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-1134/ieu-a-1134.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-1134/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 08:41:52 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1134/ieu-a-1134.vcf.gz ...
Read summary statistics for 9231031 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, 1219312 SNPs remain.
After merging with regression SNP LD, 1219312 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1133 (0.0215)
Lambda GC: 1.0378
Mean Chi^2: 1.046
Intercept: 0.9983 (0.0063)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 08:43:23 2020
Total time elapsed: 1.0m:30.09s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.95,
    "inflation_factor": 1.0193,
    "mean_EFFECT": -1.0698,
    "n": 21814,
    "n_snps": 9231031,
    "n_clumped_hits": 8,
    "n_p_sig": 262,
    "n_mono": 0,
    "n_ns": 574490,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 122039,
    "n_est": 19653.8177,
    "ratio_se_n": 0.9492,
    "mean_diff": 1.0687,
    "ratio_diff": 3.2824,
    "sd_y_est1": 3.4503,
    "sd_y_est2": 3.2751,
    "r2_sum1": 0.2171,
    "r2_sum2": 0.0182,
    "r2_sum3": 0.0202,
    "r2_sum4": 0.0194,
    "ldsc_nsnp_merge_refpanel_ld": 1219312,
    "ldsc_nsnp_merge_regression_ld": 1219312,
    "ldsc_observed_scale_h2_beta": 0.1133,
    "ldsc_observed_scale_h2_se": 0.0215,
    "ldsc_intercept_beta": 0.9983,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0378,
    "ldsc_mean_chisq": 1.046,
    "ldsc_ratio": -0.037
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 TRUE
mean_EFFECT_01 TRUE
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 47 0 9231030 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 99 0 28515 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 103 0 15300 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.502432e+00 5.865206e+00 1.00000e+00 4.000000e+00 7.000000e+00 1.300000e+01 2.400000e+01 ▇▆▂▃▁
numeric POS 0 1.0000000 NA NA NA NA NA 7.910659e+07 5.710948e+07 8.28000e+02 3.220316e+07 6.897145e+07 1.153241e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.069792e+00 7.806430e+01 -9.53037e+03 -4.320000e-02 -1.900000e-03 3.720000e-02 8.496310e+03 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.507967e+00 4.723225e+02 2.43000e-02 3.550000e-02 5.290000e-02 1.123000e-01 5.905330e+04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.974100e-01 2.893408e-01 0.00000e+00 2.466000e-01 4.958999e-01 7.484004e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.974099e-01 2.893413e-01 0.00000e+00 2.466125e-01 4.958744e-01 7.483963e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.434325e-01 2.642222e-01 1.00000e-02 3.220000e-02 1.280000e-01 3.870000e-01 9.900000e-01 ▇▂▂▁▁
numeric AF_reference 122039 0.9867795 NA NA NA NA NA 2.399872e-01 2.524035e-01 1.99700e-04 3.314700e-02 1.443690e-01 3.785940e-01 9.996010e-01 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.181400e+04 0.000000e+00 2.18140e+04 2.181400e+04 2.181400e+04 2.181400e+04 2.181400e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 14933 rs199856693 G A -0.0434 0.1794 0.8087999 0.8088441 0.0401 0.0283546 21814
1 16949 rs199745162 A C 0.6086 0.3208 0.0577803 0.0578105 0.0142 0.0139776 21814
1 51479 rs116400033 T A 0.2885 0.0818 0.0004234 0.0004205 0.2163 0.1281950 21814
1 54490 rs141149254 G A 0.2234 0.0927 0.0159199 0.0159558 0.1513 0.0960463 21814
1 55164 rs3091274 C A 0.3111 0.3698 0.4003004 0.4001992 0.9779 0.9233230 21814
1 55326 rs3107975 T C 0.0951 0.3514 0.7866001 0.7866743 0.0229 0.0459265 21814
1 55545 rs28396308 C T -0.2236 0.0840 0.0077660 0.0077700 0.2363 0.2392170 21814
