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-20114_101/ukb-d-20114_101.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-20114_101/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 15:00:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20114_101/ukb-d-20114_101.vcf.gz ...
Read summary statistics for 10051535 SNPs.
Dropped 7768 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, 1278098 SNPs remain.
After merging with regression SNP LD, 1278098 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.6206 (0.2405)
Lambda GC: 1.0115
Mean Chi^2: 1.0091
Intercept: 0.987 (0.0058)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 15:01:51 2019
Total time elapsed: 1.0m:41.38s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9417,
    "inflation_factor": 1.008,
    "mean_EFFECT": -0.0001,
    "n": 1807,
    "n_snps": 10051535,
    "n_clumped_hits": 0,
    "n_p_sig": 4,
    "n_mono": 0,
    "n_ns": 1085505,
    "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": 198700,
    "n_est": 1817.7604,
    "ratio_se_n": 1.003,
    "mean_diff": -0.0001,
    "ratio_diff": 26.5253,
    "sd_y_est1": 0.3687,
    "sd_y_est2": 0.3698,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1278098,
    "ldsc_nsnp_merge_regression_ld": 1278098,
    "ldsc_observed_scale_h2_beta": 0.6206,
    "ldsc_observed_scale_h2_se": 0.2405,
    "ldsc_intercept_beta": 0.987,
    "ldsc_intercept_se": 0.0058,
    "ldsc_lambda_gc": 1.0115,
    "ldsc_mean_chisq": 1.0091,
    "ldsc_ratio": -1.4286
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 10044323 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 48297 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30200 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.079061e+00 6.178435e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.876203e+07 5.608820e+07 302.0000000 3.249198e+07 6.966690e+07 1.147406e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -7.990000e-05 2.990660e-02 -0.4297740 -1.350370e-02 2.091000e-04 1.392840e-02 3.724970e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.553450e-02 1.567820e-02 0.0099117 1.352880e-02 1.847110e-02 3.306180e-02 9.682800e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.989252e-01 2.886773e-01 0.0000000 2.487156e-01 4.982898e-01 7.488055e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.988355e-01 2.887311e-01 0.0000000 2.485609e-01 4.982016e-01 7.487680e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.533836e-01 2.629531e-01 0.0079267 3.764550e-02 1.476370e-01 4.044380e-01 9.920730e-01 ▇▂▂▁▁
numeric AF_reference 198700 0.9802319 NA NA NA NA NA 2.530218e-01 2.537830e-01 0.0000000 4.153350e-02 1.635380e-01 4.005590e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.807000e+03 0.000000e+00 1807.0000000 1.807000e+03 1.807000e+03 1.807000e+03 1.807000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0102528 0.0215048 0.6335881 0.6335274 0.1135810 0.1894970 1807
1 693731 rs12238997 A G 0.0117896 0.0197225 0.5500675 0.5499907 0.1220470 0.1417730 1807
1 707522 rs371890604 G C 0.0038060 0.0218006 0.8614290 0.8614089 0.1041030 0.1293930 1807
1 717587 rs144155419 G A 0.0411183 0.0540138 0.4466065 0.4465045 0.0161106 0.0045926 1807
1 730087 rs148120343 T C 0.0125089 0.0273094 0.6469772 0.6469210 0.0588615 0.0127796 1807
1 731718 rs142557973 T C 0.0088158 0.0188368 0.6398335 0.6397778 0.1271820 0.1543530 1807
1 732032 rs61770163 A C 0.0075827 0.0200200 0.7049154 0.7048700 0.1273490 0.1555510 1807
1 734349 rs141242758 T C 0.0087383 0.0188245 0.6425619 0.6425046 0.1266450 0.1525560 1807
1 749963 rs529266287 T TAA -0.0065033 0.0185010 0.7252488 0.7252068 0.8643410 0.7641770 1807
1 751343 rs28544273 T A 0.0099197 0.0183191 0.5882338 0.5881672 0.1300140 0.2426120 1807
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0035373 0.0213000 0.8681211 0.8681023 0.0618792 0.0309934 1807
23 154923374 rs111332691 T A 0.0137930 0.0244001 0.5719525 0.5718802 0.0456558 0.0116556 1807
23 154925045 rs509981 C T 0.0006674 0.0118355 0.9550370 0.9550310 0.2487560 0.3634440 1807
23 154925895 rs538470 C T -0.0028002 0.0121143 0.8172230 0.8171977 0.2440520 0.3634440 1807
23 154927581 rs644138 G A -0.0003281 0.0110217 0.9762551 0.9762519 0.3109120 0.4635760 1807
23 154929412 rs557132 C T 0.0003647 0.0118503 0.9754491 0.9754457 0.2482760 0.3568210 1807
23 154929637 rs35185538 CT C -0.0042643 0.0123035 0.7289387 0.7288981 0.2344150 0.3011920 1807
23 154929952 rs4012982 CAA C 0.0044850 0.0124338 0.7183565 0.7183148 0.2417540 0.3165560 1807
23 154930230 rs781880 A G -0.0000248 0.0118531 0.9983330 0.9983327 0.2478940 0.3618540 1807
23 154930487 rs781879 T A 0.0379479 0.0389307 0.3298139 0.3296817 0.0221416 0.1263580 1807

