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-3446_3/ukb-d-3446_3.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-3446_3/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 16:49:59 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-3446_3/ukb-d-3446_3.vcf.gz ...
Read summary statistics for 10458915 SNPs.
Dropped 8327 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, 1280488 SNPs remain.
After merging with regression SNP LD, 1280488 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0222 (0.0147)
Lambda GC: 1.0216
Mean Chi^2: 1.015
Intercept: 1.0031 (0.0057)
Ratio: 0.2089 (0.3785)
Analysis finished at Mon Nov 25 16:51:44 2019
Total time elapsed: 1.0m:44.55s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9438,
    "inflation_factor": 1.0215,
    "mean_EFFECT": -2.5952e-06,
    "n": 27583,
    "n_snps": 10458915,
    "n_clumped_hits": 0,
    "n_p_sig": 2,
    "n_mono": 0,
    "n_ns": 1109536,
    "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": 205805,
    "n_est": 27672.2046,
    "ratio_se_n": 1.0016,
    "mean_diff": -6.2812e-06,
    "ratio_diff": 3.8915,
    "sd_y_est1": 0.247,
    "sd_y_est2": 0.2474,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1280488,
    "ldsc_nsnp_merge_regression_ld": 1280488,
    "ldsc_observed_scale_h2_beta": 0.0222,
    "ldsc_observed_scale_h2_se": 0.0147,
    "ldsc_intercept_beta": 1.0031,
    "ldsc_intercept_se": 0.0057,
    "ldsc_lambda_gc": 1.0216,
    "ldsc_mean_chisq": 1.015,
    "ldsc_ratio": 0.2067
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
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 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 94 0 10451152 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 49581 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30712 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.075965e+00 6.178127e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.878581e+07 5.605264e+07 3.02000e+02 3.255454e+07 6.972527e+07 1.147304e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.600000e-06 5.688200e-03 -5.34061e-02 -2.473000e-03 -2.140000e-05 2.430000e-03 6.210950e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 4.713800e-03 3.121700e-03 1.69180e-03 2.338000e-03 3.282200e-03 6.188100e-03 1.784200e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.966627e-01 2.893202e-01 0.00000e+00 2.454929e-01 4.954205e-01 7.468425e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.966569e-01 2.893236e-01 0.00000e+00 2.454833e-01 4.954144e-01 7.468406e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.443103e-01 2.626494e-01 6.21580e-03 3.129210e-02 1.345270e-01 3.908800e-01 9.937840e-01 ▇▂▂▁▁
numeric AF_reference 205805 0.9803225 NA NA NA NA NA 2.441679e-01 2.535877e-01 0.00000e+00 3.274760e-02 1.513580e-01 3.877800e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.758300e+04 0.000000e+00 2.75830e+04 2.758300e+04 2.758300e+04 2.758300e+04 2.758300e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0050884 0.0036888 0.1677799 0.1677689 0.1100050 0.1894970 27583
1 693731 rs12238997 A G 0.0008289 0.0034838 0.8119390 0.8119370 0.1148600 0.1417730 27583
1 707522 rs371890604 G C 0.0037411 0.0039396 0.3423103 0.3423021 0.0955608 0.1293930 27583
1 717587 rs144155419 G A -0.0035858 0.0092490 0.6982453 0.6982418 0.0159292 0.0045926 27583
1 730087 rs148120343 T C 0.0014488 0.0048339 0.7644023 0.7644001 0.0568384 0.0127796 27583
1 731718 rs142557973 T C 0.0018270 0.0032914 0.5788406 0.5788359 0.1214620 0.1543530 27583
1 732032 rs61770163 A C 0.0016389 0.0035210 0.6416069 0.6416038 0.1199310 0.1555510 27583
1 734349 rs141242758 T C 0.0017327 0.0032939 0.5988679 0.5988641 0.1206270 0.1525560 27583
1 749963 rs529266287 T TAA -0.0018448 0.0032603 0.5715063 0.5715010 0.8706360 0.7641770 27583
1 751343 rs28544273 T A 0.0021392 0.0032204 0.5065228 0.5065165 0.1225040 0.2426120 27583
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0028312 0.0037481 0.4500347 0.4500282 0.0555972 0.0309934 27583
23 154923374 rs111332691 T A 0.0012542 0.0042077 0.7656530 0.7656496 0.0431788 0.0116556 27583
23 154925045 rs509981 C T -0.0004899 0.0019743 0.8040201 0.8040180 0.2466770 0.3634440 27583
23 154925895 rs538470 C T -0.0008447 0.0020171 0.6753859 0.6753827 0.2435400 0.3634440 27583
23 154927581 rs644138 G A -0.0010424 0.0018580 0.5747765 0.5747743 0.3026300 0.4635760 27583
23 154929412 rs557132 C T -0.0004571 0.0019750 0.8169660 0.8169643 0.2464860 0.3568210 27583
23 154929637 rs35185538 CT C -0.0003044 0.0020600 0.8825359 0.8825351 0.2309790 0.3011920 27583
23 154929952 rs4012982 CAA C -0.0014789 0.0020749 0.4760011 0.4759943 0.2408190 0.3165560 27583
23 154930230 rs781880 A G -0.0006232 0.0019738 0.7522012 0.7521992 0.2471770 0.3618540 27583
23 154930487 rs781879 T A 0.0042084 0.0069711 0.5460495 0.5460447 0.0186709 0.1263580 27583

