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-86/ieu-a-86.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-86/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 19:11:03 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-86/ieu-a-86.vcf.gz ...
Read summary statistics for 1964238 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, 967509 SNPs remain.
After merging with regression SNP LD, 967509 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 1.0375 (0.0757)
Lambda GC: 1.0536
Mean Chi^2: 1.1913
Intercept: 0.8823 (0.011)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 19:11:28 2020
Total time elapsed: 25.35s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8826,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0.0005,
    "n": 16196,
    "n_snps": 1964238,
    "n_clumped_hits": 47,
    "n_p_sig": 1277,
    "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": 2024,
    "n_miss_AF_reference": 15815,
    "n_est": 16238.8524,
    "ratio_se_n": 1.0013,
    "mean_diff": 0.0003,
    "ratio_diff": 15.6229,
    "sd_y_est1": 2.3886,
    "sd_y_est2": 2.3918,
    "r2_sum1": 0.7451,
    "r2_sum2": 0.1306,
    "r2_sum3": 0.1302,
    "r2_sum4": 0.1339,
    "ldsc_nsnp_merge_refpanel_ld": 967509,
    "ldsc_nsnp_merge_regression_ld": 967509,
    "ldsc_observed_scale_h2_beta": 1.0375,
    "ldsc_observed_scale_h2_se": 0.0757,
    "ldsc_intercept_beta": 0.8823,
    "ldsc_intercept_se": 0.011,
    "ldsc_lambda_gc": 1.0536,
    "ldsc_mean_chisq": 1.1913,
    "ldsc_ratio": -0.6153
}

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 TRUE
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 1964238 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 8.574742e+00 5.653820e+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 7.883531e+07 5.574094e+07 1.1543e+04 3.251916e+07 7.018843e+07 1.145197e+08 2.491722e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.419000e-04 3.875130e-02 -3.8000e-01 -2.300000e-02 -3.000000e-04 2.200000e-02 3.500000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.441500e-02 1.126170e-02 1.0000e-04 2.600000e-02 3.000000e-02 4.000000e-02 1.100000e-01 ▁▇▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.883858e-01 2.949341e-01 0.0000e+00 2.300001e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.882660e-01 2.949701e-01 0.0000e+00 2.301393e-01 4.887441e-01 7.443586e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 2024 0.9989696 NA NA NA NA NA 3.986918e-01 2.410092e-01 8.0000e-03 1.920000e-01 3.500000e-01 5.830000e-01 9.920000e-01 ▇▇▆▅▂
numeric AF_reference 15815 0.9919485 NA NA NA NA NA 3.957127e-01 2.310578e-01 1.9970e-04 2.028750e-01 3.528350e-01 5.680910e-01 1.000000e+00 ▆▇▆▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.345411e+04 2.355651e+03 8.0929e+03 1.159800e+04 1.425480e+04 1.557160e+04 1.619600e+04 ▂▂▂▃▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 990380 rs3121561 C T 0.088 0.046 0.0560003 0.0557425 0.267 0.343450 11620.40
1 998501 rs3813193 G C 0.044 0.045 0.3200000 0.3281842 0.150 0.206669 9735.15
1 1003629 rs4075116 C T -0.064 0.036 0.0729995 0.0754404 0.737 0.720647 13874.70
1 1005806 rs3934834 C T 0.025 0.042 0.5600000 0.5516843 0.119 0.223442 9070.00
1 1017170 rs3766193 C G -0.082 0.032 0.0109999 0.0103922 0.569 0.575479 15302.90
1 1017197 rs3766192 C T -0.074 0.030 0.0150000 0.0136377 0.576 0.511182 15365.20
1 1017587 rs3766191 C T 0.038 0.051 0.4500005 0.4562125 0.096 0.171126 8751.80
1 1018562 rs9442371 C T -0.070 0.030 0.0189998 0.0196307 0.592 0.530152 15384.20
1 1018704 rs9442372 A G -0.071 0.030 0.0170000 0.0179491 0.602 0.611022 15225.10
1 1021346 rs10907177 A G 0.049 0.053 0.3500000 0.3552113 0.127 0.178914 8652.90
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51156933 rs6010063 A G 0.0026 0.027 0.9199999 0.9232853 0.442 0.4960060 15069.6
22 51158017 rs6010065 G C -0.0016 0.027 0.9500000 0.9527456 0.442 0.5475240 15259.6
22 51162059 rs10451 G A -0.0005 0.036 0.9900000 0.9889186 0.284 0.3865810 10035.6
22 51163138 rs715586 C T -0.0012 0.044 0.9800000 0.9782422 0.150 0.0902556 10953.0
22 51165664 rs8137951 G A 0.0080 0.030 0.7899998 0.7897258 0.275 0.4063500 14315.0
22 51171693 rs756638 G A -0.0270 0.036 0.4500005 0.4532547 0.283 0.3049120 11396.0
22 51212875 rs2238837 A C 0.0470 0.047 0.3200000 0.3173105 0.392 0.3724040 8741.0
22 51217134 rs117417021 A G 0.0360 0.048 0.4600002 0.4532547 0.442 0.2671730 8633.0
23 35921591 rs2204667 C G 0.0072 0.041 0.8600001 0.8606005 0.167 NA 11435.0
23 118495837 rs12882977 G A -0.0110 0.025 0.6600001 0.6599371 0.509 0.2307280 15981.0

