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-13994/UKB-b-13994_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13994/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:43:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13994/UKB-b-13994_data.vcf.gz ...
Read summary statistics for 2720714 SNPs.
Dropped 328 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, 683688 SNPs remain.
After merging with regression SNP LD, 683688 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0033 (0.0016)
Lambda GC: 1.1906
Mean Chi^2: 1.1858
Intercept: 1.1503 (0.011)
Ratio: 0.8091 (0.059)
Analysis finished at Thu Oct 17 14:43:42 2019
Total time elapsed: 36.37s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7924,
    "inflation_factor": 1.1999,
    "mean_EFFECT": -1.9641e-07,
    "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": 21567,
    "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": 683688,
    "ldsc_nsnp_merge_regression_ld": 683688,
    "ldsc_observed_scale_h2_beta": 0.0033,
    "ldsc_observed_scale_h2_se": 0.0016,
    "ldsc_intercept_beta": 1.1503,
    "ldsc_intercept_se": 0.011,
    "ldsc_lambda_gc": 1.1906,
    "ldsc_mean_chisq": 1.1858,
    "ldsc_ratio": 0.8089
}

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 1.000000 4 58 0 2720389 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 2720714 0.000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA NA NA 8.661581e+00 5.768973e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.000000 NA NA NA NA NA NA NA 7.854292e+07 5.662637e+07 5687.0000000 3.171176e+07 6.895728e+07 1.147123e+08 2.492013e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA NA NA -2.000000e-07 1.443000e-04 -0.0007362 -9.770000e-05 -7.000000e-07 9.650000e-05 6.911000e-04 ▁▂▇▂▁
numeric SE 0 1.000000 NA NA NA NA NA NA NA 1.322000e-04 8.400000e-06 0.0001187 1.250000e-04 1.298000e-04 1.381000e-04 2.708000e-04 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA NA NA 4.723303e-01 2.947887e-01 0.0000001 2.099999e-01 4.600002e-01 7.300002e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA NA NA 4.723305e-01 2.947662e-01 0.0000001 2.101065e-01 4.612078e-01 7.268267e-01 9.999997e-01 ▇▇▆▆▆
numeric AF 0 1.000000 NA NA NA NA NA NA NA 4.453519e-01 1.623281e-01 0.2136760 3.026120e-01 4.192200e-01 5.742780e-01 7.863240e-01 ▇▆▅▃▃
numeric AF_reference 21567 0.992073 NA NA NA NA NA NA NA 4.278638e-01 1.832808e-01 0.0001997 2.819490e-01 4.091450e-01 5.623000e-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 -0.0000230 0.0002184 0.9199999 0.9161214 0.623765 0.7821490 NA
1 54676 rs2462492 C T 0.0000059 0.0002163 0.9800000 0.9783414 0.400401 NA NA
1 91536 rs6702460 G T -0.0001825 0.0002130 0.3900004 0.3914241 0.456846 0.4207270 NA
1 534192 rs6680723 C T -0.0002613 0.0002433 0.2800000 0.2828972 0.240959 NA NA
1 706368 rs55727773 A G 0.0001928 0.0001510 0.2000000 0.2016730 0.515645 0.2751600 NA
1 763394 rs369924889 G A 0.0000452 0.0001771 0.8000000 0.7985641 0.706753 0.6176120 NA
1 768253 rs2977608 A C 0.0000700 0.0001445 0.6300007 0.6282552 0.761297 0.4894170 NA
1 776546 rs12124819 A G 0.0001651 0.0001614 0.3100002 0.3065074 0.265385 0.0756789 NA
1 808631 rs11240779 G A 0.0000746 0.0001467 0.6100002 0.6112934 0.772619 0.4534740 NA
1 808928 rs11240780 C T 0.0000868 0.0001470 0.5500004 0.5548519 0.772847 0.4522760 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51180501 rs5770999 T C -0.0001182 0.0001422 0.4100001 0.4060310 0.713656 0.6369810 NA
22 51181919 rs9616825 G C -0.0001005 0.0001415 0.4799997 0.4775056 0.695470 0.6194090 NA
22 51182485 rs6009961 A G -0.0001339 0.0001427 0.3500000 0.3480489 0.715502 0.6383790 NA
22 51186143 rs2879914 T C -0.0001791 0.0001323 0.1800002 0.1757275 0.381825 0.2733630 NA
22 51186228 rs3865766 C T -0.0001269 0.0001290 0.3300000 0.3250345 0.451061 0.4532750 NA
22 51197266 rs61290853 A G -0.0001192 0.0001331 0.3700002 0.3707494 0.386333 0.4229230 NA
22 51198027 rs34939255 A G -0.0001032 0.0001507 0.4899999 0.4934783 0.254562 0.0984425 NA
22 51211106 rs9628250 T C 0.0000319 0.0001494 0.8300000 0.8310624 0.271547 0.1671330 NA
22 51212875 rs2238837 A C -0.0001275 0.0001420 0.3700002 0.3691699 0.331457 0.3724040 NA
22 51237063 rs3896457 T C -0.0003388 0.0001453 0.0200000 0.0197677 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  -2.29978e-05:0.00021836:0.0362122:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  5.87292e-06:0.000216327:0.00877392:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  -0.000182549:0.000213:0.408935:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000261267:0.000243303:0.552842:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  0.000192844:0.000151037:0.69897:0.515645:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  4.51911e-05:0.000177077:0.09691:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  6.99772e-05:0.000144526:0.200659:0.761297:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  0.000165085:0.00016144:0.508638:0.265385:rs12124819
