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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    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_20002_1537.vcf.gz --id UKB-b:4122 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20002_1537.txt.gz --cohort_cases 1555 --cohort_controls 461378 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
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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-4122/UKB-b-4122_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4122/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:44:02 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4122/UKB-b-4122_data.vcf.gz ...
Read summary statistics for 2590226 SNPs.
Dropped 305 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, 653897 SNPs remain.
After merging with regression SNP LD, 653897 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0006 (0.0011)
Lambda GC: 1.0131
Mean Chi^2: 1.0055
Intercept: 0.9986 (0.0089)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:44:36 2019
Total time elapsed: 34.76s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7787,
    "inflation_factor": 1,
    "mean_EFFECT": -1.1449e-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": 20548,
    "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": 653897,
    "ldsc_nsnp_merge_regression_ld": 653897,
    "ldsc_observed_scale_h2_beta": 0.0006,
    "ldsc_observed_scale_h2_se": 0.0011,
    "ldsc_intercept_beta": 0.9986,
    "ldsc_intercept_se": 0.0089,
    "ldsc_lambda_gc": 1.0131,
    "ldsc_mean_chisq": 1.0055,
    "ldsc_ratio": -0.2545
}
 

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 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 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 4 58 0 2589924 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 2590226 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 8.658220e+00 5.766938e+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 7.855758e+07 5.662021e+07 5687.0000000 3.170900e+07 6.896851e+07 1.147410e+08 2.491917e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.100000e-06 1.291000e-04 -0.0005929 -8.800000e-05 -1.000000e-06 8.640000e-05 7.118000e-04 ▁▃▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.284000e-04 7.400000e-06 0.0001160 1.221000e-04 1.263000e-04 1.336000e-04 2.516000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.967809e-01 2.890398e-01 0.0000026 2.399999e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.967847e-01 2.890159e-01 0.0000026 2.437783e-01 4.963438e-01 7.470482e-01 9.999996e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.500679e-01 1.560638e-01 0.2250810 3.127830e-01 4.263300e-01 5.747615e-01 7.749190e-01 ▇▆▅▃▃
numeric AF_reference 20548 0.9920671 NA NA NA NA NA NA NA 4.321121e-01 1.792135e-01 0.0001997 2.901360e-01 4.151360e-01 5.632990e-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 0.0000001 0.0002136 1.0000000 0.9995062 0.623763 0.7821490 NA
1 54676 rs2462492 C T 0.0000525 0.0002116 0.8000000 0.8038711 0.400401 NA NA
1 91536 rs6702460 G T 0.0002207 0.0002083 0.2900000 0.2894280 0.456851 0.4207270 NA
1 534192 rs6680723 C T 0.0004981 0.0002380 0.0359998 0.0363392 0.240960 NA NA
1 706368 rs55727773 A G -0.0001639 0.0001477 0.2700001 0.2671267 0.515650 0.2751600 NA
1 763394 rs369924889 G A -0.0000223 0.0001732 0.9000000 0.8976368 0.706753 0.6176120 NA
1 768253 rs2977608 A C -0.0003188 0.0001414 0.0239999 0.0241338 0.761304 0.4894170 NA
1 776546 rs12124819 A G -0.0001273 0.0001579 0.4199997 0.4201143 0.265390 0.0756789 NA
