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-20548_5/ukb-d-20548_5.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-20548_5/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 16:47:25 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20548_5/ukb-d-20548_5.vcf.gz ...
Read summary statistics for 11551021 SNPs.
Dropped 9853 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, 1282673 SNPs remain.
After merging with regression SNP LD, 1282673 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0182 (0.0044)
Lambda GC: 1.0469
Mean Chi^2: 1.0381
Intercept: 0.9959 (0.0073)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:49:19 2019
Total time elapsed: 1.0m:54.52s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9477,
    "inflation_factor": 1.0435,
    "mean_EFFECT": 0,
    "n": 114422,
    "n_snps": 11551021,
    "n_clumped_hits": 2,
    "n_p_sig": 9,
    "n_mono": 0,
    "n_ns": 1164206,
    "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": 246841,
    "n_est": 114628.8165,
    "ratio_se_n": 1.0009,
    "mean_diff": 0.0001,
    "ratio_diff": 87.3833,
    "sd_y_est1": 0.1788,
    "sd_y_est2": 0.179,
    "r2_sum1": 0,
    "r2_sum2": 0.0006,
    "r2_sum3": 0.0006,
    "r2_sum4": 0.0006,
    "ldsc_nsnp_merge_refpanel_ld": 1282673,
    "ldsc_nsnp_merge_regression_ld": 1282673,
    "ldsc_observed_scale_h2_beta": 0.0182,
    "ldsc_observed_scale_h2_se": 0.0044,
    "ldsc_intercept_beta": 0.9959,
    "ldsc_intercept_se": 0.0073,
    "ldsc_lambda_gc": 1.0469,
    "ldsc_mean_chisq": 1.0381,
    "ldsc_ratio": -0.1076
}

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 11541774 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 52367 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 31766 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.073241e+00 6.184125e+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 7.885661e+07 5.599604e+07 3.02000e+02 3.264838e+07 6.986802e+07 1.147336e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.210000e-05 2.632800e-03 -2.54795e-02 -9.758000e-04 -1.200000e-06 9.676000e-04 3.961730e-02 ▁▇▅▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.065900e-03 1.614700e-03 6.19000e-04 8.506000e-04 1.299600e-03 2.811900e-03 9.376000e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.936395e-01 2.889947e-01 0.00000e+00 2.427270e-01 4.908231e-01 7.429062e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.936381e-01 2.889955e-01 0.00000e+00 2.427241e-01 4.908218e-01 7.429055e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.225875e-01 2.605939e-01 3.30950e-03 1.890090e-02 1.036910e-01 3.552950e-01 9.966900e-01 ▇▂▁▁▁
numeric AF_reference 246841 0.9786304 NA NA NA NA NA 2.233257e-01 2.518752e-01 0.00000e+00 1.597440e-02 1.224040e-01 3.554310e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.144220e+05 0.000000e+00 1.14422e+05 1.144220e+05 1.144220e+05 1.144220e+05 1.144220e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0010511 0.0013027 0.4197223 0.4197172 0.1117110 0.1894970 114422
1 693731 rs12238997 A G 0.0002473 0.0012342 0.8411691 0.8411695 0.1166780 0.1417730 114422
1 707522 rs371890604 G C 0.0011127 0.0013845 0.4215887 0.4215864 0.0983298 0.1293930 114422
1 717587 rs144155419 G A 0.0011285 0.0033174 0.7337194 0.7337171 0.0157526 0.0045926 114422
1 730087 rs148120343 T C -0.0016019 0.0017170 0.3508238 0.3508237 0.0568713 0.0127796 114422
1 731718 rs142557973 T C 0.0007480 0.0011711 0.5230136 0.5230148 0.1226010 0.1543530 114422
1 732032 rs61770163 A C 0.0008850 0.0012480 0.4782632 0.4782605 0.1222220 0.1555510 114422
1 734349 rs141242758 T C 0.0007179 0.0011717 0.5400699 0.5400681 0.1218520 0.1525560 114422
1 740284 rs61770167 C T 0.0039474 0.0053432 0.4600478 0.4600464 0.0058609 0.0023962 114422
1 749963 rs529266287 T TAA -0.0009445 0.0011542 0.4132007 0.4132009 0.8690450 0.7641770 114422
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0021003 0.0013768 0.1271531 0.1271498 0.0553623 0.0309934 114422
23 154923374 rs111332691 T A 0.0003987 0.0014987 0.7902163 0.7902150 0.0448384 0.0116556 114422
23 154925045 rs509981 C T 0.0001657 0.0007223 0.8185620 0.8185612 0.2446210 0.3634440 114422
23 154925895 rs538470 C T 0.0003897 0.0007387 0.5978442 0.5978421 0.2409890 0.3634440 114422
23 154927581 rs644138 G A 0.0006598 0.0006796 0.3316248 0.3316230 0.3003390 0.4635760 114422
23 154929412 rs557132 C T 0.0001488 0.0007224 0.8368189 0.8368191 0.2444980 0.3568210 114422
23 154929637 rs35185538 CT C 0.0001683 0.0007546 0.8235510 0.8235503 0.2287980 0.3011920 114422
23 154929952 rs4012982 CAA C -0.0000671 0.0007604 0.9297179 0.9297177 0.2385330 0.3165560 114422
23 154930230 rs781880 A G 0.0001474 0.0007223 0.8382891 0.8382890 0.2449060 0.3618540 114422
23 154930487 rs781879 T A 0.0005895 0.0024511 0.8099509 0.8099504 0.0197245 0.1263580 114422

