Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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/public/UKB-b-2341/UKB-b-2341_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2341/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:29 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2341/UKB-b-2341_data.vcf.gz ...
Read summary statistics for 5690354 SNPs.
Dropped 2305 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1190738 SNPs remain.
After merging with regression SNP LD, 1190738 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0102 (0.0067)
Lambda GC: 1.0291
Mean Chi^2: 1.0291
Intercept: 1.0157 (0.0067)
Ratio: 0.5403 (0.2294)
Analysis finished at Thu Oct 17 14:43:36 2019
Total time elapsed: 1.0m:6.76s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.92,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -4.0299e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 50574,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NA",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1190738,
    "ldsc_nsnp_merge_regression_ld": 1190738,
    "ldsc_observed_scale_h2_beta": 0.0102,
    "ldsc_observed_scale_h2_se": 0.0067,
    "ldsc_intercept_beta": 1.0157,
    "ldsc_intercept_se": 0.0067,
    "ldsc_lambda_gc": 1.0291,
    "ldsc_mean_chisq": 1.0291,
    "ldsc_ratio": 0.5395
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 5688065 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 5690354 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.670685e+00 5.762462e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 <U+2587><U+2585><U+2585><U+2582><U+2582>
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.860063e+07 5.656327e+07 828.0000000 3.198413e+07 6.903033e+07 1.145502e+08 2.492385e+08 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -4.000000e-06 2.764800e-03 -0.0209007 -1.691400e-03 -2.010000e-05 1.675500e-03 1.992050e-02 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.614700e-03 7.796000e-04 0.0017923 1.967200e-03 2.318500e-03 3.080400e-03 8.570500e-03 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.953890e-01 2.898153e-01 0.0000002 2.399999e-01 4.899999e-01 7.499995e-01 1.000000e+00 <U+2587><U+2587><U+2587><U+2587><U+2587>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.953909e-01 2.897915e-01 0.0000002 2.433801e-01 4.941249e-01 7.462716e-01 9.999999e-01 <U+2587><U+2587><U+2587><U+2587><U+2587>
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.237591e-01 2.497144e-01 0.0418670 1.108850e-01 2.466590e-01 4.902020e-01 9.581330e-01 <U+2587><U+2583><U+2582><U+2582><U+2581>
numeric AF_reference 50574 0.9911123 NA NA NA NA NA NA NA 3.194497e-01 2.436891e-01 0.0000000 1.190100e-01 2.527960e-01 4.802320e-01 1.000000e+00 <U+2587><U+2585><U+2583><U+2582><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C 0.0002652 0.0033033 0.9400001 0.9360187 0.623812 0.7821490 NA
1 54676 rs2462492 C T -0.0032505 0.0032937 0.3200000 0.3237113 0.399144 NA NA
1 86028 rs114608975 T C 0.0047608 0.0052431 0.3599996 0.3638737 0.103536 0.0277556 NA
1 91536 rs6702460 G T -0.0019714 0.0032396 0.5400003 0.5428475 0.455916 0.4207270 NA
1 234313 rs8179466 C T -0.0025587 0.0064068 0.6899999 0.6896127 0.074455 NA NA
1 534192 rs6680723 C T -0.0014547 0.0036898 0.6899999 0.6933973 0.242057 NA NA
1 546697 rs12025928 A G 0.0067908 0.0045782 0.1400000 0.1379950 0.912862 NA NA
1 693731 rs12238997 A G 0.0011322 0.0030766 0.7099994 0.7128635 0.117313 0.1417730 NA
1 705882 rs72631875 G A 0.0001570 0.0044845 0.9699999 0.9720750 0.067698 0.0315495 NA
1 706368 rs55727773 A G -0.0008589 0.0022837 0.7099994 0.7068422 0.513304 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218224 rs9616975 C A -0.0001169 0.0036154 0.9699999 0.9742036 0.071497 0.0619010 NA
22 51218377 rs2519461 G C -0.0000801 0.0036107 0.9800000 0.9823106 0.071792 0.0826677 NA
22 51219006 rs28729663 G A 0.0045243 0.0027776 0.1000000 0.1033482 0.136315 0.2052720 NA
22 51219387 rs9616832 T C -0.0002734 0.0036203 0.9400001 0.9397956 0.071797 0.0654952 NA
22 51221190 rs369304721 G A -0.0024444 0.0048502 0.6100002 0.6142789 0.048372 NA NA
22 51221731 rs115055839 T C -0.0000538 0.0036211 0.9900000 0.9881519 0.071348 0.0625000 NA
22 51222100 rs114553188 G T 0.0088689 0.0041961 0.0350002 0.0345477 0.054850 0.0880591 NA
22 51223637 rs375798137 G A 0.0093490 0.0042180 0.0269998 0.0266600 0.054470 0.0788738 NA
22 51229805 rs9616985 T C -0.0004248 0.0036323 0.9100000 0.9069020 0.071253 0.0730831 NA
22 51237063 rs3896457 T C 0.0009925 0.0021928 0.6499995 0.6508180 0.298393 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623812 ES:SE:LP:AF:ID  0.000265175:0.00330334:0.0268721:0.623812:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399144 ES:SE:LP:AF:ID  -0.00325045:0.00329373:0.49485:0.399144:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103536 ES:SE:LP:AF:ID  0.00476078:0.0052431:0.443698:0.103536:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.455916 ES:SE:LP:AF:ID  -0.00197135:0.00323962:0.267606:0.455916:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074455 ES:SE:LP:AF:ID  -0.00255874:0.00640677:0.161151:0.074455:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.242057 ES:SE:LP:AF:ID  -0.00145468:0.00368975:0.161151:0.242057:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.912862 ES:SE:LP:AF:ID  0.00679081:0.00457818:0.853872:0.912862:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.117313 ES:SE:LP:AF:ID  0.00113224:0.00307663:0.148742:0.117313:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067698 ES:SE:LP:AF:ID  0.000156985:0.00448452:0.0132283:0.067698:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.513304 ES:SE:LP:AF:ID  -0.000858897:0.00228369:0.148742:0.513304:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.102736 ES:SE:LP:AF:ID  -0.00161595:0.00372669:0.180456:0.102736:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.95809  ES:SE:LP:AF:ID  -0.00568836:0.00492751:0.60206:0.95809:rs2977670