1 57292 rs201418760 C T -0.0655 0.3617 0.8562000 0.8562975 0.0217 0.0337460 21814
1 58814 rs114420996 G A 0.0672 0.1378 0.6258006 0.6257884 0.0939 0.1090260 21814
1 61920 rs62637820 G A 0.0733 0.2359 0.7560996 0.7560098 0.0260 0.0115815 21814
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51234799 rs191117135 G A 0.3137 0.2575 0.2230001 0.2231281 0.0142 0.0059904 21814
22 51235959 rs200189535 T C 0.1752 0.0641 0.0062340 0.0062717 0.1907 0.1996810 21814
22 51236013 rs200507571 A AT 0.0636 0.0556 0.2528000 0.2526714 0.2364 0.1487620 21814
22 51237063 rs3896457 T C -0.0416 0.0544 0.4442005 0.4444467 0.2901 0.2050720 21814
22 51237364 rs200607599 A G 0.5465 0.2180 0.0121599 0.0121802 0.0189 0.0187700 21814
22 51237712 rs370652263 G A 0.0186 0.0897 0.8360000 0.8357304 0.0644 0.0690895 21814
23 75822996 rs147134110 C T 0.0614 0.0856 0.4727995 0.4731953 0.0336 0.0773510 21814
23 75980185 rs112961710 G A 0.0061 0.0904 0.9465000 0.9462013 0.9635 NA 21814
23 100784211 rs188350543 C A -0.0366 0.0371 0.3231000 0.3238766 0.7664 0.6498010 21814
24 13537468 rs7203107 A G -0.2305 0.4949 0.6414001 0.6413940 0.9808 NA 21814

bcf preview

1   14933   rs199856693 G   A   .   PASS    AF=0.0401   ES:SE:LP:AF:SS:ID   -0.0434:0.1794:0.0921589:0.0401:21814:rs199856693
1   16949   rs199745162 A   C   .   PASS    AF=0.0142   ES:SE:LP:AF:SS:ID   0.6086:0.3208:1.23822:0.0142:21814:rs199745162
1   51479   rs116400033 T   A   .   PASS    AF=0.2163   ES:SE:LP:AF:SS:ID   0.2885:0.0818:3.37325:0.2163:21814:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.1513   ES:SE:LP:AF:SS:ID   0.2234:0.0927:1.79806:0.1513:21814:rs141149254
1   55164   rs3091274   C   A   .   PASS    AF=0.9779   ES:SE:LP:AF:SS:ID   0.3111:0.3698:0.397614:0.9779:21814:rs3091274
1   55326   rs3107975   T   C   .   PASS    AF=0.0229   ES:SE:LP:AF:SS:ID   0.0951:0.3514:0.104246:0.0229:21814:rs3107975
1   55545   rs28396308  C   T   .   PASS    AF=0.2363   ES:SE:LP:AF:SS:ID   -0.2236:0.084:2.1098:0.2363:21814:rs28396308
1   57292   rs201418760 C   T   .   PASS    AF=0.0217   ES:SE:LP:AF:SS:ID   -0.0655:0.3617:0.0674248:0.0217:21814:rs201418760
1   58814   rs114420996 G   A   .   PASS    AF=0.0939   ES:SE:LP:AF:SS:ID   0.0672:0.1378:0.203564:0.0939:21814:rs114420996
1   61920   rs62637820  G   A   .   PASS    AF=0.026    ES:SE:LP:AF:SS:ID   0.0733:0.2359:0.121421:0.026:21814:rs62637820
1   63093   rs200092917 G   A   .   PASS    AF=0.0208   ES:SE:LP:AF:SS:ID   0.3315:0.3316:0.49812:0.0208:21814:rs200092917
1   64649   rs181431124 A   C   .   PASS    AF=0.0243   ES:SE:LP:AF:SS:ID   0.0165:0.246:0.0239253:0.0243:21814:rs181431124
1   66219   rs181028663 A   T   .   PASS    AF=0.0198   ES:SE:LP:AF:SS:ID   0.0925:0.2886:0.125808:0.0198:21814:rs181028663
1   68082   rs367789441 T   C   .   PASS    AF=0.0622   ES:SE:LP:AF:SS:ID   -0.0426:0.1462:0.113115:0.0622:21814:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.0486   ES:SE:LP:AF:SS:ID   -0.4432:0.1645:2.1523:0.0486:21814:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.066    ES:SE:LP:AF:SS:ID   -0.0843:0.1408:0.260111:0.066:21814:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.7453   ES:SE:LP:AF:SS:ID   0.2421:0.0808:2.56511:0.7453:21814:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.0275   ES:SE:LP:AF:SS:ID   0.3732:0.2552:0.842846:0.0275:21814:rs13328700
1   74792   rs13328684  G   A   .   PASS    AF=0.0275   ES:SE:LP:AF:SS:ID   0.3732:0.2552:0.842846:0.0275:21814:rs13328684
1   76854   rs367666799 A   G   .   PASS    AF=0.0699   ES:SE:LP:AF:SS:ID   -0.3269:0.1409:1.69144:0.0699:21814:rs367666799
