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/dev/ieu-a-import/processed/ieu-a-1041/ieu-a-1041.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1041/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 17:15:42 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1041/ieu-a-1041.vcf.gz ...
Read summary statistics for 6703307 SNPs.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1171769 SNPs remain.
After merging with regression SNP LD, 1171769 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1786 (0.0426)
Lambda GC: 1.0386
Mean Chi^2: 1.0417
Intercept: 1.0016 (0.0065)
Ratio: 0.0391 (0.1568)
Analysis finished at Tue Feb  4 17:16:55 2020
Total time elapsed: 1.0m:12.87s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9442,
    "inflation_factor": 1.0288,
    "mean_EFFECT": 0.0775,
    "n": 11373,
    "n_snps": 6703307,
    "n_clumped_hits": 1,
    "n_p_sig": 114,
    "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": 93224,
    "n_est": 10992.9166,
    "ratio_se_n": 0.9831,
    "mean_diff": -0.0775,
    "ratio_diff": 8585.5092,
    "sd_y_est1": 146863.3363,
    "sd_y_est2": 144388.4108,
    "r2_sum1": 83202560.0977,
    "r2_sum2": 0.0039,
    "r2_sum3": 0.004,
    "r2_sum4": 0.0032,
    "ldsc_nsnp_merge_refpanel_ld": 1171769,
    "ldsc_nsnp_merge_regression_ld": 1171769,
    "ldsc_observed_scale_h2_beta": 0.1786,
    "ldsc_observed_scale_h2_se": 0.0426,
    "ldsc_intercept_beta": 1.0016,
    "ldsc_intercept_se": 0.0065,
    "ldsc_lambda_gc": 1.0386,
    "ldsc_mean_chisq": 1.0417,
    "ldsc_ratio": 0.0384
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
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 TRUE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 6703307 0 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
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.608047e+00 5.737544e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.938888e+07 5.619011e+07 8.28000e+02 3.327035e+07 7.033009e+07 1.150475e+08 2.492178e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 7.753160e-02 5.437774e+03 -7.13927e+04 -2.216910e+03 -1.666810e+01 2.200120e+03 7.842630e+04 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 4.336621e+03 3.239590e+03 1.80836e+03 2.123460e+03 2.902200e+03 5.279540e+03 2.662790e+04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.952621e-01 2.899759e-01 0.00000e+00 2.428002e-01 4.939000e-01 7.462992e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.952620e-01 2.899759e-01 0.00000e+00 2.427786e-01 4.939162e-01 7.463393e-01 9.999996e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.532153e-01 2.613782e-01 2.63900e-03 3.958000e-02 1.504000e-01 4.024000e-01 9.986810e-01 ▇▂▂▁▁
numeric AF_reference 93224 0.9860928 NA NA NA NA NA 2.555695e-01 2.530702e-01 0.00000e+00 4.852240e-02 1.655350e-01 4.007590e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.097062e+04 1.077650e+03 5.00100e+03 1.137300e+04 1.137300e+04 1.137300e+04 1.137300e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A 5372.10 2664.15 0.0437502 0.0437539 0.8364 0.718251 9898
1 752721 rs3131972 A G 5430.51 2744.23 0.0478300 0.0478292 0.8325 0.653355 9898
1 752894 rs3131971 T C 5965.06 2927.58 0.0415997 0.0415960 0.7955 0.753195 9898
1 753541 rs2073813 G A -6887.31 3289.00 0.0362602 0.0362561 0.1332 0.301917 9898
1 754182 rs3131969 A G 6851.83 3324.64 0.0393097 0.0393103 0.8668 0.678514 9898
1 754192 rs3131968 A G 6867.03 3350.21 0.0403896 0.0403907 0.8654 0.678514 9898
1 754334 rs3131967 T C 5888.01 4269.64 0.1679001 0.1678820 0.8377 0.684305 5455
1 754503 rs3115859 G A 5975.82 2971.69 0.0443302 0.0443343 0.8311 0.663938 9898