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  7.45723e-05:0.00014673:0.21467:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  8.67907e-05:0.000146977:0.259637:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  -0.000406635:0.000207098:1.30103:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  0.000105551:0.00013856:0.346787:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  8.72182e-05:0.000136052:0.283997:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  8.63884e-05:0.000136047:0.275724:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  8.59402e-05:0.000136054:0.275724:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  8.52497e-05:0.000136068:0.275724:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  0.00016484:0.000139775:0.619789:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  -8.55129e-05:0.000136062:0.275724:0.294377:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236703 ES:SE:LP:AF:ID  -6.78336e-05:0.000144859:0.19382:0.236703:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236691 ES:SE:LP:AF:ID  -6.75703e-05:0.00014486:0.19382:0.236691:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.23975  ES:SE:LP:AF:ID  -8.65885e-05:0.000144396:0.259637:0.23975:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236693 ES:SE:LP:AF:ID  -6.77221e-05:0.000144859:0.19382:0.236693:rs28484835
1   834832  rs4411087   G   C   .   PASS    AF=0.237178 ES:SE:LP:AF:ID  -7.69759e-05:0.000144748:0.229148:0.237178:rs4411087
1   835499  rs4422948   A   G   .   PASS    AF=0.241162 ES:SE:LP:AF:ID  -3.61019e-06:0.000143738:0.00877392:0.241162:rs4422948
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  -0.000112522:0.000138695:0.376751:0.269511:rs28705752
1   838387  rs4970384   T   C   .   PASS    AF=0.214587 ES:SE:LP:AF:ID  -0.000165027:0.000149912:0.568636:0.214587:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  -0.00018326:0.000142749:0.69897:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  -0.000105725:0.000138794:0.346787:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  -7.19495e-05:0.000125496:0.244125:0.400124:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237102 ES:SE:LP:AF:ID  -0.00014803:0.000145769:0.508638:0.237102:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.215391 ES:SE:LP:AF:ID  -0.000154937:0.000150012:0.522879:0.215391:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.235323 ES:SE:LP:AF:ID  -5.14892e-05:0.000147952:0.136677:0.235323:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  1.81453e-05:0.000155786:0.0409586:0.362606:rs11516185
1   847491  rs28407778  G   A   .   PASS    AF=0.214198 ES:SE:LP:AF:ID  -3.09767e-05:0.000150087:0.0757207:0.214198:rs28407778
1   850062  rs28723578  A   T   .   PASS    AF=0.214408 ES:SE:LP:AF:ID  -4.06511e-05:0.000149948:0.102373:0.214408:rs28723578
1   850218  rs6664536   T   A   .   PASS    AF=0.590331 ES:SE:LP:AF:ID  1.421e-06:0.00012513:0.00436481:0.590331:rs6664536
1   850371  rs6679046   G   T   .   PASS    AF=0.603723 ES:SE:LP:AF:ID  -3.52659e-05:0.000125832:0.107905:0.603723:rs6679046
1   850780  rs6657440   C   T   .   PASS    AF=0.603942 ES:SE:LP:AF:ID  -3.62976e-05:0.000125815:0.113509:0.603942:rs6657440
1   851190  rs28609852  G   A   .   PASS    AF=0.214494 ES:SE:LP:AF:ID  -4.18285e-05:0.000149929:0.107905:0.214494:rs28609852
1   851204  rs28552953  G   C   .   PASS    AF=0.224621 ES:SE:LP:AF:ID  -3.98361e-05:0.00014885:0.102373:0.224621:rs28552953
1   852037  rs4970463   G   A   .   PASS    AF=0.589686 ES:SE:LP:AF:ID  7.6327e-06:0.000125334:0.0222764:0.589686:rs4970463
1   852063  rs28436996  G   A   .   PASS    AF=0.589665 ES:SE:LP:AF:ID  6.94697e-06:0.000125277:0.0177288:0.589665:rs28436996
1   852875  rs13303369  C   T   .   PASS    AF=0.607671 ES:SE:LP:AF:ID  -2.69455e-05:0.000126096:0.0809219:0.607671:rs13303369
1   853954  rs1806509   C   A   .   PASS    AF=0.607829 ES:SE:LP:AF:ID  -2.84522e-05:0.000126113:0.0861861:0.607829:rs1806509
1   854777  rs13303019  A   G   .   PASS    AF=0.610316 ES:SE:LP:AF:ID  -4.18385e-05:0.000126237:0.130768:0.610316:rs13303019
1   854978  rs13303057  A   C   .   PASS    AF=0.603283 ES:SE:LP:AF:ID  -3.02e-05:0.000125863:0.091515:0.603283:rs13303057
1   855075  rs6673914   C   G   .   PASS    AF=0.610337 ES:SE:LP:AF:ID  -4.25894e-05:0.000126239:0.130768:0.610337:rs6673914
1   856099  rs28534711  T   G   .   PASS    AF=0.389936 ES:SE:LP:AF:ID  3.94525e-05:0.000126263:0.124939:0.389936:rs28534711
1   856108  rs28742275  A   G   .   PASS    AF=0.38992  ES:SE:LP:AF:ID  3.93875e-05:0.00012627:0.119186:0.38992:rs28742275
1   856476  rs4040605   A   G   .   PASS    AF=0.350356 ES:SE:LP:AF:ID  -2.47131e-05:0.000129715:0.0705811:0.350356:rs4040605