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-2956/ukb-d-2956.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-2956/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 17:17:06 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-2956/ukb-d-2956.vcf.gz ...
Read summary statistics for 11884243 SNPs.
Dropped 10287 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, 1282911 SNPs remain.
After merging with regression SNP LD, 1282911 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0184 (0.079)
Lambda GC: 1.0104
Mean Chi^2: 1.0065
Intercept: 1.0045 (0.0063)
Ratio: 0.6872 (0.9681)
Analysis finished at Mon Nov 25 17:19:05 2019
Total time elapsed: 1.0m:58.41s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9486,
    "inflation_factor": 1.0125,
    "mean_EFFECT": -0.0001,
    "n": 5473,
    "n_snps": 11884243,
    "n_clumped_hits": 1,
    "n_p_sig": 3,
    "n_mono": 0,
    "n_ns": 1179174,
    "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": 276661,
    "n_est": 5506.7393,
    "ratio_se_n": 1.0031,
    "mean_diff": -0.0001,
    "ratio_diff": 23.0548,
    "sd_y_est1": 0.3718,
    "sd_y_est2": 0.373,
    "r2_sum1": 0.0009,
    "r2_sum2": 0.0064,
    "r2_sum3": 0.0063,
    "r2_sum4": 0.0058,
    "ldsc_nsnp_merge_refpanel_ld": 1282911,
    "ldsc_nsnp_merge_regression_ld": 1282911,
    "ldsc_observed_scale_h2_beta": 0.0184,
    "ldsc_observed_scale_h2_se": 0.079,
    "ldsc_intercept_beta": 1.0045,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0104,
    "ldsc_mean_chisq": 1.0065,
    "ldsc_ratio": 0.6923
}

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 TRUE
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 11874575 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 53136 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32047 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.070880e+00 6.185514e+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 7.888816e+07 5.597890e+07 302.0000000 3.269210e+07 6.992102e+07 1.147481e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -6.110000e-05 2.712300e-02 -0.3592140 -9.185400e-03 1.402000e-04 9.494500e-03 2.608500e-01 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.099780e-02 1.711610e-02 0.0059356 8.149700e-03 1.280600e-02 2.885750e-02 1.036790e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.986446e-01 2.887441e-01 0.0000000 2.481733e-01 4.973224e-01 7.490383e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.986153e-01 2.887617e-01 0.0000000 2.481218e-01 4.972930e-01 7.490257e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.166566e-01 2.597124e-01 0.0027354 1.620540e-02 9.533540e-02 3.450790e-01 9.972640e-01 ▇▂▁▁▁
numeric AF_reference 276661 0.9767204 NA NA NA NA NA 2.178897e-01 2.511420e-01 0.0000000 1.297920e-02 1.146170e-01 3.466450e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 5.473000e+03 0.000000e+00 5473.0000000 5.473000e+03 5.473000e+03 5.473000e+03 5.473000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0128623 0.0125666 0.3061012 0.3060570 0.1093080 0.1894970 5473
1 693731 rs12238997 A G 0.0122991 0.0118369 0.2988292 0.2987827 0.1148770 0.1417730 5473
1 707522 rs371890604 G C 0.0024120 0.0132772 0.8558540 0.8558470 0.0978723 0.1293930 5473
1 717587 rs144155419 G A 0.0103541 0.0314509 0.7420053 0.7419934 0.0154738 0.0045926 5473
1 730087 rs148120343 T C 0.0074634 0.0163920 0.6489063 0.6488885 0.0570182 0.0127796 5473
1 731718 rs142557973 T C 0.0111077 0.0112562 0.3237822 0.3237371 0.1202440 0.1543530 5473
1 732032 rs61770163 A C 0.0070816 0.0119761 0.5543384 0.5543120 0.1208180 0.1555510 5473
1 734349 rs141242758 T C 0.0114531 0.0112622 0.3092232 0.3091770 0.1195310 0.1525560 5473
1 740284 rs61770167 C T 0.0210453 0.0519359 0.6853336 0.6853181 0.0056291 0.0023962 5473
1 749963 rs529266287 T TAA -0.0138964 0.0110717 0.2094860 0.2094323 0.8697600 0.7641770 5473
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0070089 0.0128162 0.5844832 0.5844614 0.0593272 0.0309934 5473
23 154923374 rs111332691 T A 0.0271063 0.0143439 0.0588451 0.0587922 0.0449479 0.0116556 5473
23 154925045 rs509981 C T -0.0015568 0.0069594 0.8230069 0.8229982 0.2474110 0.3634440 5473
23 154925895 rs538470 C T -0.0006536 0.0071243 0.9269071 0.9269035 0.2437650 0.3634440 5473
23 154927581 rs644138 G A -0.0030820 0.0065407 0.6375144 0.6374966 0.3069180 0.4635760 5473
23 154929412 rs557132 C T -0.0017003 0.0069629 0.8070889 0.8070804 0.2471720 0.3568210 5473
23 154929637 rs35185538 CT C -0.0005143 0.0073045 0.9438690 0.9438668 0.2304540 0.3011920 5473
23 154929952 rs4012982 CAA C -0.0009118 0.0073149 0.9008011 0.9007963 0.2407230 0.3165560 5473
23 154930230 rs781880 A G -0.0009627 0.0069649 0.8900740 0.8900686 0.2475780 0.3618540 5473
23 154930487 rs781879 T A -0.0626402 0.0244141 0.0103221 0.0102956 0.0204745 0.1263580 5473

