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-16946/UKB-b-16946_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16946/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:45:24 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16946/UKB-b-16946_data.vcf.gz ...
Read summary statistics for 2405335 SNPs.
Dropped 272 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, 610351 SNPs remain.
After merging with regression SNP LD, 610351 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0004 (0.0013)
Lambda GC: 1.0074
Mean Chi^2: 1.0054
Intercept: 1.0094 (0.0101)
Ratio: 1.762 (1.8871)
Analysis finished at Thu Oct 17 14:45:57 2019
Total time elapsed: 33.1s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7566,
    "inflation_factor": 1,
    "mean_EFFECT": -1.3719e-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": 19021,
    "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": 610351,
    "ldsc_nsnp_merge_regression_ld": 610351,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0094,
    "ldsc_intercept_se": 0.0101,
    "ldsc_lambda_gc": 1.0074,
    "ldsc_mean_chisq": 1.0054,
    "ldsc_ratio": 1.7407
}
 

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 4 58 0 2405066 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 2405335 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 8.651163e+00 5.766595e+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 7.858645e+07 5.662931e+07 5687.0000000 3.172215e+07 6.902188e+07 1.147695e+08 2.491722e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.400000e-06 1.231000e-04 -0.0006771 -8.440000e-05 -1.800000e-06 8.140000e-05 7.513000e-04 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.228000e-04 6.200000e-06 0.0001119 1.175000e-04 1.210000e-04 1.270000e-04 2.423000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.989749e-01 2.887629e-01 0.0000006 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.989724e-01 2.887351e-01 0.0000006 2.486779e-01 4.984621e-01 7.481355e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.565957e-01 1.468604e-01 0.2420480 3.273900e-01 4.358410e-01 5.749085e-01 7.579520e-01 ▇▆▅▅▃
numeric AF_reference 19021 0.9920922 NA NA NA NA NA NA NA 4.378484e-01 1.734067e-01 0.0001997 3.015180e-01 4.235220e-01 5.644970e-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 -0.0000746 0.0002060 0.7199992 0.7172908 0.623765 0.7821490 NA
1 54676 rs2462492 C T -0.0001734 0.0002040 0.4000000 0.3952863 0.400401 NA NA
1 91536 rs6702460 G T -0.0004474 0.0002009 0.0259998 0.0259491 0.456846 0.4207270 NA
1 706368 rs55727773 A G 0.0000535 0.0001425 0.7099994 0.7072764 0.515645 0.2751600 NA
1 763394 rs369924889 G A 0.0001136 0.0001670 0.5000000 0.4962588 0.706753 0.6176120 NA
1 776546 rs12124819 A G 0.0001214 0.0001523 0.4299995 0.4254121 0.265385 0.0756789 NA
1 814495 rs74461805 C A -0.0001160 0.0001953 0.5500004 0.5524916 0.340396 NA NA
1 830181 rs28444699 A G -0.0000867 0.0001307 0.5099998 0.5068946 0.697255 0.6912940 NA
1 831489 rs4970385 C T -0.0000856 0.0001283 0.5000000 0.5048568 0.705397 0.6491610 NA
1 831909 rs9697642 C T -0.0000848 0.0001283 0.5099998 0.5085415 0.705442 0.6485620 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51180501 rs5770999 T C 0.0001248 0.0001341 0.3500000 0.3517884 0.713656 0.6369810 NA
22 51181919 rs9616825 G C 0.0000387 0.0001334 0.7700005 0.7718824 0.695470 0.6194090 NA
22 51182485 rs6009961 A G 0.0001094 0.0001345 0.4199997 0.4159197 0.715502 0.6383790 NA
22 51186143 rs2879914 T C 0.0000824 0.0001247 0.5099998 0.5088789 0.381825 0.2733630 NA
22 51186228 rs3865766 C T 0.0001035 0.0001216 0.3900004 0.3946684 0.451061 0.4532750 NA
22 51197266 rs61290853 A G 0.0000409 0.0001255 0.7400005 0.7445104 0.386333 0.4229230 NA
22 51198027 rs34939255 A G -0.0000588 0.0001421 0.6800001 0.6791354 0.254562 0.0984425 NA
22 51211106 rs9628250 T C -0.0000740 0.0001408 0.5999997 0.5991547 0.271547 0.1671330 NA
22 51212875 rs2238837 A C 0.0001234 0.0001338 0.3599996 0.3564274 0.331457 0.3724040 NA
22 51237063 rs3896457 T C 0.0001319 0.0001370 0.3400001 0.3355435 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  -7.45715e-05:0.000205952:0.142668:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -0.000173444:0.000204035:0.39794:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  -0.00044739:0.000200896:1.58503:0.456846:rs6702460
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  5.34942e-05:0.000142455:0.148742:0.515645:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  0.000113635:0.000167015:0.30103:0.706753:rs3115847
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  0.000121367:0.000152267:0.366532:0.265385:rs12124819
