0.7450080 104963
1 776546 rs12124819 A G 0.0030 0.0018 0.0920005 0.0955807 0.288 0.0756789 109251
1 777122 rs2980319 A T 0.0012 0.0017 0.4899999 0.4802613 0.866 0.7472040 116970
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C -0.0015 0.00140 0.2900000 0.2839768 0.385 0.3724040 107172
22 51216564 rs9616970 T C -0.0021 0.00190 0.2700001 0.2690456 0.146 0.1563500 119983
22 51217134 rs117417021 A G -0.0011 0.00140 0.4600002 0.4320349 0.415 0.2671730 108423
22 51222100 rs114553188 G T 0.0006 0.00280 0.8200001 0.8303243 0.062 0.0880591 106604
22 51223637 rs375798137 G A 0.0005 0.00280 0.8600001 0.8582742 0.062 0.0788738 105540
22 51229805 rs9616985 T C -0.0031 0.00290 0.2800000 0.2850852 0.092 0.0730831 95960
23 35921591 rs2204667 C G 0.0006 0.00120 0.6200004 0.6170751 0.162 NA 128033
23 51666786 rs14115 A G -0.0024 0.00190 0.2200002 0.2065324 0.027 NA 131759
23 70163799 rs1626496 A C -0.0007 0.00170 0.6800001 0.6805119 0.069 NA 131682
23 118495837 rs12882977 G A -0.0008 0.00092 0.4199997 0.3845381 0.508 0.2307280 120629

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.032    ES:SE:LP:AF:SS:ID   -0.0045:0.0035:0.69897:0.032:105444:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.034    ES:SE:LP:AF:SS:ID   -0.0039:0.0035:0.585027:0.034:103157:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.934    ES:SE:LP:AF:SS:ID   0.0037:0.0036:0.537602:0.934:99915:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.062    ES:SE:LP:AF:SS:ID   0.0072:0.0048:0.853872:0.062:89781:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.835    ES:SE:LP:AF:SS:ID   0.0013:0.0015:0.420216:0.835:114684:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   0.0013:0.0019:0.30103:0.885:102660:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   0.0014:0.0023:0.259637:0.102:106355:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.885    ES:SE:LP:AF:SS:ID   0.0022:0.0019:0.619789:0.885:104963:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.288    ES:SE:LP:AF:SS:ID   0.003:0.0018:1.03621:0.288:109251:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.866    ES:SE:LP:AF:SS:ID   0.0012:0.0017:0.309804:0.866:116970:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   -0.0019:0.0019:0.481486:0.133:99471:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.877    ES:SE:LP:AF:SS:ID   0.0014:0.0017:0.376751:0.877:113743:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0.0012:0.0017:0.309804:0.868:114683:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0.0012:0.0017:0.327902:0.868:116970:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   -0.0072:0.0029:1.92082:0.9:101781:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.108    ES:SE:LP:AF:SS:ID   0.0074:0.003:1.95861:0.108:100841:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.219    ES:SE:LP:AF:SS:ID   0.0004:0.0016:0.0861861:0.219:116109:rs11240777
1   846864  rs950122    G   C   .   PASS    AF=0.138    ES:SE:LP:AF:SS:ID   0.0009:0.0023:0.161151:0.138:95152:rs950122
1   882033  rs2272756   G   A   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   -0.0032:0.0019:1.01323:0.23:107444:rs2272756
1   962210  rs3128126   A   G   .   PASS    AF=0.415    ES:SE:LP:AF:SS:ID   -0.0014:0.0015:0.443698:0.415:111506:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.254    ES:SE:LP:AF:SS:ID   -0.0012:0.0014:0.366532:0.254:119588:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.146    ES:SE:LP:AF:SS:ID   -0.0013:0.0015:0.408935:0.146:130566:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.734    ES:SE:LP:AF:SS:ID   0.0006:0.0012:0.221849:0.734:131825:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   -0.0013:0.0015:0.408935:0.124:131017:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.587    ES:SE:LP:AF:SS:ID   0.0014:0.001:0.769551:0.587:123266:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.571    ES:SE:LP:AF:SS:ID   0.0014:0.001:0.79588:0.571:123266:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.124    ES:SE:LP:AF:SS:ID   -0.0015:0.0015:0.508638:0.124:132802:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.608    ES:SE:LP:AF:SS:ID   0.0015:0.001:0.920819:0.608:132823:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.588    ES:SE:LP:AF:SS:ID   0.0014:0.001:0.823909:0.588:132820:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.137    ES:SE:LP:AF:SS:ID   -0.0017:0.0015:0.60206:0.137:132806:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.735    ES:SE:LP:AF:SS:ID   0.0013:0.001:0.677781:0.735:133806:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.112    ES:SE:LP:AF:SS:ID   -0.0017:0.0015:0.585027:0.112:130514:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.726    ES:SE:LP:AF:SS:ID   0.0011:0.0011:0.468521:0.726:133714:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.585    ES:SE:LP:AF:SS:ID   0.002:0.001:1.29243:0.585:132737:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.952    ES:SE:LP:AF:SS:ID   -0.0071:0.0039:1.17393:0.952:101520:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.623    ES:SE:LP:AF:SS:ID   0.0021:0.0011:1.31876:0.623:127309:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.133    ES:SE:LP:AF:SS:ID   0.0003:0.0013:0.09691:0.133:132932:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.134    ES:SE:LP:AF:SS:ID   0.0004:0.0013:0.119186:0.134:129618:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   0.0023:0.0011:1.4318:0.717:129702:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.046    ES:SE:LP:AF:SS:ID   -0.0005:0.0015:0.130768:0.046:132862:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   0.0003:0.0014:0.0861861:0.115:132855:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.062    ES:SE:LP:AF:SS:ID   0.0002:0.0014:0.0457575:0.062:132855:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.088    ES:SE:LP:AF:SS:ID   -0.0009:0.0015:0.259637:0.088:132933:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.115    ES:SE:LP:AF:SS:ID   -0.0002:0.0014:0.0555173:0.115:132922:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.093    ES:SE:LP:AF:SS:ID   -0.001:0.0015:0.275724:0.093:131921:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.314    ES:SE:LP:AF:SS:ID   -0.0014:0.0012:0.568636:0.314:117589:rs7548798
1   1060608 rs17160824  G   A   .   PASS    AF=0.097    ES:SE:LP:AF:SS:ID   -0.0007:0.0015:0.187087:0.097:132834:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.051    ES:SE:LP:AF:SS:ID   -0.001:0.0015:0.283997:0.051:132861:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.055    ES:SE:LP:AF:SS:ID   -0.0011:0.0015:0.309804:0.055:131921:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.389    ES:SE:LP:AF:SS:ID   -0.0021:0.0011:1.20066:0.389:132825:rs11807848