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.109308 ES:SE:LP:AF:SS:ID   0.0128623:0.0125666:0.514135:0.109308:5473:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.114877 ES:SE:LP:AF:SS:ID   0.0122991:0.0118369:0.524577:0.114877:5473:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978723    ES:SE:LP:AF:SS:ID   0.00241198:0.0132772:0.0676003:0.0978723:5473:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0154738    ES:SE:LP:AF:SS:ID   0.0103541:0.0314509:0.129593:0.0154738:5473:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0570182    ES:SE:LP:AF:SS:ID   0.00746339:0.016392:0.187818:0.0570182:5473:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.120244 ES:SE:LP:AF:SS:ID   0.0111077:0.0112562:0.489747:0.120244:5473:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.120818 ES:SE:LP:AF:SS:ID   0.0070816:0.0119761:0.256225:0.120818:5473:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.119531 ES:SE:LP:AF:SS:ID   0.0114531:0.0112622:0.509728:0.119531:5473:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00562906   ES:SE:LP:AF:SS:ID   0.0210453:0.0519359:0.164098:0.00562906:5473:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.86976  ES:SE:LP:AF:SS:ID   -0.0138964:0.0110717:0.678845:0.86976:5473:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.12365  ES:SE:LP:AF:SS:ID   0.0131586:0.010947:0.639397:0.12365:5473:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.141634 ES:SE:LP:AF:SS:ID   0.0120475:0.0108674:0.57242:0.141634:5473:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123778 ES:SE:LP:AF:SS:ID   0.0130895:0.0109342:0.6358:0.123778:5473:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87034  ES:SE:LP:AF:SS:ID   -0.0122413:0.0106741:0.599453:0.87034:5473:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874182 ES:SE:LP:AF:SS:ID   -0.00959911:0.0107997:0.426973:0.874182:5473:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128886 ES:SE:LP:AF:SS:ID   0.0138147:0.0107298:0.703403:0.128886:5473:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0337109    ES:SE:LP:AF:SS:ID   0.00718335:0.0199589:0.143313:0.0337109:5473:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87002  ES:SE:LP:AF:SS:ID   -0.0124339:0.010668:0.612867:0.87002:5473:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870416 ES:SE:LP:AF:SS:ID   -0.0127428:0.0106903:0.632057:0.870416:5473:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870013 ES:SE:LP:AF:SS:ID   -0.0124287:0.0106674:0.612566:0.870013:5473:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0061901    ES:SE:LP:AF:SS:ID   0.00800927:0.0495765:0.0596514:0.0061901:5473:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00616861   ES:SE:LP:AF:SS:ID   0.00835348:0.0496997:0.0622179:0.00616861:5473:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00586444   ES:SE:LP:AF:SS:ID   -0.133224:0.0518198:1.99271:0.00586444:5473:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869917 ES:SE:LP:AF:SS:ID   -0.0122436:0.0106367:0.602489:0.869917:5473:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126531 ES:SE:LP:AF:SS:ID   0.0129694:0.0108844:0.631737:0.126531:5473:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869267 ES:SE:LP:AF:SS:ID   -0.0121814:0.0106086:0.600484:0.869267:5473:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868834 ES:SE:LP:AF:SS:ID   -0.0133284:0.0105948:0.681021:0.868834:5473:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869671 ES:SE:LP:AF:SS:ID   -0.0123195:0.0106229:0.608678:0.869671:5473:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869676 ES:SE:LP:AF:SS:ID   -0.0123237:0.0106238:0.608894:0.869676:5473:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869688 ES:SE:LP:AF:SS:ID   -0.0123397:0.0106244:0.609933:0.869688:5473:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870055 ES:SE:LP:AF:SS:ID   -0.0119856:0.0106459:0.584553:0.870055:5473:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0988371    ES:SE:LP:AF:SS:ID   0.0088095:0.0123624:0.322283:0.0988371:5473:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00631442   ES:SE:LP:AF:SS:ID   -0.142826:0.0483449:2.50208:0.00631442:5473:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874056 ES:SE:LP:AF:SS:ID   -0.00967954:0.010798:0.431717:0.874056:5473:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864019 ES:SE:LP:AF:SS:ID   -0.0127216:0.0105829:0.639444:0.864019:5473:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869081 ES:SE:LP:AF:SS:ID   -0.0118887:0.0107046:0.573842:0.869081:5473:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865702 ES:SE:LP:AF:SS:ID   -0.0120825:0.0107058:0.586494:0.865702:5473:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0980636    ES:SE:LP:AF:SS:ID   0.00816943:0.0128446:0.280015:0.0980636:5473:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870895 ES:SE:LP:AF:SS:ID   -0.0090071:0.0108167:0.392495:0.870895:5473:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870894 ES:SE:LP:AF:SS:ID   -0.00900805:0.0108167:0.392547:0.870894:5473:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870891 ES:SE:LP:AF:SS:ID   -0.00900656:0.0108168:0.392459:0.870891:5473:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871177 ES:SE:LP:AF:SS:ID   -0.00953618:0.0108218:0.422222:0.871177:5473:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125754 ES:SE:LP:AF:SS:ID   0.0125754:0.0108626:0.60722:0.125754:5473:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.104115 ES:SE:LP:AF:SS:ID   0.0108298:0.0119211:0.439282:0.104115:5473:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855058 ES:SE:LP:AF:SS:ID   -0.0101905:0.0106092:0.472588:0.855058:5473:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.840853 ES:SE:LP:AF:SS:ID   0.0109757:0.0104165:0.534509:0.840853:5473:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.764673 ES:SE:LP:AF:SS:ID   0.00143657:0.00838466:0.0635023:0.764673:5473:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.10433  ES:SE:LP:AF:SS:ID   -0.0185992:0.0115666:0.967015:0.10433:5473:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00760489   ES:SE:LP:AF:SS:ID   0.0709011:0.0429264:1.00588:0.00760489:5473:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129246 ES:SE:LP:AF:SS:ID   0.0151922:0.0107177:0.805766:0.129246:5473:rs762168062