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-22604_3/ukb-d-22604_3.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-22604_3/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 16:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22604_3/ukb-d-22604_3.vcf.gz ...
Read summary statistics for 13563393 SNPs.
Dropped 12678 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, 1283500 SNPs remain.
After merging with regression SNP LD, 1283500 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0117 (0.006)
Lambda GC: 1.0189
Mean Chi^2: 1.0268
Intercept: 1.0093 (0.0059)
Ratio: 0.3474 (0.2182)
Analysis finished at Mon Nov 25 16:43:03 2019
Total time elapsed: 2.0m:44.17s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0082,
    "mean_EFFECT": 0,
    "n": 75177,
    "n_snps": 13563393,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1251060,
    "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": 562172,
    "n_est": 75447.4324,
    "ratio_se_n": 1.0018,
    "mean_diff": 0,
    "ratio_diff": 15.2663,
    "sd_y_est1": 0.4567,
    "sd_y_est2": 0.4575,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283500,
    "ldsc_nsnp_merge_regression_ld": 1283500,
    "ldsc_observed_scale_h2_beta": 0.0117,
    "ldsc_observed_scale_h2_se": 0.006,
    "ldsc_intercept_beta": 1.0093,
    "ldsc_intercept_se": 0.0059,
    "ldsc_lambda_gc": 1.0189,
    "ldsc_mean_chisq": 1.0268,
    "ldsc_ratio": 0.347
}

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 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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 94 0 13551378 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57038 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33329 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051500e+00 6.185025e+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 7.902521e+07 5.591715e+07 3.02000e+02 3.292786e+07 7.013476e+07 1.148632e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.640000e-05 1.371480e-02 -1.79049e-01 -3.608100e-03 3.830000e-05 3.671700e-03 1.518390e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 9.852800e-03 9.493300e-03 1.95740e-03 2.816500e-03 5.178300e-03 1.414460e-02 4.788470e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.984398e-01 2.897649e-01 3.00000e-07 2.468590e-01 4.982519e-01 7.497405e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.984377e-01 2.897662e-01 3.00000e-07 2.468557e-01 4.982505e-01 7.497408e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.911163e-01 2.544894e-01 1.00000e-03 7.513700e-03 6.035730e-02 2.958730e-01 9.989990e-01 ▇▂▁▁▁
numeric AF_reference 562172 0.9585523 NA NA NA NA NA 1.965590e-01 2.471553e-01 0.00000e+00 5.790700e-03 8.446490e-02 3.085060e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 7.517700e+04 0.000000e+00 7.51770e+04 7.517700e+04 7.517700e+04 7.517700e+04 7.517700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0004819 0.0041175 0.9068330 0.9068328 0.1115640 0.1894970 75177
1 693731 rs12238997 A G 0.0001451 0.0038985 0.9703180 0.9703176 0.1164770 0.1417730 75177
1 707522 rs371890604 G C 0.0024742 0.0043817 0.5722937 0.5722925 0.0977849 0.1293930 75177
1 717587 rs144155419 G A -0.0152731 0.0103963 0.1418120 0.1418084 0.0159063 0.0045926 75177
1 723329 rs189787166 A T 0.0812959 0.0304837 0.0076579 0.0076563 0.0017753 0.0003994 75177
1 730087 rs148120343 T C 0.0015023 0.0054056 0.7810809 0.7810797 0.0569733 0.0127796 75177
1 731718 rs142557973 T C 0.0012222 0.0036982 0.7410423 0.7410403 0.1223380 0.1543530 75177
1 732032 rs61770163 A C 0.0004622 0.0039467 0.9067641 0.9067640 0.1218660 0.1555510 75177
1 734349 rs141242758 T C 0.0012048 0.0037004 0.7447388 0.7447366 0.1216090 0.1525560 75177
1 740284 rs61770167 C T 0.0258827 0.0167605 0.1225279 0.1225235 0.0058807 0.0023962 75177
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0009955 0.0043820 0.8202920 0.8202914 0.0546566 0.0309934 75177
23 154923374 rs111332691 T A -0.0046962 0.0047244 0.3202071 0.3202047 0.0450404 0.0116556 75177
23 154925045 rs509981 C T 0.0010986 0.0022854 0.6307278 0.6307269 0.2443920 0.3634440 75177
23 154925895 rs538470 C T 0.0018802 0.0023364 0.4209747 0.4209728 0.2408890 0.3634440 75177
23 154927581 rs644138 G A 0.0007790 0.0021522 0.7173944 0.7173934 0.2994310 0.4635760 75177
23 154929412 rs557132 C T 0.0010369 0.0022860 0.6501177 0.6501141 0.2442760 0.3568210 75177
23 154929637 rs35185538 CT C -0.0010162 0.0023866 0.6702580 0.6702562 0.2287170 0.3011920 75177
23 154929952 rs4012982 CAA C 0.0008077 0.0024053 0.7370246 0.7370235 0.2382650 0.3165560 75177
23 154930230 rs781880 A G 0.0011629 0.0022854 0.6108534 0.6108514 0.2447030 0.3618540 75177
23 154930487 rs781879 T A -0.0098442 0.0077654 0.2049099 0.2049063 0.0195950 0.1263580 75177

