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-10490/UKB-b-10490_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-10490/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-10490/UKB-b-10490_data.vcf.gz ...
Read summary statistics for 3417950 SNPs.
Dropped 510 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, 837622 SNPs remain.
After merging with regression SNP LD, 837622 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0021 (0.0012)
Lambda GC: 1.0733
Mean Chi^2: 1.07
Intercept: 1.0479 (0.0091)
Ratio: 0.6838 (0.1307)
Analysis finished at Thu Oct 17 14:41:02 2019
Total time elapsed: 43.54s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8463,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 1.0727e-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": 27419,
    "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": 837622,
    "ldsc_nsnp_merge_regression_ld": 837622,
    "ldsc_observed_scale_h2_beta": 0.0021,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.0479,
    "ldsc_intercept_se": 0.0091,
    "ldsc_lambda_gc": 1.0733,
    "ldsc_mean_chisq": 1.07,
    "ldsc_ratio": 0.6843
}

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 3417443 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 3417950 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 8.662787e+00 5.774014e+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 7.855199e+07 5.672907e+07 828.0000000 3.158660e+07 6.892617e+07 1.147462e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.100000e-06 1.669000e-04 -0.0009756 -1.102000e-04 1.000000e-06 1.123000e-04 9.553000e-04 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.608000e-04 1.590000e-05 0.0001385 1.470000e-04 1.558000e-04 1.720000e-04 3.632000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.899753e-01 2.914353e-01 0.0000027 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 4.899726e-01 2.914083e-01 0.0000027 2.350036e-01 4.856672e-01 7.426071e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.184675e-01 1.923821e-01 0.1577290 2.496892e-01 3.810655e-01 5.656560e-01 8.422700e-01 ▇▆▅▃▂
numeric AF_reference 27419 0.9919779 NA NA NA NA NA NA NA 4.044722e-01 2.029077e-01 0.0000000 2.394170e-01 3.742010e-01 5.529150e-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 -0.0001165 0.0002549 0.6499995 0.6477459 0.623765 0.782149 NA
1 54676 rs2462492 C T 0.0001169 0.0002525 0.6400000 0.6433139 0.400401 NA NA
1 91536 rs6702460 G T -0.0000775 0.0002486 0.7600007 0.7553757 0.456846 0.420727 NA
1 534192 rs6680723 C T -0.0002588 0.0002840 0.3599996 0.3621639 0.240959 NA NA
1 706368 rs55727773 A G 0.0000741 0.0001763 0.6700003 0.6741340 0.515645 0.275160 NA
1 752566 rs3094315 G A 0.0000196 0.0001998 0.9199999 0.9218941 0.838945 0.718251 NA
1 752721 rs3131972 A G 0.0000273 0.0001995 0.8900000 0.8912181 0.838573 0.653355 NA
1 754503 rs3115859 G A 0.0000320 0.0001990 0.8700001 0.8724166 0.838026 0.663938 NA
1 754964 rs3131966 C T 0.0000312 0.0001995 0.8800001 0.8759498 0.838657 0.663339 NA
1 755775 rs3131965 A G 0.0000159 0.0002022 0.9400001 0.9375033 0.839770 NA NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51182485 rs6009961 A G 0.0001949 0.0001665 0.2399999 0.2415509 0.715502 0.6383790 NA
22 51186143 rs2879914 T C 0.0003078 0.0001544 0.0460002 0.0461612 0.381825 0.2733630 NA
22 51186228 rs3865766 C T 0.0003102 0.0001504 0.0389996 0.0392201 0.451061 0.4532750 NA
22 51192586 rs5771006 G A 0.0001315 0.0002027 0.5199996 0.5165738 0.167627 0.0848642 NA
22 51193227 rs34608236 T G -0.0002570 0.0002072 0.2099999 0.2148887 0.168490 0.0692891 NA
22 51197266 rs61290853 A G 0.0003398 0.0001553 0.0290001 0.0287017 0.386333 0.4229230 NA
22 51198027 rs34939255 A G -0.0001583 0.0001758 0.3700002 0.3678531 0.254562 0.0984425 NA
22 51211106 rs9628250 T C -0.0001994 0.0001743 0.2500000 0.2526646 0.271547 0.1671330 NA
22 51212875 rs2238837 A C 0.0003172 0.0001656 0.0549997 0.0554726 0.331457 0.3724040 NA
22 51237063 rs3896457 T C 0.0003030 0.0001696 0.0739997 0.0739445 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  -0.00011646:0.000254894:0.187087:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000116935:0.000252521:0.19382:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  -7.74651e-05:0.000248637:0.119186:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000258804:0.00028401:0.443698:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  7.41342e-05:0.000176308:0.173925:0.515645:rs12029736
1   752566  rs3094315   G   A   .   PASS    AF=0.838945 ES:SE:LP:AF:ID  1.95855e-05:0.000199754:0.0362122:0.838945:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838573 ES:SE:LP:AF:ID  2.72897e-05:0.00019954:0.05061:0.838573:rs3131972