1   725060  rs865924913 A   T   .   PASS    AF=0.052723 ES:SE:LP:AF:ID  0.00110209:0.00726783:0.0555173:0.052723:rs865924913
1   729679  rs4951859   C   G   .   PASS    AF=0.841441 ES:SE:LP:AF:ID  -0.00184751:0.00266071:0.309804:0.841441:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056334 ES:SE:LP:AF:ID  0.00195813:0.00432218:0.187087:0.056334:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123078 ES:SE:LP:AF:ID  0.000868715:0.00292244:0.113509:0.123078:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.12233  ES:SE:LP:AF:ID  0.000668682:0.00292338:0.0861861:0.12233:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.134139 ES:SE:LP:AF:ID  0.00232297:0.00286978:0.376751:0.134139:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.837029 ES:SE:LP:AF:ID  -0.00164416:0.00257392:0.283997:0.837029:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836733 ES:SE:LP:AF:ID  -0.00159774:0.00257203:0.275724:0.836733:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.868562 ES:SE:LP:AF:ID  -0.000373127:0.00276378:0.05061:0.868562:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.131004 ES:SE:LP:AF:ID  0.000523579:0.00277088:0.0705811:0.131004:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.867976 ES:SE:LP:AF:ID  -0.000313332:0.00275934:0.0409586:0.867976:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.86805  ES:SE:LP:AF:ID  -0.00024578:0.00276047:0.0315171:0.86805:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.867987 ES:SE:LP:AF:ID  -0.000330176:0.00275927:0.0457575:0.867987:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.836159 ES:SE:LP:AF:ID  -0.00179317:0.00256451:0.318759:0.836159:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.836793 ES:SE:LP:AF:ID  -0.00188844:0.00257153:0.337242:0.836793:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.838109 ES:SE:LP:AF:ID  -0.00180911:0.00260773:0.309804:0.838109:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.868228 ES:SE:LP:AF:ID  -0.00042827:0.00275572:0.0555173:0.868228:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.867742 ES:SE:LP:AF:ID  -0.000332243:0.00274841:0.0457575:0.867742:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.866644 ES:SE:LP:AF:ID  -0.000717136:0.00274338:0.102373:0.866644:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.867911 ES:SE:LP:AF:ID  -0.00043315:0.0027512:0.0604807:0.867911:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.867923 ES:SE:LP:AF:ID  -0.0004377:0.00275139:0.0604807:0.867923:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.867932 ES:SE:LP:AF:ID  -0.000444634:0.00275149:0.0604807:0.867932:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.868398 ES:SE:LP:AF:ID  -0.000385621:0.00275873:0.05061:0.868398:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.836369 ES:SE:LP:AF:ID  -0.0019562:0.00255811:0.356547:0.836369:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.836495 ES:SE:LP:AF:ID  -0.00191656:0.00255985:0.346787:0.836495:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.860851 ES:SE:LP:AF:ID  -0.00112283:0.00274174:0.167491:0.860851:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.705804 ES:SE:LP:AF:ID  0.00295124:0.00267546:0.568636:0.705804:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.106094 ES:SE:LP:AF:ID  0.000748167:0.00307862:0.091515:0.106094:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.758252 ES:SE:LP:AF:ID  0.00137802:0.00216848:0.275724:0.758252:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.108262 ES:SE:LP:AF:ID  -0.00354947:0.00298462:0.638272:0.108262:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.13066  ES:SE:LP:AF:ID  0.000763548:0.00276982:0.107905:0.13066:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.867852 ES:SE:LP:AF:ID  -0.000568181:0.00275469:0.0757207:0.867852:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.130756 ES:SE:LP:AF:ID  0.000854427:0.00276797:0.119186:0.130756:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.867878 ES:SE:LP:AF:ID  -0.000597506:0.00275485:0.0809219:0.867878:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.263729 ES:SE:LP:AF:ID  0.000562406:0.0024503:0.0861861:0.263729:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.869067 ES:SE:LP:AF:ID  -0.000973952:0.0027621:0.142668:0.869067:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.096639 ES:SE:LP:AF:ID  -0.00319732:0.00318152:0.508638:0.096639:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.129594 ES:SE:LP:AF:ID  0.00117991:0.00277264:0.173925:0.129594:rs1055606