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/ukb-d-import/processed/ukb-d-30860_raw/ukb-d-30860_raw.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/ukb-d-import/processed/ukb-d-30860_raw/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 16:44:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30860_raw/ukb-d-30860_raw.vcf.gz ...
Read summary statistics for 13585297 SNPs.
Dropped 12710 SNPs with duplicated rs numbers.
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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1346 (0.0083)
Lambda GC: 1.5118
Mean Chi^2: 1.9751
Intercept: 1.1288 (0.0184)
Ratio: 0.132 (0.0189)
Analysis finished at Mon Nov 25 16:46:36 2019
Total time elapsed: 2.0m:19.01s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.3208,
    "mean_EFFECT": 0.0001,
    "n": 314921,
    "n_snps": 13585297,
    "n_clumped_hits": 249,
    "n_p_sig": 54141,
    "n_mono": 0,
    "n_ns": 1251738,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 568980,
    "n_est": 316132.6853,
    "ratio_se_n": 1.0019,
    "mean_diff": -0.0001,
    "ratio_diff": 79.783,
    "sd_y_est1": 4.0346,
    "sd_y_est2": 4.0424,
    "r2_sum1": 0.9859,
    "r2_sum2": 0.0606,
    "r2_sum3": 0.0603,
    "r2_sum4": 0.0596,
    "ldsc_nsnp_merge_refpanel_ld": 1283502,
    "ldsc_nsnp_merge_regression_ld": 1283502,
    "ldsc_observed_scale_h2_beta": 0.1346,
    "ldsc_observed_scale_h2_se": 0.0083,
    "ldsc_intercept_beta": 1.1288,
    "ldsc_intercept_se": 0.0184,
    "ldsc_lambda_gc": 1.5118,
    "ldsc_mean_chisq": 1.9751,
    "ldsc_ratio": 0.1321
}

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 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 1.000000 3 94 0 13573251 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 100 0 57080 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 342 0 33334 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.051281e+00 6.184965e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.902516e+07 5.591503e+07 3.02000e+02 3.293038e+07 7.013894e+07 1.148598e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 1.388000e-04 6.277540e-02 -1.28390e+00 -1.888800e-02 4.240000e-05 1.897300e-02 9.304400e-01 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 4.271130e-02 4.119890e-02 8.34810e-03 1.216200e-02 2.241000e-02 6.137600e-02 2.080000e-01 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.532425e-01 3.026863e-01 0.00000e+00 1.792999e-01 4.382501e-01 7.158796e-01 1.000000e+00 ▇▆▆▅▅
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.532420e-01 3.026866e-01 0.00000e+00 1.792976e-01 4.382481e-01 7.158806e-01 9.999998e-01 ▇▆▆▅▅
numeric AF 0 1.000000 NA NA NA NA NA 1.908201e-01 2.544081e-01 1.00000e-03 7.433700e-03 6.004400e-02 2.953300e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 568980 0.958118 NA NA NA NA NA 1.963466e-01 2.471053e-01 0.00000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.000000 NA NA NA NA NA 3.149210e+05 0.000000e+00 3.14921e+05 3.149210e+05 3.149210e+05 3.149210e+05 3.149210e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0046493 0.017804 0.7939808 0.7939861 0.1105500 0.1894970 314921
1 693731 rs12238997 A G 0.0018880 0.016819 0.9106200 0.9106220 0.1158600 0.1417730 314921
1 707522 rs371890604 G C 0.0087993 0.018924 0.6419497 0.6419451 0.0972210 0.1293930 314921
1 717587 rs144155419 G A 0.0512420 0.045063 0.2555001 0.2554885 0.0157110 0.0045926 314921
1 723329 rs189787166 A T -0.1231000 0.133190 0.3553702 0.3553595 0.0017318 0.0003994 314921
1 730087 rs148120343 T C 0.0037888 0.023430 0.8715299 0.8715364 0.0564790 0.0127796 314921
1 731718 rs142557973 T C 0.0058391 0.015954 0.7143598 0.7143681 0.1217400 0.1543530 314921
1 732032 rs61770163 A C 0.0111270 0.017026 0.5134203 0.5134147 0.1210900 0.1555510 314921
1 734349 rs141242758 T C 0.0057539 0.015962 0.7185004 0.7184920 0.1209700 0.1525560 314921
1 740284 rs61770167 C T -0.0474010 0.073187 0.5172006 0.5171986 0.0057554 0.0023962 314921
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0023032 0.0184220 0.9005099 0.9005042 0.056102 0.0309934 314921
23 154923374 rs111332691 T A 0.0222950 0.0201580 0.2687200 0.2687211 0.045013 0.0116556 314921
23 154925045 rs509981 C T 0.0081681 0.0097336 0.4013803 0.4013765 0.245720 0.3634440 314921
23 154925895 rs538470 C T 0.0074794 0.0099572 0.4525598 0.4525594 0.242010 0.3634440 314921
23 154927581 rs644138 G A 0.0064497 0.0091548 0.4811195 0.4811117 0.302210 0.4635760 314921
23 154929412 rs557132 C T 0.0076550 0.0097365 0.4317397 0.4317405 0.245570 0.3568210 314921
23 154929637 rs35185538 CT C 0.0010409 0.0101610 0.9184100 0.9184069 0.229950 0.3011920 314921
23 154929952 rs4012982 CAA C 0.0058786 0.0102400 0.5659004 0.5659123 0.239500 0.3165560 314921
23 154930230 rs781880 A G 0.0069625 0.0097354 0.4744998 0.4745018 0.245950 0.3618540 314921
23 154930487 rs781879 T A 0.0322110 0.0334570 0.3356704 0.3356689 0.019469 0.1263580 314921