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110005 ES:SE:LP:AF:SS:ID   0.00508843:0.00368885:0.77526:0.110005:27583:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11486  ES:SE:LP:AF:SS:ID   0.000828891:0.00348379:0.0904766:0.11486:27583:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0955608    ES:SE:LP:AF:SS:ID   0.00374112:0.00393957:0.46558:0.0955608:27583:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0159292    ES:SE:LP:AF:SS:ID   -0.00358579:0.009249:0.155992:0.0159292:27583:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0568384    ES:SE:LP:AF:SS:ID   0.00144876:0.00483391:0.116678:0.0568384:27583:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121462 ES:SE:LP:AF:SS:ID   0.00182701:0.0032914:0.237441:0.121462:27583:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.119931 ES:SE:LP:AF:SS:ID   0.00163889:0.00352103:0.192731:0.119931:27583:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120627 ES:SE:LP:AF:SS:ID   0.00173269:0.00329387:0.222669:0.120627:27583:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.870636 ES:SE:LP:AF:SS:ID   -0.00184481:0.00326029:0.242979:0.870636:27583:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.122504 ES:SE:LP:AF:SS:ID   0.00213924:0.00322043:0.295401:0.122504:27583:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143502 ES:SE:LP:AF:SS:ID   0.00222246:0.00316816:0.316055:0.143502:27583:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12255  ES:SE:LP:AF:SS:ID   0.00219988:0.00321692:0.306204:0.12255:27583:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.871449 ES:SE:LP:AF:SS:ID   -0.0036847:0.00313656:0.619606:0.871449:27583:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87633  ES:SE:LP:AF:SS:ID   -0.00213449:0.00318783:0.298316:0.87633:27583:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128345 ES:SE:LP:AF:SS:ID   0.0034647:0.00313964:0.568948:0.128345:27583:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0365805    ES:SE:LP:AF:SS:ID   0.00750724:0.00569609:0.726938:0.0365805:27583:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.871139 ES:SE:LP:AF:SS:ID   -0.00380208:0.00313227:0.648167:0.871139:27583:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.871234 ES:SE:LP:AF:SS:ID   -0.00359801:0.00313318:0.600619:0.871234:27583:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.871125 ES:SE:LP:AF:SS:ID   -0.00380452:0.00313202:0.648815:0.871125:27583:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.871121 ES:SE:LP:AF:SS:ID   -0.00376842:0.00312798:0.641471:0.871121:27583:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125557 ES:SE:LP:AF:SS:ID   0.00328403:0.00319133:0.517889:0.125557:27583:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870699 ES:SE:LP:AF:SS:ID   -0.00377261:0.00312123:0.644374:0.870699:27583:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.870017 ES:SE:LP:AF:SS:ID   -0.00375638:0.00311731:0.641663:0.870017:27583:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870903 ES:SE:LP:AF:SS:ID   -0.00388163:0.00312416:0.669426:0.870903:27583:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870912 ES:SE:LP:AF:SS:ID   -0.0038811:0.00312441:0.669225:0.870912:27583:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870912 ES:SE:LP:AF:SS:ID   -0.00388023:0.00312437:0.669029:0.870912:27583:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.871332 ES:SE:LP:AF:SS:ID   -0.00373227:0.00313189:0.631916:0.871332:27583:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0978378    ES:SE:LP:AF:SS:ID   0.00267274:0.00365043:0.333416:0.0978378:27583:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00629586   ES:SE:LP:AF:SS:ID   0.0146443:0.0143934:0.510103:0.00629586:27583:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.875526 ES:SE:LP:AF:SS:ID   -0.00259064:0.00317941:0.381758:0.875526:27583:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864818 ES:SE:LP:AF:SS:ID   -0.00407509:0.0031174:0.718619:0.864818:27583:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.870067 ES:SE:LP:AF:SS:ID   -0.00377294:0.00314907:0.636608:0.870067:27583:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866746 ES:SE:LP:AF:SS:ID   -0.00354482:0.00314803:0.584764:0.866746:27583:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0982305    ES:SE:LP:AF:SS:ID   0.0022187:0.00376442:0.255232:0.0982305:27583:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.872339 ES:SE:LP:AF:SS:ID   -0.00220291:0.00318593:0.310435:0.872339:27583:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.872339 ES:SE:LP:AF:SS:ID   -0.00220287:0.00318593:0.310428:0.872339:27583:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.872354 ES:SE:LP:AF:SS:ID   -0.00221652:0.00318659:0.31274:0.872354:27583:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87266  ES:SE:LP:AF:SS:ID   -0.00211145:0.00318819:0.294306:0.87266:27583:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125094 ES:SE:LP:AF:SS:ID   0.00303535:0.0031857:0.467632:0.125094:27583:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.104772 ES:SE:LP:AF:SS:ID   0.0032789:0.00347593:0.461517:0.104772:27583:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855328 ES:SE:LP:AF:SS:ID   -0.00363605:0.00311494:0.614211:0.855328:27583:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.835305 ES:SE:LP:AF:SS:ID   -0.00443637:0.00305818:0.833014:0.835305:27583:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.761034 ES:SE:LP:AF:SS:ID   -0.00422975:0.00247222:1.05994:0.761034:27583:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.108726 ES:SE:LP:AF:SS:ID   0.0033263:0.00338314:0.487425:0.108726:27583:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00755971   ES:SE:LP:AF:SS:ID   0.0207003:0.0128644:0.968176:0.00755971:27583:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.128631 ES:SE:LP:AF:SS:ID   0.00372395:0.00314088:0.627502:0.128631:27583:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.128284 ES:SE:LP:AF:SS:ID   0.00359816:0.00313732:0.599573:0.128284:27583:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.108004 ES:SE:LP:AF:SS:ID   0.00340327:0.00340764:0.497655:0.108004:27583:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00901443   ES:SE:LP:AF:SS:ID   -0.0116858:0.012168:0.472526:0.00901443:27583:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00756448   ES:SE:LP:AF:SS:ID   0.018506:0.0129221:0.817814:0.00756448:27583:rs112563271