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/public/UKB-b-6144/UKB-b-6144_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6144/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:45:46 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6144/UKB-b-6144_data.vcf.gz ...
Read summary statistics for 5145372 SNPs.
Dropped 1572 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, 1133906 SNPs remain.
After merging with regression SNP LD, 1133906 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.002 (0.0011)
Lambda GC: 1.0559
Mean Chi^2: 1.055
Intercept: 1.0366 (0.0069)
Ratio: 0.6652 (0.1245)
Analysis finished at Thu Oct 17 14:46:38 2019
Total time elapsed: 52.31s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9096,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -1.9778e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "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": 44229,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1133906,
    "ldsc_nsnp_merge_regression_ld": 1133906,
    "ldsc_observed_scale_h2_beta": 0.002,
    "ldsc_observed_scale_h2_se": 0.0011,
    "ldsc_intercept_beta": 1.0366,
    "ldsc_intercept_se": 0.0069,
    "ldsc_lambda_gc": 1.0559,
    "ldsc_mean_chisq": 1.055,
    "ldsc_ratio": 0.6655
}

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 5143811 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 5145372 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 8.672588e+00 5.764250e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.853172e+07 5.660050e+07 828.0000000 3.189815e+07 6.891768e+07 1.144888e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -2.000000e-06 3.346000e-04 -0.0027522 -2.126000e-04 -2.200000e-06 2.087000e-04 2.784500e-03 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.166000e-04 7.540000e-05 0.0002326 2.530000e-04 2.893000e-04 3.640000e-04 9.091000e-04 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.915721e-01 2.905566e-01 0.0000000 2.399999e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.915713e-01 2.905306e-01 0.0000000 2.380721e-01 4.885466e-01 7.426943e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.456590e-01 2.410825e-01 0.0602100 1.382780e-01 2.776030e-01 5.124552e-01 9.397900e-01 ▇▅▃▂▂
numeric AF_reference 44229 0.9914041 NA NA NA NA NA NA NA 3.395518e-01 2.371391e-01 0.0000000 1.439700e-01 2.807510e-01 5.017970e-01 1.000000e+00 ▇▆▃▂▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0001764 0.0004281 0.6800001 0.6802829 0.623743 0.7821490 NA
1 54676 rs2462492 C T 0.0007439 0.0004241 0.0790005 0.0794347 0.400427 NA NA
1 86028 rs114608975 T C 0.0000506 0.0006781 0.9400001 0.9404802 0.103535 0.0277556 NA
1 91536 rs6702460 G T -0.0005508 0.0004175 0.1900002 0.1870449 0.456851 0.4207270 NA
1 234313 rs8179466 C T 0.0006855 0.0008238 0.4100001 0.4053336 0.074444 NA NA
1 534192 rs6680723 C T 0.0007420 0.0004770 0.1199999 0.1197940 0.240934 NA NA
1 546697 rs12025928 A G 0.0008970 0.0005951 0.1299999 0.1316974 0.913484 NA NA
1 693731 rs12238997 A G -0.0001068 0.0003998 0.7899998 0.7893662 0.116361 0.1417730 NA
1 705882 rs72631875 G A -0.0006374 0.0005858 0.2800000 0.2765425 0.067335 0.0315495 NA
1 706368 rs55727773 A G 0.0004320 0.0002961 0.1400000 0.1445977 0.515728 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51213613 rs34726907 C T 0.0000947 0.0003664 0.8000000 0.7960937 0.127885 0.1727240 NA
22 51216564 rs9616970 T C 0.0000993 0.0003648 0.7899998 0.7853947 0.128406 0.1563500 NA
22 51217954 rs9616974 G A -0.0002899 0.0004629 0.5300002 0.5311896 0.073344 0.0621006 NA
22 51218224 rs9616975 C A -0.0002945 0.0004631 0.5199996 0.5248791 0.073365 0.0619010 NA
22 51218377 rs2519461 G C -0.0002996 0.0004626 0.5199996 0.5172271 0.073647 0.0826677 NA
22 51219006 rs28729663 G A -0.0000438 0.0003571 0.9000000 0.9023935 0.138007 0.2052720 NA
22 51219387 rs9616832 T C -0.0003194 0.0004635 0.4899999 0.4907231 0.073774 0.0654952 NA
22 51221731 rs115055839 T C -0.0002874 0.0004638 0.5400003 0.5354117 0.073270 0.0625000 NA
22 51229805 rs9616985 T C -0.0002485 0.0004655 0.5900000 0.5934758 0.073108 0.0730831 NA
22 51237063 rs3896457 T C 0.0005022 0.0002848 0.0779992 0.0777952 0.298164 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623743 ES:SE:LP:AF:ID  -0.00017639:0.000428051:0.167491:0.623743:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400427 ES:SE:LP:AF:ID  0.000743861:0.0004241:1.10237:0.400427:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103535 ES:SE:LP:AF:ID  5.06283e-05:0.000678061:0.0268721:0.103535:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  -0.000550835:0.000417498:0.721246:0.456851:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074444 ES:SE:LP:AF:ID  0.00068549:0.000823774:0.387216:0.074444:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240934 ES:SE:LP:AF:ID  0.000742004:0.000476977:0.920819:0.240934:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913484 ES:SE:LP:AF:ID  0.000897038:0.000595073:0.886057:0.913484:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116361 ES:SE:LP:AF:ID  -0.000106807:0.000399826:0.102373:0.116361:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067335 ES:SE:LP:AF:ID  -0.000637405:0.000585786:0.552842:0.067335:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515728 ES:SE:LP:AF:ID  0.000432042:0.000296146:0.853872:0.515728:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.101239 ES:SE:LP:AF:ID  -0.000271163:0.00048858:0.236572:0.101239:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.843131 ES:SE:LP:AF:ID  9.17722e-05:0.000346462:0.102373:0.843131:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.122349 ES:SE:LP:AF:ID  -4.4743e-06:0.000379228:0.00436481:0.122349:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121591 ES:SE:LP:AF:ID  -9.02929e-06:0.000379386:0.00877392:0.121591:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132404 ES:SE:LP:AF:ID  6.65277e-05:0.00037387:0.0655015:0.132404:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.838819 ES:SE:LP:AF:ID  4.29359e-05:0.000335443:0.0457575:0.838819:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838441 ES:SE:LP:AF:ID  2.597e-05:0.000335068:0.0268721:0.838441:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869695 ES:SE:LP:AF:ID  -0.000117156:0.000359571:0.130768:0.869695:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129968 ES:SE:LP:AF:ID  0.000104205:0.000360287:0.113509:0.129968:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.869034 ES:SE:LP:AF:ID  -0.000145986:0.000358856:0.167491:0.869034:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869135 ES:SE:LP:AF:ID  -0.000137762:0.000359002:0.154902:0.869135:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869038 ES:SE:LP:AF:ID  -0.000148095:0.00035885:0.167491:0.869038:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.83789  ES:SE:LP:AF:ID  3.30232e-05:0.000334136:0.0362122:0.83789:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838522 ES:SE:LP:AF:ID  8.13868e-06:0.000335075:0.00877392:0.838522:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.839641 ES:SE:LP:AF:ID  4.33334e-06:0.000339626:0.00436481:0.839641:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869324 ES:SE:LP:AF:ID  -0.000113242:0.000358453:0.124939:0.869324:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868876 ES:SE:LP:AF:ID  -0.000133977:0.000357568:0.148742:0.868876:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867818 ES:SE:LP:AF:ID  -0.000180681:0.000356859:0.21467:0.867818:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869015 ES:SE:LP:AF:ID  -0.000130866:0.000357853:0.148742:0.869015:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869024 ES:SE:LP:AF:ID  -0.000130851:0.00035788:0.148742:0.869024:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869031 ES:SE:LP:AF:ID  -0.000131321:0.000357889:0.148742:0.869031:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869507 ES:SE:LP:AF:ID  -0.000127256:0.000358859:0.142668:0.869507:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.838176 ES:SE:LP:AF:ID  1.92547e-05:0.000333517:0.0222764:0.838176:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838295 ES:SE:LP:AF:ID  1.45121e-05:0.000333753:0.0132283:0.838295:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862176 ES:SE:LP:AF:ID  -8.72528e-05:0.000356605:0.091515:0.862176:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.706654 ES:SE:LP:AF:ID  -2.71639e-05:0.000347177:0.0268721:0.706654:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.105166 ES:SE:LP:AF:ID  0.000462899:0.000399971:0.60206:0.105166:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.76134  ES:SE:LP:AF:ID  0.000198832:0.000283492:0.318759:0.76134:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.106382 ES:SE:LP:AF:ID  -0.00052167:0.000390823:0.744727:0.106382:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.129655 ES:SE:LP:AF:ID  0.000152701:0.000360115:0.173925:0.129655:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.868838 ES:SE:LP:AF:ID  -0.000152389:0.000358194:0.173925:0.868838:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129755 ES:SE:LP:AF:ID  0.000127742:0.000359881:0.142668:0.129755:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.868848 ES:SE:LP:AF:ID  -0.000156559:0.000358201:0.180456:0.868848:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.265289 ES:SE:LP:AF:ID  -0.000459816:0.000316585:0.823909:0.265289:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.869996 ES:SE:LP:AF:ID  -0.000146328:0.000358956:0.167491:0.869996:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.095068 ES:SE:LP:AF:ID  -0.00041282:0.000416223:0.49485:0.095068:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.128623 ES:SE:LP:AF:ID  0.000130053:0.000360374:0.142668:0.128623:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128919 ES:SE:LP:AF:ID  0.000118558:0.000359769:0.130768:0.128919:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.868735 ES:SE:LP:AF:ID  -0.000123265:0.000358001:0.136677:0.868735:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.101866 ES:SE:LP:AF:ID  0.000434576:0.000405721:0.552842:0.101866:rs61768199