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11055  ES:SE:LP:AF:SS:ID   0.0046493:0.017804:0.10019:0.11055:314921:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11586  ES:SE:LP:AF:SS:ID   0.001888:0.016819:0.0406628:0.11586:314921:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097221 ES:SE:LP:AF:SS:ID   0.0087993:0.018924:0.192499:0.097221:314921:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015711 ES:SE:LP:AF:SS:ID   0.051242:0.045063:0.592609:0.015711:314921:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017318    ES:SE:LP:AF:SS:ID   -0.1231:0.13319:0.449319:0.0017318:314921:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056479 ES:SE:LP:AF:SS:ID   0.0037888:0.02343:0.0597177:0.056479:314921:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12174  ES:SE:LP:AF:SS:ID   0.0058391:0.015954:0.146083:0.12174:314921:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12109  ES:SE:LP:AF:SS:ID   0.011127:0.017026:0.289527:0.12109:314921:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12097  ES:SE:LP:AF:SS:ID   0.0057539:0.015962:0.143573:0.12097:314921:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0057554    ES:SE:LP:AF:SS:ID   -0.047401:0.073187:0.286341:0.0057554:314921:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018557    ES:SE:LP:AF:SS:ID   0.047135:0.13895:0.13405:0.0018557:314921:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86972  ES:SE:LP:AF:SS:ID   -0.013436:0.015736:0.405398:0.86972:314921:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015197    ES:SE:LP:AF:SS:ID   -0.26396:0.14299:1.18782:0.0015197:314921:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12294  ES:SE:LP:AF:SS:ID   0.0046715:0.015586:0.116691:0.12294:314921:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14276  ES:SE:LP:AF:SS:ID   0.0043412:0.015402:0.108992:0.14276:314921:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12305  ES:SE:LP:AF:SS:ID   0.0051154:0.015564:0.129356:0.12305:314921:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87094  ES:SE:LP:AF:SS:ID   -0.0075361:0.01517:0.208057:0.87094:314921:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87547  ES:SE:LP:AF:SS:ID   -0.0054458:0.015418:0.140303:0.87547:314921:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12862  ES:SE:LP:AF:SS:ID   0.006676:0.015207:0.180029:0.12862:314921:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036323 ES:SE:LP:AF:SS:ID   -0.015657:0.027599:0.243744:0.036323:314921:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87052  ES:SE:LP:AF:SS:ID   -0.0072757:0.015154:0.199874:0.87052:314921:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87063  ES:SE:LP:AF:SS:ID   -0.006645:0.015162:0.17968:0.87063:314921:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87052  ES:SE:LP:AF:SS:ID   -0.0071358:0.015154:0.195377:0.87052:314921:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050401    ES:SE:LP:AF:SS:ID   0.10042:0.077727:0.706947:0.0050401:314921:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050067    ES:SE:LP:AF:SS:ID   0.10133:0.077937:0.713207:0.0050067:314921:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0055143    ES:SE:LP:AF:SS:ID   0.11787:0.075816:0.920783:0.0055143:314921:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87061  ES:SE:LP:AF:SS:ID   -0.0066036:0.015128:0.178834:0.87061:314921:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12595  ES:SE:LP:AF:SS:ID   0.0081738:0.015434:0.22447:0.12595:314921:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87018  ES:SE:LP:AF:SS:ID   -0.0065579:0.015092:0.177891:0.87018:314921:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   -0.0061987:0.015079:0.166847:0.86946:314921:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87033  ES:SE:LP:AF:SS:ID   -0.0063104:0.015105:0.169976:0.87033:314921:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87034  ES:SE:LP:AF:SS:ID   -0.0063145:0.015106:0.170092:0.87034:314921:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87035  ES:SE:LP:AF:SS:ID   -0.006402:0.015107:0.172812:0.87035:314921:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87079  ES:SE:LP:AF:SS:ID   -0.0068598:0.015145:0.186693:0.87079:314921:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098818 ES:SE:LP:AF:SS:ID   -0.0027376:0.017601:0.0572976:0.098818:314921:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0063971    ES:SE:LP:AF:SS:ID   0.089679:0.068509:0.720037:0.0063971:314921:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87464  ES:SE:LP:AF:SS:ID   -0.0068739:0.015367:0.183997:0.87464:314921:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86407  ES:SE:LP:AF:SS:ID   -0.0069807:0.015074:0.191586:0.86407:314921:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   -0.0074065:0.015217:0.203107:0.86946:314921:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86641  ES:SE:LP:AF:SS:ID   -0.0037566:0.01522:0.0941771:0.86641:314921:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098816 ES:SE:LP:AF:SS:ID   0.0081233:0.018214:0.183354:0.098816:314921:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0069778:0.015393:0.186873:0.87158:314921:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0069767:0.015393:0.18684:0.87158:314921:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0069994:0.015393:0.187541:0.87158:314921:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87194  ES:SE:LP:AF:SS:ID   -0.0066021:0.015401:0.175113:0.87194:314921:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12557  ES:SE:LP:AF:SS:ID   0.006275:0.015413:0.165001:0.12557:314921:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10539  ES:SE:LP:AF:SS:ID   -0.0037478:0.016788:0.0844155:0.10539:314921:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85541  ES:SE:LP:AF:SS:ID   -0.007138:0.015067:0.196761:0.85541:314921:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016498    ES:SE:LP:AF:SS:ID   -0.11046:0.13356:0.389095:0.0016498:314921:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83825  ES:SE:LP:AF:SS:ID   -0.00071726:0.014824:0.0170914:0.83825:314921:rs376645387