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-8388/UKB-b-8388_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8388/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:41:34 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8388/UKB-b-8388_data.vcf.gz ...
Read summary statistics for 3736159 SNPs.
Dropped 644 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, 902402 SNPs remain.
After merging with regression SNP LD, 902402 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1246 (0.0423)
Lambda GC: 1.0576
Mean Chi^2: 1.0779
Intercept: 1.0175 (0.0112)
Ratio: 0.2244 (0.1442)
Analysis finished at Thu Oct 17 14:42:23 2019
Total time elapsed: 49.18s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8639,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 9,
    "n_p_sig": 8738,
    "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": 30221,
    "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": 902402,
    "ldsc_nsnp_merge_regression_ld": 902402,
    "ldsc_observed_scale_h2_beta": 0.1246,
    "ldsc_observed_scale_h2_se": 0.0423,
    "ldsc_intercept_beta": 1.0175,
    "ldsc_intercept_se": 0.0112,
    "ldsc_lambda_gc": 1.0576,
    "ldsc_mean_chisq": 1.0779,
    "ldsc_ratio": 0.2246
}
 

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 TRUE
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 3 58 0 3735518 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 3736159 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 8.663840e+00 5.770444e+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 7.854937e+07 5.675336e+07 828.0000000 3.159218e+07 6.890210e+07 1.147166e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 4.260000e-05 4.231900e-03 -0.0661569 -2.460300e-03 -6.000000e-06 2.476100e-03 1.477540e-01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.590100e-03 4.270000e-04 0.0030091 3.219600e-03 3.452900e-03 3.887500e-03 1.097960e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.892107e-01 2.932202e-01 0.0000000 2.300001e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.892116e-01 2.931963e-01 0.0000000 2.319425e-01 4.868317e-01 7.439129e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.053167e-01 2.040385e-01 0.1350310 2.268470e-01 3.622210e-01 5.587495e-01 8.649690e-01 ▇▅▃▃▂
numeric AF_reference 30221 0.9919112 NA NA NA NA NA NA NA 3.929471e-01 2.108370e-01 0.0000000 2.200480e-01 3.572280e-01 5.461260e-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 0.0085174 0.0055701 0.1299999 0.1262364 0.623063 0.782149 NA
1 54676 rs2462492 C T 0.0013178 0.0054833 0.8100000 0.8100792 0.402242 NA NA
1 91536 rs6702460 G T 0.0070738 0.0054248 0.1900002 0.1922444 0.458495 0.420727 NA
1 534192 rs6680723 C T 0.0055874 0.0061720 0.3700002 0.3653139 0.241507 NA NA
1 706368 rs55727773 A G -0.0030740 0.0038533 0.4299995 0.4250093 0.513571 0.275160 NA
1 729679 rs4951859 C G 0.0002776 0.0045016 0.9500000 0.9508221 0.843741 0.639976 NA
1 752566 rs3094315 G A -0.0012962 0.0043609 0.7700005 0.7662985 0.839663 0.718251 NA
1 752721 rs3131972 A G -0.0011116 0.0043507 0.8000000 0.7983398 0.839108 0.653355 NA
1 754503 rs3115859 G A -0.0010307 0.0043423 0.8100000 0.8123687 0.838654 0.663938 NA
1 754964 rs3131966 C T -0.0012782 0.0043550 0.7700005 0.7691424 0.839288 0.663339 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51186143 rs2879914 T C -0.0051355 0.0033960 0.1299999 0.1304741 0.383075 0.2733630 NA
22 51186228 rs3865766 C T -0.0042367 0.0033007 0.2000000 0.1992975 0.452633 0.4532750 NA
22 51192586 rs5771006 G A -0.0009128 0.0044435 0.8400000 0.8372496 0.167760 0.0848642 NA
22 51193227 rs34608236 T G 0.0050746 0.0045277 0.2599998 0.2623773 0.169087 0.0692891 NA
22 51197266 rs61290853 A G -0.0043891 0.0033888 0.2000000 0.1952570 0.387148 0.4229230 NA
22 51198027 rs34939255 A G 0.0054463 0.0038581 0.1600000 0.1580536 0.253011 0.0984425 NA
22 51211106 rs9628250 T C 0.0065458 0.0038141 0.0860003 0.0861252 0.269402 0.1671330 NA
22 51212875 rs2238837 A C -0.0056476 0.0036392 0.1199999 0.1206958 0.333027 0.3724040 NA
22 51219006 rs28729663 G A 0.0031669 0.0046428 0.5000000 0.4951667 0.138458 0.2052720 NA
22 51237063 rs3896457 T C -0.0073614 0.0037173 0.0479999 0.0476716 0.298098 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623063 ES:SE:LP:AF:ID  0.00851736:0.00557013:0.886057:0.623063:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.402242 ES:SE:LP:AF:ID  0.00131777:0.00548331:0.091515:0.402242:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.458495 ES:SE:LP:AF:ID  0.00707378:0.00542481:0.721246:0.458495:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.241507 ES:SE:LP:AF:ID  0.00558738:0.00617195:0.431798:0.241507:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.513571 ES:SE:LP:AF:ID  -0.00307398:0.00385326:0.366532:0.513571:rs12029736
1   729679  rs4951859   C   G   .   PASS    AF=0.843741 ES:SE:LP:AF:ID  0.000277632:0.00450157:0.0222764:0.843741:rs4951859
1   752566  rs3094315   G   A   .   PASS    AF=0.839663 ES:SE:LP:AF:ID  -0.00129615:0.00436091:0.113509:0.839663:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.839108 ES:SE:LP:AF:ID  -0.00111158:0.00435067:0.09691:0.839108:rs3131972
