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-1099/ieu-a-1099.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-1099/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 10:11:13 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1099/ieu-a-1099.vcf.gz ...
Read summary statistics for 2450940 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, 1042439 SNPs remain.
After merging with regression SNP LD, 1042439 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0238 (0.0232)
Lambda GC: 1.006
Mean Chi^2: 1.0155
Intercept: 1.0078 (0.0072)
Ratio: 0.5055 (0.465)
Analysis finished at Tue Feb  4 10:11:46 2020
Total time elapsed: 32.66s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8049,
    "inflation_factor": 1,
    "mean_EFFECT": 0,
    "n": 16474,
    "n_snps": 2450940,
    "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": 21855,
    "n_miss_AF_reference": 18861,
    "n_est": 15886.1323,
    "ratio_se_n": 0.982,
    "mean_diff": 0.0002,
    "ratio_diff": 1.2848,
    "sd_y_est1": 0.319,
    "sd_y_est2": 0.3133,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1042439,
    "ldsc_nsnp_merge_regression_ld": 1042439,
    "ldsc_observed_scale_h2_beta": 0.0238,
    "ldsc_observed_scale_h2_se": 0.0232,
    "ldsc_intercept_beta": 1.0078,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.006,
    "ldsc_mean_chisq": 1.0155,
    "ldsc_ratio": 0.5032
}

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 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 3 42 0 2450940 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 8.576092e+00 5.678612e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.900730e+07 5.585682e+07 1.1523e+04 3.268585e+07 7.025685e+07 1.147090e+08 2.492107e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.570000e-05 5.229100e-03 -6.5000e-02 -3.100000e-03 0.000000e+00 3.100000e-03 5.500000e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 4.915200e-03 1.736100e-03 3.2000e-03 3.700000e-03 4.300000e-03 5.600000e-03 3.000000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.989140e-01 2.891484e-01 5.0000e-07 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.984839e-01 2.892802e-01 6.0000e-07 2.469070e-01 4.987419e-01 7.496136e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 21855 0.9910830 NA NA NA NA NA 3.693823e-01 2.734008e-01 3.0000e-03 1.360000e-01 2.940000e-01 5.740000e-01 9.970000e-01 ▇▅▃▃▂
numeric AF_reference 18861 0.9923046 NA NA NA NA NA 3.538257e-01 2.637972e-01 1.9970e-04 1.311900e-01 2.887380e-01 5.417330e-01 1.000000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.547843e+04 1.973557e+03 5.0020e+03 1.546100e+04 1.640600e+04 1.645500e+04 1.647400e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 723819 rs11804171 T A 0.0081 0.0069 0.2399999 0.2404299 0.387 0.1345850 10964
1 723891 rs2977670 G C -0.0078 0.0068 0.2500000 0.2513573 0.508 0.7799520 10384
1 740857 rs12082473 G A 0.0036 0.0057 0.5199996 0.5276620 0.181 0.0585064 12289
1 750235 rs12138618 G A 0.0077 0.0092 0.4000000 0.4026170 0.067 NA 14881
1 752566 rs3094315 G A 0.0027 0.0035 0.4400003 0.4404529 0.303 0.7182510 16412
1 754192 rs3131968 A G 0.0054 0.0039 0.1600000 0.1661701 0.266 0.6785140 16416
1 777122 rs2980319 A T 0.0057 0.0035 0.1100001 0.1034038 0.361 0.7472040 15417
1 779322 rs4040617 A G -0.0072 0.0036 0.0460002 0.0455003 0.541 0.2264380 16402
1 780027 rs2977613 G T -0.0067 0.0084 0.4299995 0.4250916 0.929 0.9796330 13554
