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/ukb-d-import/processed/ukb-d-20445/ukb-d-20445.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/ukb-d-import/processed/ukb-d-20445/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 17:18:04 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20445/ukb-d-20445.vcf.gz ...
Read summary statistics for 11982119 SNPs.
Dropped 10436 SNPs with duplicated rs numbers.
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, 1283008 SNPs remain.
After merging with regression SNP LD, 1283008 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0045 (0.0103)
Lambda GC: 1.0107
Mean Chi^2: 1.0076
Intercept: 1.0042 (0.0061)
Ratio: 0.5508 (0.8123)
Analysis finished at Mon Nov 25 17:20:26 2019
Total time elapsed: 2.0m:21.73s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9489,
    "inflation_factor": 1.007,
    "mean_EFFECT": 0,
    "n": 38007,
    "n_snps": 11982119,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1183703,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 281849,
    "n_est": 37803.4411,
    "ratio_se_n": 0.9973,
    "mean_diff": 0.0001,
    "ratio_diff": 986.4916,
    "sd_y_est1": 0.336,
    "sd_y_est2": 0.3351,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283008,
    "ldsc_nsnp_merge_regression_ld": 1283008,
    "ldsc_observed_scale_h2_beta": 0.0045,
    "ldsc_observed_scale_h2_se": 0.0103,
    "ldsc_intercept_beta": 1.0042,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 1.0107,
    "ldsc_mean_chisq": 1.0076,
    "ldsc_ratio": 0.5526
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 94 0 11972306 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 53342 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32134 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.068752e+00 6.184299e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.889382e+07 5.598039e+07 3.02000e+02 3.269833e+07 6.992076e+07 1.147614e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.610000e-05 9.535300e-03 -1.00304e-01 -3.264100e-03 -2.370000e-05 3.218300e-03 1.358960e-01 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 7.348900e-03 6.058400e-03 2.35550e-03 2.800700e-03 4.438100e-03 1.013150e-02 3.855240e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.988812e-01 2.888324e-01 2.00000e-07 2.488273e-01 4.985067e-01 7.489365e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.988770e-01 2.888349e-01 2.00000e-07 2.488194e-01 4.985023e-01 7.489344e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.149873e-01 2.594454e-01 2.58590e-03 1.548780e-02 9.293850e-02 3.419930e-01 9.974140e-01 ▇▂▁▁▁
numeric AF_reference 281849 0.9764775 NA NA NA NA NA 2.163301e-01 2.509150e-01 0.00000e+00 1.218050e-02 1.124200e-01 3.440500e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.800700e+04 0.000000e+00 3.80070e+04 3.800700e+04 3.800700e+04 3.800700e+04 3.800700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0015644 0.0042174 0.7106978 0.7106947 0.1118270 0.1894970 38007
1 693731 rs12238997 A G 0.0006231 0.0039987 0.8761721 0.8761709 0.1167120 0.1417730 38007
1 707522 rs371890604 G C 0.0029297 0.0044773 0.5128885 0.5128841 0.0983852 0.1293930 38007
1 717587 rs144155419 G A -0.0053258 0.0107447 0.6201347 0.6201302 0.0158577 0.0045926 38007
1 730087 rs148120343 T C 0.0056940 0.0055535 0.3052242 0.3052177 0.0573553 0.0127796 38007
1 731718 rs142557973 T C 0.0015339 0.0037899 0.6856871 0.6856842 0.1227190 0.1543530 38007
1 732032 rs61770163 A C 0.0003495 0.0040337 0.9309580 0.9309574 0.1224230 0.1555510 38007
1 734349 rs141242758 T C 0.0008921 0.0037915 0.8139760 0.8139745 0.1219450 0.1525560 38007
1 740284 rs61770167 C T 0.0001999 0.0172807 0.9907720 0.9907718 0.0058293 0.0023962 38007
1 749963 rs529266287 T TAA -0.0013811 0.0037261 0.7108926 0.7108903 0.8685600 0.7641770 38007
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0031513 0.0052692 0.5498041 0.5498004 0.0570043 0.0309934 38007
23 154923374 rs111332691 T A -0.0136862 0.0059026 0.0204169 0.0204117 0.0438209 0.0116556 38007
23 154925045 rs509981 C T 0.0019463 0.0028167 0.4895826 0.4895789 0.2444680 0.3634440 38007
23 154925895 rs538470 C T 0.0017270 0.0028822 0.5490375 0.5490336 0.2407020 0.3634440 38007
23 154927581 rs644138 G A 0.0007958 0.0026447 0.7634841 0.7634827 0.3019570 0.4635760 38007
23 154929412 rs557132 C T 0.0019921 0.0028172 0.4794927 0.4794882 0.2443710 0.3568210 38007
23 154929637 rs35185538 CT C 0.0016209 0.0029512 0.5828436 0.5828426 0.2277640 0.3011920 38007
23 154929952 rs4012982 CAA C 0.0019464 0.0029691 0.5121262 0.5121210 0.2381350 0.3165560 38007
23 154930230 rs781880 A G 0.0015851 0.0028173 0.5736883 0.5736860 0.2446060 0.3618540 38007
23 154930487 rs781879 T A -0.0086803 0.0097744 0.3745122 0.3745062 0.0190270 0.1263580 38007