1 754964 rs3131966 C T 5619.05 3300.72 0.0886890 0.0886858 0.8074 0.663339 9348
1 755775 rs3131965 A G 4917.80 3818.20 0.1977002 0.1977498 0.7942 NA 6368
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51165390 rs76268556 C T -8661.380 8878.64 0.3293002 0.3292974 0.025070 0.0515176 7487
22 51165664 rs8137951 G A 1889.300 2162.26 0.3822003 0.3822480 0.281000 0.4063500 10495
22 51167604 rs150488734 C T 5972.280 11463.20 0.6024001 0.6023696 0.007916 0.0055910 9049
22 51169045 rs8140772 C T -6133.760 8629.14 0.4771995 0.4771962 0.027700 0.0632987 7487
22 51171667 rs41281537 G A -6098.180 8632.35 0.4799003 0.4799187 0.027700 0.0577077 7487
22 51171693 rs756638 G A 915.771 2384.70 0.7010000 0.7009641 0.259900 0.3049120 9748
22 51171783 rs115712102 C T 8963.370 12642.60 0.4782996 0.4783359 0.015830 0.0067891 5851
22 51172460 rs5770824 T C -6171.420 8666.14 0.4764003 0.4763842 0.027700 0.0684904 7487
22 51175626 rs3810648 A G 2294.730 4207.55 0.5855001 0.5854895 0.052770 0.1084270 10755
22 51178090 rs2285395 G A 2221.810 4385.47 0.6123997 0.6124146 0.051450 0.0666933 10755

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.8364   ES:SE:LP:AF:SS:ID   5372.1:2664.15:1.35902:0.8364:9898:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.8325   ES:SE:LP:AF:SS:ID   5430.51:2744.23:1.3203:0.8325:9898:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.7955   ES:SE:LP:AF:SS:ID   5965.06:2927.58:1.38091:0.7955:9898:rs3131971
1   753541  rs2073813   G   A   .   PASS    AF=0.1332   ES:SE:LP:AF:SS:ID   -6887.31:3289:1.44057:0.1332:9898:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.8668   ES:SE:LP:AF:SS:ID   6851.83:3324.64:1.4055:0.8668:9898:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8654   ES:SE:LP:AF:SS:ID   6867.03:3350.21:1.39373:0.8654:9898:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.8377   ES:SE:LP:AF:SS:ID   5888.01:4269.64:0.774949:0.8377:5455:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.8311   ES:SE:LP:AF:SS:ID   5975.82:2971.69:1.3533:0.8311:9898:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.8074   ES:SE:LP:AF:SS:ID   5619.05:3300.72:1.05213:0.8074:9348:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.7942   ES:SE:LP:AF:SS:ID   4917.8:3818.2:0.703993:0.7942:6368:rs3131965
1   756604  rs3131962   A   G   .   PASS    AF=0.8351   ES:SE:LP:AF:SS:ID   4698.73:4112.12:0.596536:0.8351:5741:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.8668   ES:SE:LP:AF:SS:ID   5373.86:4167.27:0.705093:0.8668:5936:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8681   ES:SE:LP:AF:SS:ID   5398.47:4168.29:0.709298:0.8681:5936:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8668   ES:SE:LP:AF:SS:ID   5389.3:4167.18:0.707966:0.8668:5936:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.8391   ES:SE:LP:AF:SS:ID   4200.66:3687.11:0.594142:0.8391:7276:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8641   ES:SE:LP:AF:SS:ID   6632.21:4385.99:0.884389:0.8641:5069:rs3131954
1   768448  rs12562034  G   A   .   PASS    AF=0.09763  ES:SE:LP:AF:SS:ID   -2492.23:3639.43:0.306713:0.09763:7192:rs12562034
1   769963  rs7518545   G   A   .   PASS    AF=0.09499  ES:SE:LP:AF:SS:ID   -2680.49:3813.49:0.316863:0.09499:7192:rs7518545
1   798400  rs10900604  A   G   .   PASS    AF=0.2203   ES:SE:LP:AF:SS:ID   -1649.25:3527.97:0.193684:0.2203:5884:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.2269   ES:SE:LP:AF:SS:ID   -1717.43:3284.97:0.221053:0.2269:5884:rs11240777
1   876499  rs4372192   A   G   .   PASS    AF=0.94987  ES:SE:LP:AF:SS:ID   3037.97:6363.45:0.198528:0.94987:6697:rs4372192