1 785050 rs2905062 G A 0.0021 0.0041 0.6100002 0.6085145 0.119 0.6269970 16474
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C -0.0025 0.0047 0.5999997 0.5947849 0.349 0.1563500 16453
22 51217134 rs117417021 A G -0.0026 0.0037 0.4799997 0.4822410 0.476 0.2671730 15808
22 51222100 rs114553188 G T 0.0031 0.0063 0.6200004 0.6226745 0.238 0.0880591 11801
23 35921591 rs2204667 C G -0.0062 0.0047 0.1900002 0.1871193 0.151 NA 15866
23 51115886 rs17864968 C G 0.0001 0.0057 0.9900000 0.9860027 0.190 NA 13012
23 51666786 rs14115 A G -0.0036 0.0038 0.3400001 0.3434511 0.358 NA 15750
23 57663373 rs28962478 A G -0.0013 0.0074 0.8600001 0.8605487 0.040 NA 13005
23 70163799 rs1626496 A C -0.0048 0.0047 0.3100002 0.3071234 0.159 NA 15885
23 91415872 rs6562597 G A -0.0008 0.0063 0.9000000 0.8989530 0.119 0.0021192 14881
23 118495837 rs12882977 G A 0.0043 0.0041 0.2999998 0.2942792 0.123 0.2307280 14881

bcf preview

1   723819  rs11804171  T   A   .   PASS    AF=0.387    ES:SE:LP:AF:SS:ID   0.0081:0.0069:0.619789:0.387:10964:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.508    ES:SE:LP:AF:SS:ID   -0.0078:0.0068:0.60206:0.508:10384:rs2977670
1   740857  rs12082473  G   A   .   PASS    AF=0.181    ES:SE:LP:AF:SS:ID   0.0036:0.0057:0.283997:0.181:12289:rs12082473
1   750235  rs12138618  G   A   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.0077:0.0092:0.39794:0.067:14881:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.303    ES:SE:LP:AF:SS:ID   0.0027:0.0035:0.356547:0.303:16412:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.266    ES:SE:LP:AF:SS:ID   0.0054:0.0039:0.79588:0.266:16416:rs3131968
1   777122  rs2980319   A   T   .   PASS    AF=0.361    ES:SE:LP:AF:SS:ID   0.0057:0.0035:0.958607:0.361:15417:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.541    ES:SE:LP:AF:SS:ID   -0.0072:0.0036:1.33724:0.541:16402:rs4040617
1   780027  rs2977613   G   T   .   PASS    AF=0.929    ES:SE:LP:AF:SS:ID   -0.0067:0.0084:0.366532:0.929:13554:rs2977613
1   785050  rs2905062   G   A   .   PASS    AF=0.119    ES:SE:LP:AF:SS:ID   0.0021:0.0041:0.21467:0.119:16474:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.093    ES:SE:LP:AF:SS:ID   0.0018:0.004:0.180456:0.093:16250:rs2980300
1   792480  rs2905036   C   T   .   PASS    AF=0.908    ES:SE:LP:AF:SS:ID   -0.0029:0.0067:0.180456:0.908:14033:rs2905036
1   798026  rs4951864   C   T   .   PASS    AF=0.825    ES:SE:LP:AF:SS:ID   -0.0083:0.0078:0.537602:0.825:13892:rs4951864
1   798959  rs11240777  G   A   .   PASS    AF=0.789    ES:SE:LP:AF:SS:ID   -0.0012:0.0037:0.124939:0.789:16432:rs11240777
1   799463  rs4245756   T   C   .   PASS    AF=0.905    ES:SE:LP:AF:SS:ID   0.0035:0.0067:0.221849:0.905:13552:rs4245756
1   800007  rs6681049   T   C   .   PASS    AF=0.897    ES:SE:LP:AF:SS:ID   0.0044:0.007:0.275724:0.897:13595:rs6681049
1   990380  rs3121561   C   T   .   PASS    AF=0.563    ES:SE:LP:AF:SS:ID   0.0063:0.0068:0.455932:0.563:11854:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.381    ES:SE:LP:AF:SS:ID   0.0045:0.0058:0.366532:0.381:15461:rs3813193
1   998874  rs7526509   A   T   .   PASS    AF=0.153    ES:SE:LP:AF:SS:ID   -0.0028:0.0068:0.167491:0.153:13539:rs7526509
1   1003629 rs4075116   C   T   .   PASS    AF=0.49 ES:SE:LP:AF:SS:ID   -0.0026:0.004:0.29243:0.49:16214:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.441    ES:SE:LP:AF:SS:ID   0.001:0.0046:0.0809219:0.441:16432:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.403    ES:SE:LP:AF:SS:ID   -0.0022:0.0042:0.21467:0.403:14967:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.163    ES:SE:LP:AF:SS:ID   -0.0061:0.0044:0.769551:0.163:16406:rs3766192
