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-22601_11353225/ukb-d-22601_11353225.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-22601_11353225/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 15:49:58 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_11353225/ukb-d-22601_11353225.vcf.gz ...
Read summary statistics for 9528836 SNPs.
Dropped 7090 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, 1273548 SNPs remain.
After merging with regression SNP LD, 1273548 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0106 (0.0046)
Lambda GC: 0.9923
Mean Chi^2: 0.9914
Intercept: 1.0103 (0.0062)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 15:51:22 2019
Total time elapsed: 1.0m:23.7s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.939,
    "inflation_factor": 0.9978,
    "mean_EFFECT": -5.5942e-06,
    "n": 89866,
    "n_snps": 9528836,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1052632,
    "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": 190538,
    "n_est": 89846.4626,
    "ratio_se_n": 0.9999,
    "mean_diff": -0,
    "ratio_diff": 56.677,
    "sd_y_est1": 0.1128,
    "sd_y_est2": 0.1128,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1273548,
    "ldsc_nsnp_merge_regression_ld": 1273548,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0103,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 0.9923,
    "ldsc_mean_chisq": 0.9914,
    "ldsc_ratio": -1.1977
}

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 9522283 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 46496 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29468 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.080394e+00 6.174411e+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 7.871028e+07 5.611348e+07 3.02000e+02 3.241640e+07 6.958210e+07 1.147301e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.600000e-06 1.157700e-03 -1.04379e-02 -5.741000e-04 -1.130000e-05 5.562000e-04 1.191250e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.012600e-03 5.577000e-04 4.40100e-04 5.810000e-04 7.671000e-04 1.288300e-03 3.145300e-03 ▇▂▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.002436e-01 2.885835e-01 1.00000e-07 2.500858e-01 5.004815e-01 7.501394e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.002419e-01 2.885846e-01 1.00000e-07 2.500830e-01 5.004793e-01 7.501386e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.658279e-01 2.627728e-01 1.08507e-02 4.749700e-02 1.654530e-01 4.224872e-01 9.891490e-01 ▇▂▂▁▁
numeric AF_reference 190538 0.9800041 NA NA NA NA NA 2.652157e-01 2.535666e-01 0.00000e+00 5.431310e-02 1.801120e-01 4.173320e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 8.986600e+04 0.000000e+00 8.98660e+04 8.986600e+04 8.986600e+04 8.986600e+04 8.986600e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0009964 0.0009297 0.2838102 0.2838075 0.1114870 0.1894970 89866
1 693731 rs12238997 A G -0.0011405 0.0008806 0.1952949 0.1952910 0.1164980 0.1417730 89866
1 707522 rs371890604 G C -0.0020877 0.0009900 0.0349687 0.0349659 0.0978285 0.1293930 89866
1 717587 rs144155419 G A 0.0037689 0.0023582 0.1099981 0.1099952 0.0158090 0.0045926 89866
1 730087 rs148120343 T C -0.0018782 0.0012211 0.1240249 0.1240212 0.0569661 0.0127796 89866
1 731718 rs142557973 T C -0.0011472 0.0008357 0.1698349 0.1698298 0.1223780 0.1543530 89866
1 732032 rs61770163 A C -0.0013825 0.0008909 0.1207299 0.1207266 0.1220530 0.1555510 89866
1 734349 rs141242758 T C -0.0011386 0.0008363 0.1733521 0.1733500 0.1216170 0.1525560 89866
1 749963 rs529266287 T TAA 0.0009337 0.0008228 0.2564519 0.2564485 0.8689590 0.7641770 89866
1 751343 rs28544273 T A -0.0011895 0.0008157 0.1447541 0.1447514 0.1236780 0.2426120 89866
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0019609 0.0009781 0.0449925 0.0449900 0.0553576 0.0309934 89866
23 154923374 rs111332691 T A 0.0019306 0.0010649 0.0698345 0.0698303 0.0449113 0.0116556 89866
23 154925045 rs509981 C T -0.0003510 0.0005136 0.4943095 0.4943080 0.2444280 0.3634440 89866
23 154925895 rs538470 C T -0.0003714 0.0005251 0.4794419 0.4794396 0.2408760 0.3634440 89866
23 154927581 rs644138 G A 0.0001495 0.0004831 0.7568887 0.7568879 0.3001910 0.4635760 89866
23 154929412 rs557132 C T -0.0003450 0.0005137 0.5018975 0.5018964 0.2442750 0.3568210 89866
23 154929637 rs35185538 CT C -0.0000862 0.0005364 0.8723129 0.8723131 0.2286930 0.3011920 89866
23 154929952 rs4012982 CAA C -0.0004563 0.0005406 0.3986814 0.3986784 0.2381980 0.3165560 89866
23 154930230 rs781880 A G -0.0003523 0.0005136 0.4927345 0.4927331 0.2447120 0.3618540 89866
23 154930487 rs781879 T A -0.0009752 0.0017421 0.5756175 0.5756155 0.0196791 0.1263580 89866

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   -0.000996423:0.000929668:0.546972:0.111487:89866:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116498 ES:SE:LP:AF:SS:ID   -0.00114051:0.000880645:0.709309:0.116498:89866:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978285    ES:SE:LP:AF:SS:ID   -0.00208771:0.000990021:1.45632:0.0978285:89866:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015809 ES:SE:LP:AF:SS:ID   0.00376891:0.0023582:0.958615:0.015809:89866:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569661    ES:SE:LP:AF:SS:ID   -0.00187825:0.00122114:0.906491:0.0569661:89866:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122378 ES:SE:LP:AF:SS:ID   -0.00114719:0.000835687:0.769973:0.122378:89866:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122053 ES:SE:LP:AF:SS:ID   -0.00138249:0.000890934:0.918185:0.122053:89866:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121617 ES:SE:LP:AF:SS:ID   -0.00113865:0.000836309:0.761071:0.121617:89866:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868959 ES:SE:LP:AF:SS:ID   0.00093374:0.000822805:0.590994:0.868959:89866:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123678 ES:SE:LP:AF:SS:ID   -0.00118954:0.00081569:0.839369:0.123678:89866:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143191 ES:SE:LP:AF:SS:ID   -0.00121111:0.000807578:0.873865:0.143191:89866:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123813 ES:SE:LP:AF:SS:ID   -0.00118332:0.000814513:0.834797:0.123813:89866:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869927 ES:SE:LP:AF:SS:ID   0.000935782:0.00079363:0.622776:0.869927:89866:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87461  ES:SE:LP:AF:SS:ID   0.00112101:0.000806566:0.783633:0.87461:89866:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12951  ES:SE:LP:AF:SS:ID   -0.000995888:0.000796055:0.675868:0.12951:89866:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0357365    ES:SE:LP:AF:SS:ID   -0.000317963:0.0014564:0.0824:0.0357365:89866:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869574 ES:SE:LP:AF:SS:ID   0.000919438:0.000792931:0.608645:0.869574:89866:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869652 ES:SE:LP:AF:SS:ID   0.000909002:0.000793284:0.598856:0.869652:89866:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86957  ES:SE:LP:AF:SS:ID   0.000920303:0.000792899:0.609462:0.86957:89866:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.869566 ES:SE:LP:AF:SS:ID   0.000960297:0.000791327:0.647951:0.869566:89866:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126879 ES:SE:LP:AF:SS:ID   -0.00117331:0.000807818:0.834515:0.126879:89866:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869094 ES:SE:LP:AF:SS:ID   0.00100981:0.000789274:0.697334:0.869094:89866:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868498 ES:SE:LP:AF:SS:ID   0.000987699:0.000788792:0.676723:0.868498:89866:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869245 ES:SE:LP:AF:SS:ID   0.000974283:0.000789996:0.662589:0.869245:89866:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869251 ES:SE:LP:AF:SS:ID   0.000974853:0.000790049:0.663064:0.869251:89866:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869252 ES:SE:LP:AF:SS:ID   0.000975317:0.000790054:0.663496:0.869252:89866:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869724 ES:SE:LP:AF:SS:ID   0.000957925:0.000792156:0.644807:0.869724:89866:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991203    ES:SE:LP:AF:SS:ID   -0.00156171:0.000922194:1.04398:0.0991203:89866:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873732 ES:SE:LP:AF:SS:ID   0.00106883:0.000803922:0.735938:0.873732:89866:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863116 ES:SE:LP:AF:SS:ID   0.00102519:0.000788525:0.713187:0.863116:89866:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868511 ES:SE:LP:AF:SS:ID   0.00117347:0.0007964:0.851925:0.868511:89866:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86539  ES:SE:LP:AF:SS:ID   0.00129663:0.000796515:0.984829:0.86539:89866:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0994301    ES:SE:LP:AF:SS:ID   -0.000783273:0.000953839:0.385582:0.0994301:89866:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870696 ES:SE:LP:AF:SS:ID   0.00125718:0.000805679:0.925666:0.870696:89866:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870695 ES:SE:LP:AF:SS:ID   0.00125719:0.000805679:0.925674:0.870695:89866:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870693 ES:SE:LP:AF:SS:ID   0.00125733:0.000805681:0.925813:0.870693:89866:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871061 ES:SE:LP:AF:SS:ID   0.00121834:0.000806062:0.883817:0.871061:89866:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126484 ES:SE:LP:AF:SS:ID   -0.00115768:0.000806877:0.819997:0.126484:89866:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106022 ES:SE:LP:AF:SS:ID   -0.00195418:0.000877128:1.5869:0.106022:89866:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854451 ES:SE:LP:AF:SS:ID   0.0013457:0.000788332:1.05639:0.854451:89866:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839008 ES:SE:LP:AF:SS:ID   -0.000838429:0.000778797:0.55025:0.839008:89866:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.76317  ES:SE:LP:AF:SS:ID   -0.000163873:0.000626152:0.10043:0.76317:89866:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.10519  ES:SE:LP:AF:SS:ID   0.00164582:0.000862916:1.24804:0.10519:89866:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129876 ES:SE:LP:AF:SS:ID   -0.00123522:0.000795573:0.918952:0.129876:89866:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129602 ES:SE:LP:AF:SS:ID   -0.00123377:0.000794533:0.919128:0.129602:89866:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104469 ES:SE:LP:AF:SS:ID   0.00157956:0.000869572:1.15927:0.104469:89866:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.103468 ES:SE:LP:AF:SS:ID   0.00163172:0.000877117:1.20174:0.103468:89866:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.829371 ES:SE:LP:AF:SS:ID   0.00106417:0.000775526:0.769531:0.829371:89866:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.869112 ES:SE:LP:AF:SS:ID   0.00107994:0.000790702:0.764459:0.869112:89866:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129712 ES:SE:LP:AF:SS:ID   -0.00119412:0.000794078:0.877319:0.129712:89866:rs59066358