1   879676  rs6605067   G   A   .   PASS    AF=0.94987  ES:SE:LP:AF:SS:ID   2987.87:6233.81:0.199489:0.94987:6697:rs6605067
1   879687  rs2839  T   C   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2325.38:6142.05:0.151811:0.95119:7247:rs2839
1   880238  rs3748592   A   G   .   PASS    AF=0.95251  ES:SE:LP:AF:SS:ID   2360.92:6130.85:0.154778:0.95251:7247:rs3748592
1   882803  rs2340582   A   G   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   1978.51:5859.59:0.133358:0.95119:7247:rs2340582
1   884815  rs4246503   A   G   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2313.31:5649.32:0.166088:0.95119:7247:rs4246503
1   885676  rs4970377   C   A   .   PASS    AF=0.94327  ES:SE:LP:AF:SS:ID   2374.42:5584.23:0.173472:0.94327:7247:rs4970377
1   885689  rs4970452   G   A   .   PASS    AF=0.94987  ES:SE:LP:AF:SS:ID   2380.51:5734.81:0.168706:0.94987:7247:rs4970452
1   885699  rs4970376   A   G   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2296.44:5623.65:0.165579:0.95119:7247:rs4970376
1   886006  rs4970375   T   C   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2365.32:5558.4:0.173666:0.95119:7247:rs4970375
1   887801  rs3828047   A   G   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2428.78:5454.54:0.18303:0.95119:7247:rs3828047
1   888639  rs3748596   T   C   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2428.56:5442.47:0.183494:0.95119:7247:rs3748596
1   888659  rs3748597   T   C   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2434.3:5438.29:0.184157:0.95119:7247:rs3748597
1   889238  rs3828049   G   A   .   PASS    AF=0.04749  ES:SE:LP:AF:SS:ID   -2316.12:5549.55:0.169796:0.04749:7247:rs3828049
1   889713  rs13303051  C   A   .   PASS    AF=0.94063  ES:SE:LP:AF:SS:ID   2976.96:5292.61:0.241239:0.94063:7247:rs13303051
1   891021  rs13302957  G   A   .   PASS    AF=0.94591  ES:SE:LP:AF:SS:ID   2500.97:5462.69:0.189029:0.94591:7247:rs13302957
1   892745  rs13303227  G   A   .   PASS    AF=0.95119  ES:SE:LP:AF:SS:ID   2214.39:5549.89:0.161214:0.95119:7247:rs13303227
1   893280  rs4970371   G   A   .   PASS    AF=0.95251  ES:SE:LP:AF:SS:ID   2234:5679.46:0.158578:0.95251:7247:rs4970371
1   893631  rs6605069   A   G   .   PASS    AF=0.93931  ES:SE:LP:AF:SS:ID   2753.7:5465.59:0.211549:0.93931:7247:rs6605069
1   893719  rs4970445   G   A   .   PASS    AF=0.92744  ES:SE:LP:AF:SS:ID   3473.13:5618.24:0.27043:0.92744:6697:rs4970445
1   896476  rs28393498  A   G   .   PASS    AF=0.93536  ES:SE:LP:AF:SS:ID   923.597:5956.28:0.0570995:0.93536:6697:rs28393498
1   897564  rs13303229  T   C   .   PASS    AF=0.94459  ES:SE:LP:AF:SS:ID   3289.83:5926.9:0.237471:0.94459:6697:rs13303229
1   897738  rs6696971   C   T   .   PASS    AF=0.05541  ES:SE:LP:AF:SS:ID   -3438.27:5966.31:0.248413:0.05541:6697:rs6696971
1   898323  rs6605071   T   C   .   PASS    AF=0.94723  ES:SE:LP:AF:SS:ID   1749.2:6085.15:0.111371:0.94723:7247:rs6605071
1   898467  rs41285808  C   T   .   PASS    AF=0.04617  ES:SE:LP:AF:SS:ID   -1649.24:6061.37:0.104799:0.04617:7247:rs41285808
1   913889  rs2340596   G   A   .   PASS    AF=0.6003   ES:SE:LP:AF:SS:ID   2836.7:2414.78:0.619608:0.6003:8249:rs2340596
1   914940  rs13303033  T   C   .   PASS    AF=0.5858   ES:SE:LP:AF:SS:ID   3371.99:2307.32:0.841939:0.5858:8249:rs13303033
1   916834  rs6694632   G   A   .   PASS    AF=0.5989   ES:SE:LP:AF:SS:ID   3075.94:2284.72:0.749092:0.5989:8249:rs6694632
1   918384  rs13303118  G   T   .   PASS    AF=0.5871   ES:SE:LP:AF:SS:ID   3384.02:2245.02:0.880414:0.5871:8249:rs13303118
1   918573  rs2341354   A   G   .   PASS    AF=0.5963   ES:SE:LP:AF:SS:ID   3039.74:2254.75:0.750557:0.5963:8249:rs2341354