1   754503  rs3115859   G   A   .   PASS    AF=0.838026 ES:SE:LP:AF:ID  3.19551e-05:0.000198986:0.0604807:0.838026:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838657 ES:SE:LP:AF:ID  3.11501e-05:0.000199545:0.0555173:0.838657:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.83977  ES:SE:LP:AF:ID  1.58576e-05:0.000202244:0.0268721:0.83977:rs3131965
1   760912  rs1048488   C   T   .   PASS    AF=0.838306 ES:SE:LP:AF:ID  4.79957e-05:0.000198608:0.091515:0.838306:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838427 ES:SE:LP:AF:ID  5.47799e-05:0.000198749:0.107905:0.838427:rs3115850
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  0.000107365:0.000206704:0.221849:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  -2.15296e-05:0.000168707:0.0457575:0.761297:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  6.83083e-05:0.000188452:0.142668:0.265385:rs12124819
1   798400  rs10900604  A   G   .   PASS    AF=0.206591 ES:SE:LP:AF:ID  -0.000100294:0.000179975:0.236572:0.206591:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.20642  ES:SE:LP:AF:ID  -9.91516e-05:0.000180053:0.236572:0.20642:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  0.000121417:0.00017128:0.318759:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  0.000108974:0.000171569:0.275724:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  -0.000363697:0.000241748:0.886057:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  5.39382e-05:0.000161742:0.130768:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  -3.90287e-05:0.000158815:0.091515:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  -3.55573e-05:0.00015881:0.0861861:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  -3.33523e-05:0.000158817:0.0809219:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  -3.43667e-05:0.000158834:0.0809219:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  6.37919e-05:0.000163162:0.154902:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  3.3311e-05:0.000158826:0.0809219:0.294377:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236703 ES:SE:LP:AF:ID  -6.96464e-05:0.000169095:0.167491:0.236703:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236691 ES:SE:LP:AF:ID  -6.90678e-05:0.000169097:0.167491:0.236691:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.23975  ES:SE:LP:AF:ID  -8.73192e-05:0.000168555:0.221849:0.23975:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236693 ES:SE:LP:AF:ID  -6.88118e-05:0.000169096:0.167491:0.236693:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.212421 ES:SE:LP:AF:ID  -0.000189551:0.000175752:0.552842:0.212421:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.212316 ES:SE:LP:AF:ID  -0.000192414:0.000175783:0.568636:0.212316:rs28385272
1   834832  rs4411087   G   C   .   PASS    AF=0.237178 ES:SE:LP:AF:ID  -6.52556e-05:0.000168966:0.154902:0.237178:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.212962 ES:SE:LP:AF:ID  -0.000185983:0.000175533:0.537602:0.212962:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.212924 ES:SE:LP:AF:ID  -0.000185308:0.000175569:0.537602:0.212924:rs28570054
1   835499  rs4422948   A   G   .   PASS    AF=0.241162 ES:SE:LP:AF:ID  -8.82609e-05:0.000167787:0.221849:0.241162:rs4422948
1   836529  rs28731045  C   G   .   PASS    AF=0.213543 ES:SE:LP:AF:ID  -0.000193874:0.00017531:0.568636:0.213543:rs28731045
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  -0.000118469:0.000161901:0.337242:0.269511:rs28705752
1   836924  rs72890788  G   A   .   PASS    AF=0.213513 ES:SE:LP:AF:ID  -0.000189694:0.000175331:0.552842:0.213513:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.214587 ES:SE:LP:AF:ID  -0.000191069:0.000174994:0.568636:0.214587:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  -0.000210023:0.000166633:0.677781:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  -0.000129711:0.000162016:0.376751:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  0.000135509:0.000146493:0.455932:0.400124:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237102 ES:SE:LP:AF:ID  -0.000254843:0.000170158:0.886057:0.237102:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.215391 ES:SE:LP:AF:ID  -0.000192098:0.000175111:0.568636:0.215391:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.235323 ES:SE:LP:AF:ID  -0.00013739:0.000172706:0.366532:0.235323:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  -6.58361e-05:0.000181851:0.142668:0.362606:rs11516185
1   844300  rs61769713  C   G   .   PASS    AF=0.818811 ES:SE:LP:AF:ID  -0.000346946:0.000186898:1.20066:0.818811:rs61769713
1   845283  rs7366404   G   T   .   PASS    AF=0.814497 ES:SE:LP:AF:ID  -0.000260474:0.000185251:0.79588:0.814497:rs7366404