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111564 ES:SE:LP:AF:SS:ID   -0.000481889:0.0041175:0.0424727:0.111564:75177:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116477 ES:SE:LP:AF:SS:ID   0.000145064:0.00389852:0.0130859:0.116477:75177:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0977849    ES:SE:LP:AF:SS:ID   0.00247424:0.00438168:0.242381:0.0977849:75177:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0159063    ES:SE:LP:AF:SS:ID   -0.0152731:0.0103963:0.848287:0.0159063:75177:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00177526   ES:SE:LP:AF:SS:ID   0.0812959:0.0304837:2.11589:0.00177526:75177:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0569733    ES:SE:LP:AF:SS:ID   0.00150228:0.00540559:0.107304:0.0569733:75177:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122338 ES:SE:LP:AF:SS:ID   0.00122217:0.00369821:0.130157:0.122338:75177:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121866 ES:SE:LP:AF:SS:ID   0.000462246:0.00394673:0.0425057:0.121866:75177:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121609 ES:SE:LP:AF:SS:ID   0.00120481:0.00370042:0.127996:0.121609:75177:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00588068   ES:SE:LP:AF:SS:ID   0.0258827:0.0167605:0.911765:0.00588068:75177:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00180846   ES:SE:LP:AF:SS:ID   0.00792731:0.0326455:0.0925145:0.00180846:75177:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868816 ES:SE:LP:AF:SS:ID   -0.000372978:0.00364092:0.0369648:0.868816:75177:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00165878   ES:SE:LP:AF:SS:ID   0.0114037:0.0315589:0.143972:0.00165878:75177:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123758 ES:SE:LP:AF:SS:ID   -3.00165e-05:0.00360979:0.00289115:0.123758:75177:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143056 ES:SE:LP:AF:SS:ID   0.000497721:0.00357655:0.050941:0.143056:75177:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123902 ES:SE:LP:AF:SS:ID   -1.4355e-05:0.00360442:0.00138239:0.123902:75177:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869912 ES:SE:LP:AF:SS:ID   0.000554712:0.0035122:0.0582372:0.869912:75177:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874529 ES:SE:LP:AF:SS:ID   -0.000573063:0.003569:0.0592669:0.874529:75177:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129553 ES:SE:LP:AF:SS:ID   -0.000439815:0.00352342:0.0454382:0.129553:75177:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0360084    ES:SE:LP:AF:SS:ID   0.00535275:0.00641723:0.393388:0.0360084:75177:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869552 ES:SE:LP:AF:SS:ID   0.000496187:0.00350939:0.0518003:0.869552:75177:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869633 ES:SE:LP:AF:SS:ID   0.000354154:0.0035107:0.0363788:0.869633:75177:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869547 ES:SE:LP:AF:SS:ID   0.000495575:0.00350924:0.0517352:0.869547:75177:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00528791   ES:SE:LP:AF:SS:ID   -0.00203674:0.0176117:0.0419462:0.00528791:75177:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00525393   ES:SE:LP:AF:SS:ID   -0.0023259:0.017656:0.0480824:0.00525393:75177:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558736   ES:SE:LP:AF:SS:ID   -0.027436:0.0173616:0.942912:0.00558736:75177:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869525 ES:SE:LP:AF:SS:ID   0.000493251:0.00350172:0.0515963:0.869525:75177:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126948 ES:SE:LP:AF:SS:ID   -7.74108e-05:0.00357601:0.00756623:0.126948:75177:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869049 ES:SE:LP:AF:SS:ID   0.000729315:0.00349284:0.0785201:0.869049:75177:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868472 ES:SE:LP:AF:SS:ID   0.000415124:0.00349119:0.0431835:0.868472:75177:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869198 ES:SE:LP:AF:SS:ID   0.000570492:0.00349593:0.0602956:0.869198:75177:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869203 ES:SE:LP:AF:SS:ID   0.000570586:0.00349616:0.0603016:0.869203:75177:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869206 ES:SE:LP:AF:SS:ID   0.000571667:0.0034962:0.0604223:0.869206:75177:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869689 ES:SE:LP:AF:SS:ID   0.000444176:0.00350525:0.0461606:0.869689:75177:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991701    ES:SE:LP:AF:SS:ID   0.00433213:0.00407825:0.540419:0.0991701:75177:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00642849   ES:SE:LP:AF:SS:ID   -0.0134912:0.0157949:0.405581:0.00642849:75177:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873648 ES:SE:LP:AF:SS:ID   0.000171083:0.00355664:0.0169897:0.873648:75177:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863065 ES:SE:LP:AF:SS:ID   0.000850478:0.00349004:0.0928714:0.863065:75177:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868456 ES:SE:LP:AF:SS:ID   -0.000608363:0.00352341:0.064031:0.868456:75177:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865365 ES:SE:LP:AF:SS:ID   0.000331947:0.00352466:0.0338733:0.865365:75177:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995942    ES:SE:LP:AF:SS:ID   -0.00270649:0.00421774:0.283099:0.0995942:75177:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870659 ES:SE:LP:AF:SS:ID   0.000845658:0.00356451:0.0901937:0.870659:75177:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870659 ES:SE:LP:AF:SS:ID   0.000845443:0.00356451:0.0901686:0.870659:75177:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870656 ES:SE:LP:AF:SS:ID   0.00084451:0.00356453:0.0900596:0.870656:75177:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871036 ES:SE:LP:AF:SS:ID   0.000644274:0.00356627:0.0672032:0.871036:75177:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126586 ES:SE:LP:AF:SS:ID   0.000309351:0.00357024:0.0310727:0.126586:75177:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10597  ES:SE:LP:AF:SS:ID   0.00176698:0.00388125:0.187807:0.10597:75177:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854336 ES:SE:LP:AF:SS:ID   0.00142762:0.00348909:0.16595:0.854336:75177:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168869   ES:SE:LP:AF:SS:ID   0.0790958:0.0305557:2.01596:0.00168869:75177:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839618 ES:SE:LP:AF:SS:ID   0.00077556:0.00344658:0.0851483:0.839618:75177:rs376645387