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.113581 ES:SE:LP:AF:SS:ID   0.0102528:0.0215048:0.198193:0.113581:1807:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.122047 ES:SE:LP:AF:SS:ID   0.0117896:0.0197225:0.259584:0.122047:1807:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.104103 ES:SE:LP:AF:SS:ID   0.00380597:0.0218006:0.0647805:0.104103:1807:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0161106    ES:SE:LP:AF:SS:ID   0.0411183:0.0540138:0.350075:0.0161106:1807:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0588615    ES:SE:LP:AF:SS:ID   0.0125089:0.0273094:0.189111:0.0588615:1807:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.127182 ES:SE:LP:AF:SS:ID   0.0088158:0.0188368:0.193933:0.127182:1807:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.127349 ES:SE:LP:AF:SS:ID   0.00758267:0.02002:0.151863:0.127349:1807:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.126645 ES:SE:LP:AF:SS:ID   0.00873833:0.0188245:0.192085:0.126645:1807:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.864341 ES:SE:LP:AF:SS:ID   -0.00650326:0.018501:0.139513:0.864341:1807:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.130014 ES:SE:LP:AF:SS:ID   0.00991968:0.0183191:0.23045:0.130014:1807:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.152136 ES:SE:LP:AF:SS:ID   0.0188888:0.0180878:0.527978:0.152136:1807:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.13006  ES:SE:LP:AF:SS:ID   0.0101365:0.0182944:0.236874:0.13006:1807:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.864878 ES:SE:LP:AF:SS:ID   -0.00869762:0.0178692:0.203076:0.864878:1807:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.868676 ES:SE:LP:AF:SS:ID   -0.0113559:0.0181793:0.273864:0.868676:1807:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.134682 ES:SE:LP:AF:SS:ID   0.00799936:0.0178885:0.183891:0.134682:1807:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0359712    ES:SE:LP:AF:SS:ID   -0.0476784:0.0335404:0.808717:0.0359712:1807:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.864781 ES:SE:LP:AF:SS:ID   -0.00832662:0.0178725:0.192904:0.864781:1807:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.864769 ES:SE:LP:AF:SS:ID   -0.00834745:0.017872:0.193475:0.864769:1807:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.864762 ES:SE:LP:AF:SS:ID   -0.00827907:0.0178719:0.191624:0.864762:1807:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.864475 ES:SE:LP:AF:SS:ID   -0.00698606:0.0178124:0.158043:0.864475:1807:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.131945 ES:SE:LP:AF:SS:ID   0.00853464:0.0181384:0.195156:0.131945:1807:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.864139 ES:SE:LP:AF:SS:ID   -0.00701956:0.0177545:0.159506:0.864139:1807:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.863289 ES:SE:LP:AF:SS:ID   -0.00528074:0.0177368:0.115802:0.863289:1807:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.86431  ES:SE:LP:AF:SS:ID   -0.00669695:0.0177963:0.150746:0.86431:1807:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.864313 ES:SE:LP:AF:SS:ID   -0.00669747:0.0177972:0.150751:0.864313:1807:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.86432  ES:SE:LP:AF:SS:ID   -0.00669331:0.0177976:0.15064:0.86432:1807:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.864544 ES:SE:LP:AF:SS:ID   -0.00659638:0.0178282:0.147868:0.864544:1807:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.103879 ES:SE:LP:AF:SS:ID   -0.00385941:0.0206545:0.0696649:0.103879:1807:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.868299 ES:SE:LP:AF:SS:ID   -0.00863923:0.0181196:0.198205:0.868299:1807:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.857162 ES:SE:LP:AF:SS:ID   -0.00476051:0.0177513:0.103147:0.857162:1807:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.862577 ES:SE:LP:AF:SS:ID   -0.00602412:0.0179212:0.13265:0.862577:1807:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.860971 ES:SE:LP:AF:SS:ID   -0.00872506:0.0179108:0.203273:0.860971:1807:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.102196 ES:SE:LP:AF:SS:ID   0.0108572:0.0218121:0.208509:0.102196:1807:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.866022 ES:SE:LP:AF:SS:ID   -0.00603466:0.0181922:0.130685:0.866022:1807:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.866021 ES:SE:LP:AF:SS:ID   -0.00603633:0.018192:0.130727:0.866021:1807:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.866017 ES:SE:LP:AF:SS:ID   -0.00604107:0.0181921:0.130842:0.866017:1807:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.8662   ES:SE:LP:AF:SS:ID   -0.00570427:0.01819:0.122705:0.8662:1807:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.132186 ES:SE:LP:AF:SS:ID   0.00617875:0.0181337:0.134692:0.132186:1807:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.11062  ES:SE:LP:AF:SS:ID   0.00580615:0.0197333:0.114291:0.11062:1807:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.848718 ES:SE:LP:AF:SS:ID   -0.00760658:0.0178034:0.174414:0.848718:1807:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.829283 ES:SE:LP:AF:SS:ID   0.000264276:0.0178916:0.00514768:0.829283:1807:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.748728 ES:SE:LP:AF:SS:ID   0.00655093:0.014158:0.191361:0.748728:1807:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.114001 ES:SE:LP:AF:SS:ID   -0.0224223:0.0195685:0.59857:0.114001:1807:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.135645 ES:SE:LP:AF:SS:ID   0.00508301:0.0178639:0.110122:0.135645:1807:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.134736 ES:SE:LP:AF:SS:ID   0.00805151:0.017882:0.185367:0.134736:1807:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.113462 ES:SE:LP:AF:SS:ID   -0.0216675:0.0196781:0.567024:0.113462:1807:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.112807 ES:SE:LP:AF:SS:ID   -0.0210438:0.0198045:0.540433:0.112807:1807:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.826028 ES:SE:LP:AF:SS:ID   -0.00748328:0.0176125:0.173296:0.826028:1807:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.863718 ES:SE:LP:AF:SS:ID   -0.00726002:0.0178115:0.165189:0.863718:1807:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.135115 ES:SE:LP:AF:SS:ID   0.00591374:0.0178545:0.130464:0.135115:1807:rs59066358