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-4012_irnt/ukb-d-4012_irnt.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-4012_irnt/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 16:30:23 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-4012_irnt/ukb-d-4012_irnt.vcf.gz ...
Read summary statistics for 13449538 SNPs.
Dropped 12512 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, 1283476 SNPs remain.
After merging with regression SNP LD, 1283476 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0436 (0.0637)
Lambda GC: 1.0042
Mean Chi^2: 1.0033
Intercept: 0.9974 (0.0061)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:32:39 2019
Total time elapsed: 2.0m:15.85s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9518,
    "inflation_factor": 0.9957,
    "mean_EFFECT": 0.0001,
    "n": 6795,
    "n_snps": 13449538,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1246661,
    "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": 537027,
    "n_est": 6850.2751,
    "ratio_se_n": 1.0041,
    "mean_diff": 0,
    "ratio_diff": 2.6339,
    "sd_y_est1": 0.8854,
    "sd_y_est2": 0.889,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283476,
    "ldsc_nsnp_merge_regression_ld": 1283476,
    "ldsc_observed_scale_h2_beta": 0.0436,
    "ldsc_observed_scale_h2_se": 0.0637,
    "ldsc_intercept_beta": 0.9974,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 1.0042,
    "ldsc_mean_chisq": 1.0033,
    "ldsc_ratio": -0.7879
}

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 1.000000 3 94 0 13437686 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 100 0 56799 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 342 0 33249 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.052828e+00 6.184630e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.900932e+07 5.591735e+07 302.0000000 3.290503e+07 7.011355e+07 1.148419e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 1.366000e-04 8.620760e-02 -1.1735100 -2.284550e-02 1.595000e-04 2.322040e-02 1.109120e+00 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 6.222070e-02 5.975180e-02 0.0125613 1.810420e-02 3.290790e-02 8.886830e-02 4.039600e-01 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 5.004600e-01 2.886196e-01 0.0000001 2.502183e-01 5.009184e-01 7.503968e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 5.004365e-01 2.886337e-01 0.0000001 2.501771e-01 5.008947e-01 7.503858e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA 1.926317e-01 2.548523e-01 0.0010002 7.900000e-03 6.231770e-02 2.989510e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 537027 0.960071 NA NA NA NA NA 1.977365e-01 2.474179e-01 0.0000000 5.990400e-03 8.626200e-02 3.109030e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.000000 NA NA NA NA NA 6.795000e+03 0.000000e+00 6795.0000000 6.795000e+03 6.795000e+03 6.795000e+03 6.795000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0272560 0.0266758 0.3069347 0.3068992 0.1094850 0.1894970 6795
1 693731 rs12238997 A G 0.0051459 0.0251078 0.8376170 0.8376107 0.1154870 0.1417730 6795
1 707522 rs371890604 G C -0.0182205 0.0282503 0.5189709 0.5189488 0.0973761 0.1293930 6795
1 717587 rs144155419 G A 0.0358168 0.0695267 0.6064640 0.6064470 0.0149444 0.0045926 6795
1 723329 rs189787166 A T -0.0096235 0.1968330 0.9610071 0.9610057 0.0017513 0.0003994 6795
1 730087 rs148120343 T C -0.0248379 0.0352104 0.4805770 0.4805528 0.0562810 0.0127796 6795
1 731718 rs142557973 T C 0.0059454 0.0238249 0.8029450 0.8029381 0.1208690 0.1543530 6795
1 732032 rs61770163 A C 0.0058400 0.0253955 0.8181300 0.8181228 0.1207520 0.1555510 6795
1 734349 rs141242758 T C 0.0072046 0.0238184 0.7622966 0.7622868 0.1203000 0.1525560 6795
1 740284 rs61770167 C T -0.1130700 0.1236710 0.3606002 0.3605694 0.0045478 0.0023962 6795
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0236915 0.0277541 0.3933453 0.3933147 0.0564510 0.0309934 6795
23 154923374 rs111332691 T A -0.0201988 0.0294991 0.4935407 0.4935169 0.0468727 0.0116556 6795
23 154925045 rs509981 C T 0.0001606 0.0151278 0.9915310 0.9915312 0.2314980 0.3634440 6795
23 154925895 rs538470 C T 0.0060114 0.0154592 0.6973969 0.6973842 0.2282080 0.3634440 6795
23 154927581 rs644138 G A -0.0049587 0.0141020 0.7251252 0.7251145 0.2883160 0.4635760 6795
23 154929412 rs557132 C T 0.0001552 0.0151287 0.9918170 0.9918167 0.2314830 0.3568210 6795
23 154929637 rs35185538 CT C -0.0015705 0.0158544 0.9210949 0.9210920 0.2163060 0.3011920 6795
23 154929952 rs4012982 CAA C 0.0022996 0.0159379 0.8852801 0.8852754 0.2242230 0.3165560 6795
23 154930230 rs781880 A G 0.0010909 0.0151349 0.9425420 0.9425395 0.2317170 0.3618540 6795
23 154930487 rs781879 T A 0.0263794 0.0536370 0.6228665 0.6228512 0.0180031 0.1263580 6795