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111827 ES:SE:LP:AF:SS:ID   0.00156435:0.00421745:0.148315:0.111827:38007:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116712 ES:SE:LP:AF:SS:ID   0.000623104:0.00399874:0.0574106:0.116712:38007:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0983852    ES:SE:LP:AF:SS:ID   0.00292973:0.00447729:0.289977:0.0983852:38007:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0158577    ES:SE:LP:AF:SS:ID   -0.00532578:0.0107447:0.207514:0.0158577:38007:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0573553    ES:SE:LP:AF:SS:ID   0.00569404:0.00555349:0.515381:0.0573553:38007:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122719 ES:SE:LP:AF:SS:ID   0.00153386:0.00378994:0.163874:0.122719:38007:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122423 ES:SE:LP:AF:SS:ID   0.000349483:0.00403372:0.0310699:0.122423:38007:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121945 ES:SE:LP:AF:SS:ID   0.000892149:0.00379151:0.0893884:0.121945:38007:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00582932   ES:SE:LP:AF:SS:ID   0.000199871:0.0172807:0.00402628:0.00582932:38007:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.86856  ES:SE:LP:AF:SS:ID   -0.00138113:0.00372613:0.148196:0.86856:38007:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.124316 ES:SE:LP:AF:SS:ID   6.97554e-05:0.00369605:0.0065889:0.124316:38007:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143775 ES:SE:LP:AF:SS:ID   0.00252067:0.00365748:0.309172:0.143775:38007:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124413 ES:SE:LP:AF:SS:ID   3.13447e-05:0.00369126:0.00295236:0.124413:38007:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869374 ES:SE:LP:AF:SS:ID   -0.000673761:0.00359983:0.0697985:0.869374:38007:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87391  ES:SE:LP:AF:SS:ID   -0.000493199:0.00365794:0.0492716:0.87391:38007:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129947 ES:SE:LP:AF:SS:ID   0.000773995:0.00360979:0.0808047:0.129947:38007:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0357566    ES:SE:LP:AF:SS:ID   0.00635694:0.00663443:0.471108:0.0357566:38007:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.86898  ES:SE:LP:AF:SS:ID   -0.000534707:0.00359644:0.0546255:0.86898:38007:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869057 ES:SE:LP:AF:SS:ID   -0.00061179:0.00359738:0.063004:0.869057:38007:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.868983 ES:SE:LP:AF:SS:ID   -0.000540843:0.00359633:0.0552904:0.868983:38007:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00500852   ES:SE:LP:AF:SS:ID   -0.00152272:0.0186155:0.029278:0.00500852:38007:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00498236   ES:SE:LP:AF:SS:ID   -0.00158447:0.0186567:0.0304355:0.00498236:38007:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0058628    ES:SE:LP:AF:SS:ID   0.0119582:0.0175204:0.305476:0.0058628:38007:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869059 ES:SE:LP:AF:SS:ID   -0.000380676:0.00358998:0.0383165:0.869059:38007:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.127335 ES:SE:LP:AF:SS:ID   0.000642026:0.00366174:0.0650882:0.127335:38007:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868603 ES:SE:LP:AF:SS:ID   -0.000410936:0.0035805:0.0416139:0.868603:38007:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868002 ES:SE:LP:AF:SS:ID   -0.000367666:0.00357972:0.0370651:0.868002:38007:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868755 ES:SE:LP:AF:SS:ID   -0.000337711:0.00358417:0.0338902:0.868755:38007:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868761 ES:SE:LP:AF:SS:ID   -0.000342111:0.00358445:0.0343454:0.868761:38007:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868763 ES:SE:LP:AF:SS:ID   -0.000344081:0.00358445:0.0345504:0.868763:38007:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869131 ES:SE:LP:AF:SS:ID   -0.000390637:0.0035925:0.0393333:0.869131:38007:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100259 ES:SE:LP:AF:SS:ID   0.00296212:0.00416084:0.321912:0.100259:38007:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00689708   ES:SE:LP:AF:SS:ID   0.000328985:0.015664:0.0073387:0.00689708:38007:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873114 ES:SE:LP:AF:SS:ID   -0.000178509:0.00364619:0.0172979:0.873114:38007:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862938 ES:SE:LP:AF:SS:ID   -0.000929814:0.00358053:0.0995744:0.862938:38007:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.867883 ES:SE:LP:AF:SS:ID   -0.000615175:0.00361235:0.0630959:0.867883:38007:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.864946 ES:SE:LP:AF:SS:ID   -0.000287582:0.00361536:0.0284458:0.864946:38007:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.100483 ES:SE:LP:AF:SS:ID   0.00112059:0.0043156:0.0995635:0.100483:38007:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870015 ES:SE:LP:AF:SS:ID   -0.000293982:0.00365348:0.0287859:0.870015:38007:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870015 ES:SE:LP:AF:SS:ID   -0.000294026:0.00365347:0.0287905:0.870015:38007:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870011 ES:SE:LP:AF:SS:ID   -0.000295466:0.00365348:0.0289358:0.870011:38007:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870351 ES:SE:LP:AF:SS:ID   -0.000203744:0.003655:0.0197484:0.870351:38007:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.127017 ES:SE:LP:AF:SS:ID   0.000367544:0.00365787:0.0362296:0.127017:38007:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106782 ES:SE:LP:AF:SS:ID   0.00125657:0.00397179:0.123943:0.106782:38007:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854057 ES:SE:LP:AF:SS:ID   -0.000461656:0.00357628:0.0470677:0.854057:38007:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83754  ES:SE:LP:AF:SS:ID   -0.00154871:0.00354927:0.178756:0.83754:38007:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.761539 ES:SE:LP:AF:SS:ID   -0.00126692:0.00284446:0.183074:0.761539:38007:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.106441 ES:SE:LP:AF:SS:ID   0.00163332:0.00393046:0.168938:0.106441:38007:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00790799   ES:SE:LP:AF:SS:ID   0.0221857:0.0143889:0.909689:0.00790799:38007:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.130336 ES:SE:LP:AF:SS:ID   0.000314226:0.0036075:0.0312416:0.130336:38007:rs762168062