1   82163   rs139113303 G   A   .   PASS    AF=0.07 ES:SE:LP:AF:SS:ID   -0.3293:0.1406:1.7176:0.07:21814:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.0702   ES:SE:LP:AF:SS:ID   -0.3085:0.1398:1.56304:0.0702:21814:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3633   ES:SE:LP:AF:SS:ID   0.0392:0.0709:0.236422:0.3633:21814:rs201754587
1   86028   rs114608975 T   C   .   PASS    AF=0.0519   ES:SE:LP:AF:SS:ID   -0.1149:0.157:0.333482:0.0519:21814:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.0706   ES:SE:LP:AF:SS:ID   -0.2883:0.1403:1.39892:0.0706:21814:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.1022   ES:SE:LP:AF:SS:ID   -0.1482:0.1354:0.562725:0.1022:21814:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.0135   ES:SE:LP:AF:SS:ID   -0.1092:0.5552:0.0736061:0.0135:21814:rs188486692
1   87360   rs180907504 C   T   .   PASS    AF=0.0197   ES:SE:LP:AF:SS:ID   0.052:0.2996:0.064392:0.0197:21814:rs180907504
1   87409   rs139490478 C   T   .   PASS    AF=0.0721   ES:SE:LP:AF:SS:ID   -0.3235:0.1398:1.68424:0.0721:21814:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.2127   ES:SE:LP:AF:SS:ID   -0.0237:0.0817:0.112608:0.2127:21814:rs940550
1   88172   rs940551    G   A   .   PASS    AF=0.0612   ES:SE:LP:AF:SS:ID   -0.0303:0.1437:0.0793029:0.0612:21814:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.0602   ES:SE:LP:AF:SS:ID   -0.0245:0.1481:0.0611302:0.0602:21814:rs143215837
1   88236   rs186918018 C   T   .   PASS    AF=0.0108   ES:SE:LP:AF:SS:ID   0.2307:0.4494:0.216382:0.0108:21814:rs186918018
1   88316   rs113759966 G   A   .   PASS    AF=0.0614   ES:SE:LP:AF:SS:ID   -0.0523:0.1442:0.144723:0.0614:21814:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.0786   ES:SE:LP:AF:SS:ID   0.0385:0.1281:0.117134:0.0786:21814:rs55700207
1   88710   rs186575039 C   G   .   PASS    AF=0.0721   ES:SE:LP:AF:SS:ID   -0.3234:0.1398:1.68382:0.0721:21814:rs186575039
1   89599   rs375955515 A   T   .   PASS    AF=0.0721   ES:SE:LP:AF:SS:ID   -0.3234:0.1398:1.68382:0.0721:21814:rs375955515
1   89946   rs138808727 A   T   .   PASS    AF=0.2237   ES:SE:LP:AF:SS:ID   0.1551:0.0822:1.22922:0.2237:21814:rs138808727
1   91190   rs143856811 G   A   .   PASS    AF=0.0739   ES:SE:LP:AF:SS:ID   -0.328:0.1389:1.74017:0.0739:21814:rs143856811
1   91421   rs28619159  T   C   .   PASS    AF=0.0121   ES:SE:LP:AF:SS:ID   -0.3742:0.4808:0.360115:0.0121:21814:rs28619159
1   91515   rs376723915 A   C   .   PASS    AF=0.5509   ES:SE:LP:AF:SS:ID   0.0204:0.0694:0.113904:0.5509:21814:rs376723915
1   92633   rs149776517 C   T   .   PASS    AF=0.0293   ES:SE:LP:AF:SS:ID   -0.0021:0.1996:0.00366348:0.0293:21814:rs149776517
1   92858   rs147061536 G   T   .   PASS    AF=0.2313   ES:SE:LP:AF:SS:ID   0.194:0.0809:1.78278:0.2313:21814:rs147061536
1   99671   rs146209971 A   T   .   PASS    AF=0.0108   ES:SE:LP:AF:SS:ID   0.1917:0.3687:0.219611:0.0108:21814:rs146209971
1   99687   rs139153227 C   T   .   PASS    AF=0.0571   ES:SE:LP:AF:SS:ID   -0.0578:0.1471:0.15839:0.0571:21814:rs139153227
1   99719   rs183898652 C   T   .   PASS    AF=0.0108   ES:SE:LP:AF:SS:ID   0.0706:0.3864:0.0679831:0.0108:21814:rs183898652
1   115729  rs199999500 GCACA   G   .   PASS    AF=0.0127   ES:SE:LP:AF:SS:ID   0.687:0.3446:1.33526:0.0127:21814:rs199999500
1   115746  rs147538909 C   T   .   PASS    AF=0.0453   ES:SE:LP:AF:SS:ID   -0.4443:0.1804:1.85981:0.0453:21814:rs147538909
1   129010  rs377161483 AATG    A   .   PASS    AF=0.557    ES:SE:LP:AF:SS:ID   -0.1031:0.0684:0.879426:0.557:21814:rs377161483
1   135163  rs374499151 C   T   .   PASS    AF=0.0232   ES:SE:LP:AF:SS:ID   -0.1305:0.2649:0.206:0.0232:21814:rs374499151