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.109485 ES:SE:LP:AF:SS:ID   -0.027256:0.0266758:0.512954:0.109485:6795:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115487 ES:SE:LP:AF:SS:ID   0.00514586:0.0251078:0.0769545:0.115487:6795:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0973761    ES:SE:LP:AF:SS:ID   -0.0182205:0.0282503:0.284857:0.0973761:6795:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0149444    ES:SE:LP:AF:SS:ID   0.0358168:0.0695267:0.217195:0.0149444:6795:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00175129   ES:SE:LP:AF:SS:ID   -0.00962348:0.196833:0.0172734:0.00175129:6795:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056281 ES:SE:LP:AF:SS:ID   -0.0248379:0.0352104:0.318237:0.056281:6795:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.120869 ES:SE:LP:AF:SS:ID   0.00594542:0.0238249:0.0953142:0.120869:6795:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.120752 ES:SE:LP:AF:SS:ID   0.00583995:0.0253955:0.0871777:0.120752:6795:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.1203   ES:SE:LP:AF:SS:ID   0.00720457:0.0238184:0.117876:0.1203:6795:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00454775   ES:SE:LP:AF:SS:ID   -0.11307:0.123671:0.442974:0.00454775:6795:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00243028   ES:SE:LP:AF:SS:ID   0.141037:0.176598:0.37209:0.00243028:6795:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.870631 ES:SE:LP:AF:SS:ID   -0.00641158:0.02364:0.104449:0.870631:6795:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00164279   ES:SE:LP:AF:SS:ID   0.27373:0.203069:0.750278:0.00164279:6795:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.122187 ES:SE:LP:AF:SS:ID   0.00820718:0.0233925:0.139234:0.122187:6795:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142738 ES:SE:LP:AF:SS:ID   0.00477197:0.0229952:0.0779964:0.142738:6795:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.122291 ES:SE:LP:AF:SS:ID   0.008805:0.0233666:0.150999:0.122291:6795:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87132  ES:SE:LP:AF:SS:ID   -0.0134959:0.0226203:0.259025:0.87132:6795:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.876072 ES:SE:LP:AF:SS:ID   -0.0140063:0.0230744:0.264509:0.876072:6795:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128118 ES:SE:LP:AF:SS:ID   0.0105151:0.0227228:0.191414:0.128118:6795:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363503    ES:SE:LP:AF:SS:ID   -0.0379189:0.0411829:0.447068:0.0363503:6795:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870574 ES:SE:LP:AF:SS:ID   -0.0127744:0.0225776:0.242948:0.870574:6795:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870584 ES:SE:LP:AF:SS:ID   -0.0128597:0.0225801:0.244867:0.870584:6795:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870569 ES:SE:LP:AF:SS:ID   -0.0128895:0.0225765:0.245599:0.870569:6795:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00526916   ES:SE:LP:AF:SS:ID   0.223779:0.114023:1.30333:0.00526916:6795:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00522703   ES:SE:LP:AF:SS:ID   0.223441:0.114369:1.29431:0.00522703:6795:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0053993    ES:SE:LP:AF:SS:ID   0.0487114:0.114001:0.174456:0.0053993:6795:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87084  ES:SE:LP:AF:SS:ID   -0.0127675:0.0225484:0.243168:0.87084:6795:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125293 ES:SE:LP:AF:SS:ID   0.00982359:0.0231539:0.173032:0.125293:6795:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870272 ES:SE:LP:AF:SS:ID   -0.0126099:0.0224911:0.240297:0.870272:6795:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869209 ES:SE:LP:AF:SS:ID   -0.0105212:0.0224416:0.194356:0.869209:6795:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870498 ES:SE:LP:AF:SS:ID   -0.0124502:0.0225059:0.236461:0.870498:6795:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870507 ES:SE:LP:AF:SS:ID   -0.0124433:0.0225072:0.236288:0.870507:6795:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870508 ES:SE:LP:AF:SS:ID   -0.0124487:0.0225071:0.236415:0.870508:6795:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870994 ES:SE:LP:AF:SS:ID   -0.0131562:0.0225731:0.251789:0.870994:6795:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0985482    ES:SE:LP:AF:SS:ID   -0.0118008:0.0263072:0.184587:0.0985482:6795:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00594786   ES:SE:LP:AF:SS:ID   0.0935903:0.105519:0.42581:0.00594786:6795:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.875512 ES:SE:LP:AF:SS:ID   -0.0148315:0.0230334:0.284287:0.875512:6795:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863732 ES:SE:LP:AF:SS:ID   -0.0102565:0.0224247:0.188816:0.863732:6795:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869743 ES:SE:LP:AF:SS:ID   -0.0136551:0.0227229:0.261299:0.869743:6795:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866831 ES:SE:LP:AF:SS:ID   -0.0136858:0.0227321:0.261882:0.866831:6795:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0978294    ES:SE:LP:AF:SS:ID   0.037112:0.0272507:0.761244:0.0978294:6795:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87266  ES:SE:LP:AF:SS:ID   -0.0129737:0.0230766:0.241091:0.87266:6795:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87266  ES:SE:LP:AF:SS:ID   -0.0129737:0.0230766:0.241091:0.87266:6795:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.872656 ES:SE:LP:AF:SS:ID   -0.0129756:0.0230767:0.241131:0.872656:6795:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.873098 ES:SE:LP:AF:SS:ID   -0.0122531:0.0231089:0.224777:0.873098:6795:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12436  ES:SE:LP:AF:SS:ID   0.0120808:0.0231439:0.220621:0.12436:6795:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10575  ES:SE:LP:AF:SS:ID   -0.00133584:0.0250094:0.0189048:0.10575:6795:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855537 ES:SE:LP:AF:SS:ID   -0.010668:0.0225023:0.196916:0.855537:6795:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016829    ES:SE:LP:AF:SS:ID   -0.00500222:0.197122:0.00888207:0.0016829:6795:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.841834 ES:SE:LP:AF:SS:ID   0.00756575:0.0224921:0.132769:0.841834:6795:rs376645387