1 808631 rs11240779 G A -0.0002983 0.0001435 0.0379997 0.0376517 0.772626 0.4534740 NA
1 808928 rs11240780 C T -0.0003179 0.0001438 0.0269998 0.0269912 0.772854 0.4522760 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51180501 rs5770999 T C -0.0003489 0.0001390 0.0120000 0.0120852 0.713658 0.6369810 NA
22 51181919 rs9616825 G C -0.0002911 0.0001383 0.0350002 0.0353081 0.695471 0.6194090 NA
22 51182485 rs6009961 A G -0.0003502 0.0001395 0.0120000 0.0120271 0.715505 0.6383790 NA
22 51186143 rs2879914 T C -0.0001600 0.0001293 0.2200002 0.2160907 0.381826 0.2733630 NA
22 51186228 rs3865766 C T -0.0002225 0.0001260 0.0779992 0.0775271 0.451063 0.4532750 NA
22 51197266 rs61290853 A G -0.0001063 0.0001301 0.4100001 0.4139800 0.386333 0.4229230 NA
22 51198027 rs34939255 A G -0.0001687 0.0001473 0.2500000 0.2522472 0.254557 0.0984425 NA
22 51211106 rs9628250 T C -0.0001325 0.0001461 0.3599996 0.3644304 0.271547 0.1671330 NA
22 51212875 rs2238837 A C -0.0001071 0.0001388 0.4400003 0.4402905 0.331455 0.3724040 NA
22 51237063 rs3896457 T C -0.0000399 0.0001421 0.7800007 0.7788061 0.297971 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623763 ES:SE:LP:AF:ID  1.32164e-07:0.000213569:-0:0.623763:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  5.25436e-05:0.000211579:0.09691:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  0.000220699:0.000208329:0.537602:0.456851:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.24096  ES:SE:LP:AF:ID  0.000498083:0.000237963:1.4437:0.24096:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.51565  ES:SE:LP:AF:ID  -0.000163931:0.000147725:0.568636:0.51565:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  -2.22808e-05:0.000173193:0.0457575:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761304 ES:SE:LP:AF:ID  -0.000318759:0.000141357:1.61979:0.761304:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.26539  ES:SE:LP:AF:ID  -0.000127301:0.000157898:0.376751:0.26539:rs12124819
1   808631  rs11240779  G   A   .   PASS    AF=0.772626 ES:SE:LP:AF:ID  -0.000298312:0.000143514:1.42022:0.772626:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772854 ES:SE:LP:AF:ID  -0.000317935:0.000143755:1.56864:0.772854:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340397 ES:SE:LP:AF:ID  0.000227634:0.00020256:0.585027:0.340397:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697259 ES:SE:LP:AF:ID  1.91707e-05:0.000135518:0.05061:0.697259:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705403 ES:SE:LP:AF:ID  -1.68276e-05:0.000133067:0.0457575:0.705403:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705448 ES:SE:LP:AF:ID  -1.60783e-05:0.000133062:0.0457575:0.705448:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705634 ES:SE:LP:AF:ID  -1.86928e-05:0.000133068:0.05061:0.705634:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705662 ES:SE:LP:AF:ID  -1.91935e-05:0.000133082:0.05061:0.705662:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730134 ES:SE:LP:AF:ID  -2.6894e-05:0.000136709:0.0757207:0.730134:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294371 ES:SE:LP:AF:ID  1.84362e-05:0.000133076:0.05061:0.294371:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236696 ES:SE:LP:AF:ID  4.27276e-05:0.000141681:0.119186:0.236696:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236684 ES:SE:LP:AF:ID  4.95441e-05:0.000141682:0.136677:0.236684:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.239743 ES:SE:LP:AF:ID  2.76003e-05:0.000141228:0.0705811:0.239743:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236686 ES:SE:LP:AF:ID  4.95557e-05:0.000141681:0.136677:0.236686:rs28484835