bcf preview

1   990380  rs3121561   C   T   .   PASS    AF=0.267    ES:SE:LP:AF:SS:ID   0.088:0.046:1.25181:0.267:11620.4:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.044:0.045:0.49485:0.15:9735.15:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.737    ES:SE:LP:AF:SS:ID   -0.064:0.036:1.13668:0.737:13874.7:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.119    ES:SE:LP:AF:SS:ID   0.025:0.042:0.251812:0.119:9070:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.569    ES:SE:LP:AF:SS:ID   -0.082:0.032:1.95861:0.569:15302.9:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.576    ES:SE:LP:AF:SS:ID   -0.074:0.03:1.82391:0.576:15365.2:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.096    ES:SE:LP:AF:SS:ID   0.038:0.051:0.346787:0.096:8751.8:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.592    ES:SE:LP:AF:SS:ID   -0.07:0.03:1.72125:0.592:15384.2:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.602    ES:SE:LP:AF:SS:ID   -0.071:0.03:1.76955:0.602:15225.1:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.049:0.053:0.455932:0.127:8652.9:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   -0.073:0.032:1.63827:0.717:14559:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.113    ES:SE:LP:AF:SS:ID   0.049:0.053:0.455932:0.113:8658.6:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   -0.062:0.034:1.19382:0.725:14250.7:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.567    ES:SE:LP:AF:SS:ID   -0.092:0.032:2.37675:0.567:14114.9:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.077:0.035:1.56864:0.6:11239.3:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.048:0.046:0.537602:0.083:8885:rs6687776
1   1031540 rs9651273   A   G   .   PASS    AF=0.658    ES:SE:LP:AF:SS:ID   -0.066:0.033:1.35655:0.658:10755:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0035:0.062:0.0177288:0.05:8667:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.029:0.052:0.236572:0.075:9325.54:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.028:0.052:0.229148:0.067:9980.79:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.052    ES:SE:LP:AF:SS:ID   0.011:0.063:0.0655015:0.052:8500:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.024:0.051:0.200659:0.067:9973:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0093:0.062:0.0555173:0.05:8666.9:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.398    ES:SE:LP:AF:SS:ID   0.067:0.045:0.853872:0.398:8408.46:rs7548798
1   1060608 rs17160824  G   A   .   PASS    AF=0.058    ES:SE:LP:AF:SS:ID   0.0096:0.062:0.0555173:0.058:8838.2:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.055    ES:SE:LP:AF:SS:ID   0.0051:0.063:0.0268721:0.055:8666.7:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0041:0.064:0.0222764:0.05:8666.8:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.412    ES:SE:LP:AF:SS:ID   0.083:0.037:1.61979:0.412:10626:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.552    ES:SE:LP:AF:SS:ID   -0.07:0.036:1.25964:0.552:10593.2:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.754    ES:SE:LP:AF:SS:ID   -0.065:0.05:0.69897:0.754:9742.43:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.0081:0.052:0.0555173:0.083:8345:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.038:0.04:0.468521:0.675:10183.6:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.683    ES:SE:LP:AF:SS:ID   -0.029:0.043:0.309804:0.683:9716.96:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.924    ES:SE:LP:AF:SS:ID   0.059:0.076:0.356547:0.924:8207.5:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.912    ES:SE:LP:AF:SS:ID   -0.011:0.075:0.0555173:0.912:8729.4:rs9442380
1   1099342 rs9660710   A   C   .   PASS    AF=0.941    ES:SE:LP:AF:SS:ID   0.011:0.07:0.0604807:0.941:8221:rs9660710
1   1121794 rs11260549  G   A   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   -0.086:0.051:1.05061:0.125:9180:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.267    ES:SE:LP:AF:SS:ID   -0.045:0.033:0.769551:0.267:14026.6:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.225    ES:SE:LP:AF:SS:ID   -0.028:0.036:0.346787:0.225:13031:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   -0.079:0.052:0.886057:0.125:9017.9:rs11260554
1   1130727 rs10907175  A   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.15:0.06:1.82391:0.1:8727.7:rs10907175
1   1135242 rs9729550   A   C   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   -0.049:0.032:0.886057:0.275:14177:rs9729550
1   1140435 rs1815606   G   T   .   PASS    AF=0.31 ES:SE:LP:AF:SS:ID   -0.009:0.036:0.09691:0.31:10359.5:rs1815606
1   1152631 rs11721 C   A   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.085:0.059:0.823909:0.083:8694:rs11721
1   1156131 rs2887286   T   C   .   PASS    AF=0.183    ES:SE:LP:AF:SS:ID   0.062:0.041:0.886057:0.183:10702:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.12:0.056:1.52288:0.1:9277:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.13:0.056:1.67778:0.1:9273:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0078:0.044:0.0655015:0.15:10932:rs7515488
1   1176597 rs6675798   T   C   .   PASS    AF=0.108    ES:SE:LP:AF:SS:ID   0.032:0.057:0.236572:0.108:9440.97:rs6675798
1   1181751 rs6603783   T   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.052:0.059:0.420216:0.1:8987.9:rs6603783