1   1017216 rs6667248   A   G   .   PASS    AF=0.235    ES:SE:LP:AF:SS:ID   0.0009:0.0044:0.0809219:0.235:13971:rs6667248
1   1017587 rs3766191   C   T   .   PASS    AF=0.228    ES:SE:LP:AF:SS:ID   0.004:0.0066:0.259637:0.228:15460:rs3766191
1   1017598 rs12096277  A   G   .   PASS    AF=0.143    ES:SE:LP:AF:SS:ID   0.0007:0.0052:0.05061:0.143:12582:rs12096277
1   1018562 rs9442371   C   T   .   PASS    AF=0.145    ES:SE:LP:AF:SS:ID   -0.0048:0.0047:0.508638:0.145:16409:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.51 ES:SE:LP:AF:SS:ID   -0.0018:0.0035:0.221849:0.51:16319:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.236    ES:SE:LP:AF:SS:ID   0.0019:0.005:0.154902:0.236:16386:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.844    ES:SE:LP:AF:SS:ID   -0.0044:0.0066:0.30103:0.844:11853:rs3737728
1   1021658 rs11260588  G   A   .   PASS    AF=0.235    ES:SE:LP:AF:SS:ID   0.0025:0.0056:0.180456:0.235:12580:rs11260588
1   1021695 rs9442398   A   G   .   PASS    AF=0.507    ES:SE:LP:AF:SS:ID   0.0003:0.0045:0.0268721:0.507:15461:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.437    ES:SE:LP:AF:SS:ID   -0.0017:0.0043:0.161151:0.437:15461:rs6701114
1   1040026 rs6671356   T   C   .   PASS    AF=0.561    ES:SE:LP:AF:SS:ID   0.01:0.0071:0.79588:0.561:5430:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.571    ES:SE:LP:AF:SS:ID   0.014:0.0072:1.284:0.571:5421:rs6666280
1   1049950 rs12726255  A   G   .   PASS    AF=0.582    ES:SE:LP:AF:SS:ID   0.017:0.0073:1.67778:0.582:5389:rs12726255
1   1088534 rs12060927  T   C   .   PASS    AF=0.161    ES:SE:LP:AF:SS:ID   0.0051:0.0055:0.455932:0.161:12582:rs12060927
1   1089699 rs6686003   G   A   .   PASS    AF=0.354    ES:SE:LP:AF:SS:ID   0.0038:0.0039:0.481486:0.354:14048:rs6686003
1   1089830 rs6700376   A   G   .   PASS    AF=0.365    ES:SE:LP:AF:SS:ID   0.0035:0.004:0.420216:0.365:13564:rs6700376
1   1090557 rs7553429   A   C   .   PASS    AF=0.408    ES:SE:LP:AF:SS:ID   0.0049:0.004:0.657577:0.408:14068:rs7553429
1   1094738 rs4970362   A   G   .   PASS    AF=0.469    ES:SE:LP:AF:SS:ID   -0.0007:0.0049:0.05061:0.469:15461:rs4970362
1   1097335 rs9442385   T   G   .   PASS    AF=0.822    ES:SE:LP:AF:SS:ID   0.0003:0.0046:0.0268721:0.822:16275:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.813    ES:SE:LP:AF:SS:ID   -0.0005:0.0049:0.0362122:0.813:16423:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.81 ES:SE:LP:AF:SS:ID   -0.0015:0.005:0.107905:0.81:16424:rs1891905
1   1106112 rs6670693   A   G   .   PASS    AF=0.976    ES:SE:LP:AF:SS:ID   0.014:0.0077:1.21467:0.976:9510:rs6670693
1   1124663 rs6684820   G   A   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.0003:0.0051:0.0222764:0.675:15461:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.198    ES:SE:LP:AF:SS:ID   0.0008:0.0049:0.0604807:0.198:16454:rs10907174
1   1130727 rs10907175  A   C   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   -0.0038:0.0052:0.327902:0.129:16425:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.656    ES:SE:LP:AF:SS:ID   -0.0004:0.0048:0.0315171:0.656:15460:rs9729550
1   1138913 rs3819001   T   C   .   PASS    AF=0.534    ES:SE:LP:AF:SS:ID   0.0004:0.0051:0.0268721:0.534:15460:rs3819001