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  -0.000116032:0.00019533:0.259637:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  -8.67338e-05:0.000130686:0.29243:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  -8.55731e-05:0.000128321:0.30103:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  -8.48317e-05:0.000128317:0.29243:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  -8.65999e-05:0.000128323:0.30103:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  -8.55103e-05:0.000128336:0.29243:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  -8.69606e-05:0.000131833:0.29243:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  8.44893e-05:0.00012833:0.29243:0.294377:rs28765502
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  0.000119993:0.000130814:0.443698:0.269511:rs28705752
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  0.000132613:0.000134638:0.49485:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  0.000132531:0.000130907:0.508638:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  0.000106692:0.000118365:0.431798:0.400124:rs4970382
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  0.000174979:0.000146933:0.638272:0.362606:rs11516185
1   850218  rs6664536   T   A   .   PASS    AF=0.590331 ES:SE:LP:AF:ID  -0.000146901:0.00011802:0.677781:0.590331:rs6664536
1   850371  rs6679046   G   T   .   PASS    AF=0.603723 ES:SE:LP:AF:ID  -0.000157331:0.000118682:0.744727:0.603723:rs6679046
1   850780  rs6657440   C   T   .   PASS    AF=0.603942 ES:SE:LP:AF:ID  -0.000162984:0.000118666:0.769551:0.603942:rs6657440
1   852037  rs4970463   G   A   .   PASS    AF=0.589686 ES:SE:LP:AF:ID  -0.000141637:0.000118212:0.638272:0.589686:rs4970463
1   852063  rs28436996  G   A   .   PASS    AF=0.589665 ES:SE:LP:AF:ID  -0.000144437:0.000118159:0.657577:0.589665:rs28436996
1   852875  rs13303369  C   T   .   PASS    AF=0.607671 ES:SE:LP:AF:ID  -0.000142305:0.000118931:0.638272:0.607671:rs13303369
1   853954  rs1806509   C   A   .   PASS    AF=0.607829 ES:SE:LP:AF:ID  -0.000146185:0.000118947:0.657577:0.607829:rs1806509
1   854777  rs13303019  A   G   .   PASS    AF=0.610316 ES:SE:LP:AF:ID  -0.000158147:0.000119064:0.744727:0.610316:rs13303019
1   854978  rs13303057  A   C   .   PASS    AF=0.603283 ES:SE:LP:AF:ID  -0.000164169:0.000118711:0.769551:0.603283:rs13303057
1   855075  rs6673914   C   G   .   PASS    AF=0.610337 ES:SE:LP:AF:ID  -0.000158359:0.000119066:0.744727:0.610337:rs6673914
1   856099  rs28534711  T   G   .   PASS    AF=0.389936 ES:SE:LP:AF:ID  0.000164332:0.000119089:0.769551:0.389936:rs28534711
1   856108  rs28742275  A   G   .   PASS    AF=0.38992  ES:SE:LP:AF:ID  0.000163598:0.000119095:0.769551:0.38992:rs28742275
1   856476  rs4040605   A   G   .   PASS    AF=0.350356 ES:SE:LP:AF:ID  0.000120352:0.000122344:0.481486:0.350356:rs4040605
1   866893  rs2880024   T   C   .   PASS    AF=0.610552 ES:SE:LP:AF:ID  -0.000150126:0.000119734:0.677781:0.610552:rs2880024
1   868418  rs28546443  C   T   .   PASS    AF=0.297867 ES:SE:LP:AF:ID  0.000120258:0.000131553:0.443698:0.297867:rs28546443
1   870645  rs28576697  T   C   .   PASS    AF=0.291285 ES:SE:LP:AF:ID  2.49194e-05:0.000130506:0.0705811:0.291285:rs28576697
1   871334  rs4072383   G   T   .   PASS    AF=0.72062  ES:SE:LP:AF:ID  2.82508e-07:0.000129697:-0:0.72062:rs4072383
1   872352  rs1806780   G   C   .   PASS    AF=0.267527 ES:SE:LP:AF:ID  3.00877e-05:0.000131455:0.0861861:0.267527:rs1806780
1   873558  rs1110052   G   T   .   PASS    AF=0.715251 ES:SE:LP:AF:ID  8.37366e-06:0.000128667:0.0222764:0.715251:rs1110052
1   875770  rs4970379   A   G   .   PASS    AF=0.600085 ES:SE:LP:AF:ID  -0.000137782:0.00012073:0.60206:0.600085:rs4970379
1   877147  rs114982608 G   A   .   PASS    AF=0.242966 ES:SE:LP:AF:ID  -2.86693e-05:0.000136736:0.0809219:0.242966:rs114982608
1   881627  rs2272757   G   A   .   PASS    AF=0.652393 ES:SE:LP:AF:ID  -5.41125e-05:0.000121958:0.180456:0.652393:rs2272757
1   882033  rs2272756   G   A   .   PASS    AF=0.243918 ES:SE:LP:AF:ID  -2.07913e-06:0.00013583:0.00436481:0.243918:rs2272756
1   890104  rs28631199  G   A   .   PASS    AF=0.246771 ES:SE:LP:AF:ID  2.93833e-05:0.000135295:0.0809219:0.246771:rs28631199
1   891059  rs13303065  C   T   .   PASS    AF=0.652432 ES:SE:LP:AF:ID  -6.89107e-05:0.000121939:0.244125:0.652432:rs13303065
1   891945  rs13303106  A   G   .   PASS    AF=0.652494 ES:SE:LP:AF:ID  -6.03286e-05:0.000122081:0.207608:0.652494:rs13303106
1   900505  rs28705211  G   C   .   PASS    AF=0.271763 ES:SE:LP:AF:ID  -1.86026e-05:0.000131979:0.05061:0.271763:rs28705211
1   903245  rs28690976  A   G   .   PASS    AF=0.566938 ES:SE:LP:AF:ID  -9.74767e-05:0.000121253:0.376751:0.566938:rs28690976
1   909073  rs3892467   C   T   .   PASS    AF=0.386681 ES:SE:LP:AF:ID  -2.67689e-05:0.000120923:0.0861861:0.386681:rs3892467
1   909238  rs3829740   G   C   .   PASS    AF=0.571408 ES:SE:LP:AF:ID  2.68155e-05:0.000117111:0.0861861:0.571408:rs3829740
1   910394  rs28477686  C   T   .   PASS    AF=0.324458 ES:SE:LP:AF:ID  1.79608e-05:0.000126935:0.05061:0.324458:rs28477686