1   834832  rs4411087   G   C   .   PASS    AF=0.237171 ES:SE:LP:AF:ID  5.01094e-05:0.000141572:0.142668:0.237171:rs4411087
1   835499  rs4422948   A   G   .   PASS    AF=0.241155 ES:SE:LP:AF:ID  5.86498e-05:0.000140584:0.167491:0.241155:rs4422948
1   836896  rs28705752  T   C   .   PASS    AF=0.269503 ES:SE:LP:AF:ID  0.000144134:0.000135653:0.537602:0.269503:rs28705752
1   838555  rs4970383   C   A   .   PASS    AF=0.246197 ES:SE:LP:AF:ID  0.000155636:0.000139618:0.585027:0.246197:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.27001  ES:SE:LP:AF:ID  0.000147057:0.000135749:0.552842:0.27001:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400106 ES:SE:LP:AF:ID  -7.63848e-05:0.000122743:0.275724:0.400106:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237094 ES:SE:LP:AF:ID  0.000186565:0.000142572:0.721246:0.237094:rs1574243
1   842362  rs28540380  C   T   .   PASS    AF=0.235321 ES:SE:LP:AF:ID  8.47644e-05:0.000144704:0.251812:0.235321:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362599 ES:SE:LP:AF:ID  -0.000209883:0.000152372:0.769551:0.362599:rs11516185
1   850218  rs6664536   T   A   .   PASS    AF=0.590333 ES:SE:LP:AF:ID  0.000108218:0.000122383:0.420216:0.590333:rs6664536
1   850371  rs6679046   G   T   .   PASS    AF=0.603726 ES:SE:LP:AF:ID  0.000134846:0.00012307:0.568636:0.603726:rs6679046
1   850780  rs6657440   C   T   .   PASS    AF=0.603944 ES:SE:LP:AF:ID  0.00013973:0.000123053:0.585027:0.603944:rs6657440
1   852037  rs4970463   G   A   .   PASS    AF=0.589688 ES:SE:LP:AF:ID  0.00011147:0.000122582:0.443698:0.589688:rs4970463
1   852063  rs28436996  G   A   .   PASS    AF=0.589667 ES:SE:LP:AF:ID  0.000116752:0.000122527:0.468521:0.589667:rs28436996
1   852875  rs13303369  C   T   .   PASS    AF=0.607674 ES:SE:LP:AF:ID  9.64164e-05:0.000123328:0.366532:0.607674:rs13303369
1   853954  rs1806509   C   A   .   PASS    AF=0.607833 ES:SE:LP:AF:ID  9.57769e-05:0.000123345:0.356547:0.607833:rs1806509
1   854777  rs13303019  A   G   .   PASS    AF=0.610318 ES:SE:LP:AF:ID  0.000102862:0.000123466:0.39794:0.610318:rs13303019
1   854978  rs13303057  A   C   .   PASS    AF=0.603286 ES:SE:LP:AF:ID  0.000136331:0.0001231:0.568636:0.603286:rs13303057
1   855075  rs6673914   C   G   .   PASS    AF=0.610338 ES:SE:LP:AF:ID  0.000102183:0.000123468:0.387216:0.610338:rs6673914
1   856099  rs28534711  T   G   .   PASS    AF=0.389935 ES:SE:LP:AF:ID  -9.50404e-05:0.000123492:0.356547:0.389935:rs28534711
1   856108  rs28742275  A   G   .   PASS    AF=0.389918 ES:SE:LP:AF:ID  -9.55292e-05:0.000123498:0.356547:0.389918:rs28742275
1   856476  rs4040605   A   G   .   PASS    AF=0.350351 ES:SE:LP:AF:ID  -5.88755e-05:0.000126868:0.19382:0.350351:rs4040605
1   858801  rs7418179   A   G   .   PASS    AF=0.765845 ES:SE:LP:AF:ID  -2.90404e-05:0.000142415:0.0757207:0.765845:rs7418179
1   860416  rs61464428  G   A   .   PASS    AF=0.766637 ES:SE:LP:AF:ID  -4.88506e-05:0.000142486:0.136677:0.766637:rs61464428
1   860688  rs60837925  G   A   .   PASS    AF=0.766103 ES:SE:LP:AF:ID  -6.28823e-05:0.000142388:0.180456:0.766103:rs60837925
1   861630  rs2879816   G   A   .   PASS    AF=0.766255 ES:SE:LP:AF:ID  -6.2837e-05:0.000142422:0.180456:0.766255:rs2879816
1   862866  rs3892970   C   T   .   PASS    AF=0.763121 ES:SE:LP:AF:ID  -6.13671e-05:0.000142292:0.173925:0.763121:rs3892970
1   864938  rs2340587   G   A   .   PASS    AF=0.760005 ES:SE:LP:AF:ID  -1.16659e-05:0.000141237:0.0315171:0.760005:rs2340587