1   754503  rs3115859   G   A   .   PASS    AF=0.838654 ES:SE:LP:AF:ID  -0.00103074:0.00434231:0.091515:0.838654:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.839288 ES:SE:LP:AF:ID  -0.00127817:0.00435497:0.113509:0.839288:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.84041  ES:SE:LP:AF:ID  -0.00115724:0.00441705:0.102373:0.84041:rs3131965
1   760912  rs1048488   C   T   .   PASS    AF=0.839436 ES:SE:LP:AF:ID  -0.00115742:0.00434267:0.102373:0.839436:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.839517 ES:SE:LP:AF:ID  -0.00113565:0.00434536:0.102373:0.839517:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862978 ES:SE:LP:AF:ID  -0.0029261:0.00464524:0.275724:0.862978:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.708189 ES:SE:LP:AF:ID  -0.00149244:0.0045249:0.130768:0.708189:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761243 ES:SE:LP:AF:ID  -0.00143619:0.00370259:0.154902:0.761243:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265093 ES:SE:LP:AF:ID  -0.00418453:0.00412954:0.508638:0.265093:rs12124819
1   787399  rs2905055   G   T   .   PASS    AF=0.861364 ES:SE:LP:AF:ID  -0.00170446:0.00466208:0.148742:0.861364:rs2905055
1   787685  rs2905054   G   T   .   PASS    AF=0.861663 ES:SE:LP:AF:ID  -0.00167129:0.00466053:0.142668:0.861663:rs2905054
1   795988  rs59380221  C   T   .   PASS    AF=0.14387  ES:SE:LP:AF:ID  0.00571559:0.00482368:0.619789:0.14387:rs59380221
1   798400  rs10900604  A   G   .   PASS    AF=0.206542 ES:SE:LP:AF:ID  -0.00028843:0.00393445:0.0268721:0.206542:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.206384 ES:SE:LP:AF:ID  -0.000324565:0.00393657:0.0315171:0.206384:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.773834 ES:SE:LP:AF:ID  0.000291747:0.00376498:0.0268721:0.773834:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.773882 ES:SE:LP:AF:ID  4.55908e-05:0.00376968:0.00436481:0.773882:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340304 ES:SE:LP:AF:ID  0.00040323:0.00530675:0.0268721:0.340304:rs74461805
1   824398  rs7538305   A   C   .   PASS    AF=0.139097 ES:SE:LP:AF:ID  0.00089379:0.00466637:0.0705811:0.139097:rs7538305
1   830181  rs28444699  A   G   .   PASS    AF=0.696493 ES:SE:LP:AF:ID  -0.00616187:0.00351055:1.10237:0.696493:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.704756 ES:SE:LP:AF:ID  -0.00473071:0.00345:0.769551:0.704756:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.704844 ES:SE:LP:AF:ID  -0.00465232:0.00344991:0.744727:0.704844:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.704978 ES:SE:LP:AF:ID  -0.00470756:0.00344962:0.769551:0.704978:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705003 ES:SE:LP:AF:ID  -0.004704:0.00344973:0.769551:0.705003:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.72883  ES:SE:LP:AF:ID  -0.00636576:0.00354031:1.14267:0.72883:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.295023 ES:SE:LP:AF:ID  0.00468528:0.00344975:0.769551:0.295023:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236977 ES:SE:LP:AF:ID  0.00266496:0.00368305:0.327902:0.236977:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236973 ES:SE:LP:AF:ID  0.00264718:0.003683:0.327902:0.236973:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.239732 ES:SE:LP:AF:ID  0.00285262:0.00367177:0.356547:0.239732:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.23702  ES:SE:LP:AF:ID  0.00259069:0.0036825:0.318759:0.23702:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.213211 ES:SE:LP:AF:ID  0.00447134:0.0038168:0.619789:0.213211:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.213129 ES:SE:LP:AF:ID  0.00448272:0.00381692:0.619789:0.213129:rs28385272
1   834832  rs4411087   G   C   .   PASS    AF=0.237454 ES:SE:LP:AF:ID  0.00256429:0.00368072:0.309804:0.237454:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.213802 ES:SE:LP:AF:ID  0.00441191:0.00381205:0.60206:0.213802:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.213773 ES:SE:LP:AF:ID  0.00444098:0.00381273:0.619789:0.213773:rs28570054
1   835499  rs4422948   A   G   .   PASS    AF=0.241985 ES:SE:LP:AF:ID  0.00266428:0.00364957:0.327902:0.241985:rs4422948
1   836529  rs28731045  C   G   .   PASS    AF=0.214692 ES:SE:LP:AF:ID  0.00471826:0.00380606:0.657577:0.214692:rs28731045
1   836896  rs28705752  T   C   .   PASS    AF=0.269664 ES:SE:LP:AF:ID  0.00256083:0.00354273:0.327902:0.269664:rs28705752
1   836924  rs72890788  G   A   .   PASS    AF=0.214603 ES:SE:LP:AF:ID  0.00480125:0.00380681:0.677781:0.214603:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.21581  ES:SE:LP:AF:ID  0.00473186:0.00379812:0.677781:0.21581:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.247046 ES:SE:LP:AF:ID  0.00449913:0.0036364:0.657577:0.247046:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270302 ES:SE:LP:AF:ID  0.0026198:0.00354417:0.337242:0.270302:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400334 ES:SE:LP:AF:ID  0.00231889:0.00317945:0.327902:0.400334:rs4970382