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111711 ES:SE:LP:AF:SS:ID   0.00105114:0.00130267:0.377038:0.111711:114422:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116678 ES:SE:LP:AF:SS:ID   0.000247331:0.0012342:0.0751167:0.116678:114422:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0983298    ES:SE:LP:AF:SS:ID   0.0011127:0.00138452:0.375111:0.0983298:114422:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157526    ES:SE:LP:AF:SS:ID   0.00112853:0.0033174:0.13447:0.0157526:114422:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0568713    ES:SE:LP:AF:SS:ID   -0.00160193:0.00171698:0.454911:0.0568713:114422:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122601 ES:SE:LP:AF:SS:ID   0.000747962:0.00117106:0.281487:0.122601:114422:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122222 ES:SE:LP:AF:SS:ID   0.000884982:0.00124803:0.320333:0.122222:114422:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121852 ES:SE:LP:AF:SS:ID   0.000717894:0.00117167:0.26755:0.121852:114422:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0058609    ES:SE:LP:AF:SS:ID   0.00394742:0.00534323:0.337197:0.0058609:114422:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.869045 ES:SE:LP:AF:SS:ID   -0.000944476:0.00115423:0.383839:0.869045:114422:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123663 ES:SE:LP:AF:SS:ID   0.000798969:0.00114366:0.314437:0.123663:114422:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143266 ES:SE:LP:AF:SS:ID   0.00106002:0.00113119:0.457531:0.143266:114422:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123787 ES:SE:LP:AF:SS:ID   0.000796378:0.00114208:0.313711:0.123787:114422:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.86984  ES:SE:LP:AF:SS:ID   -0.00107618:0.00111245:0.477105:0.86984:114422:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874607 ES:SE:LP:AF:SS:ID   -0.000886963:0.00113097:0.363616:0.874607:114422:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129637 ES:SE:LP:AF:SS:ID   0.001136:0.00111547:0.510763:0.129637:114422:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0366494    ES:SE:LP:AF:SS:ID   0.00165209:0.0020218:0.383156:0.0366494:114422:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869441 ES:SE:LP:AF:SS:ID   -0.00122444:0.00111138:0.567701:0.869441:114422:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869515 ES:SE:LP:AF:SS:ID   -0.00121156:0.00111181:0.559343:0.869515:114422:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86944  ES:SE:LP:AF:SS:ID   -0.00123073:0.00111136:0.571672:0.86944:114422:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00515222   ES:SE:LP:AF:SS:ID   0.00495061:0.00565899:0.418309:0.00515222:114422:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00512096   ES:SE:LP:AF:SS:ID   0.00503373:0.00567146:0.426221:0.00512096:114422:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00569216   ES:SE:LP:AF:SS:ID   0.00244033:0.00547435:0.183255:0.00569216:114422:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869508 ES:SE:LP:AF:SS:ID   -0.00111011:0.00110933:0.498978:0.869508:114422:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126917 ES:SE:LP:AF:SS:ID   0.000995356:0.00113225:0.420961:0.126917:114422:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869029 ES:SE:LP:AF:SS:ID   -0.00110871:0.00110641:0.499893:0.869029:114422:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868436 ES:SE:LP:AF:SS:ID   -0.00122251:0.00110604:0.570201:0.868436:114422:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869215 ES:SE:LP:AF:SS:ID   -0.00115095:0.0011075:0.524765:0.869215:114422:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869222 ES:SE:LP:AF:SS:ID   -0.0011516:0.00110758:0.525114:0.869222:114422:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869224 ES:SE:LP:AF:SS:ID   -0.00115099:0.00110759:0.524734:0.869224:114422:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869663 ES:SE:LP:AF:SS:ID   -0.00114222:0.00111044:0.51761:0.869663:114422:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.099489 ES:SE:LP:AF:SS:ID   0.000970409:0.0012909:0.344656:0.099489:114422:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00655187   ES:SE:LP:AF:SS:ID   0.00116682:0.00496831:0.0892033:0.00655187:114422:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873708 ES:SE:LP:AF:SS:ID   -0.000982013:0.0011273:0.416021:0.873708:114422:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863017 ES:SE:LP:AF:SS:ID   -0.00126375:0.0011058:0.596696:0.863017:114422:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868401 ES:SE:LP:AF:SS:ID   -0.00119668:0.00111628:0.547121:0.868401:114422:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865415 ES:SE:LP:AF:SS:ID   -0.000991648:0.0011164:0.426656:0.865415:114422:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0997473    ES:SE:LP:AF:SS:ID   0.00116145:0.00133387:0.415785:0.0997473:114422:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870695 ES:SE:LP:AF:SS:ID   -0.000921899:0.00112952:0.382585:0.870695:114422:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870695 ES:SE:LP:AF:SS:ID   -0.000921889:0.00112952:0.38258:0.870695:114422:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870693 ES:SE:LP:AF:SS:ID   -0.000922452:0.00112952:0.382878:0.870693:114422:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871018 ES:SE:LP:AF:SS:ID   -0.00100094:0.00113002:0.425113:0.871018:114422:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126512 ES:SE:LP:AF:SS:ID   0.00087434:0.00113097:0.35707:0.126512:114422:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106279 ES:SE:LP:AF:SS:ID   0.000390699:0.00122899:0.124615:0.106279:114422:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854464 ES:SE:LP:AF:SS:ID   -0.00142086:0.00110546:0.701831:0.854464:114422:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839076 ES:SE:LP:AF:SS:ID   -0.000959711:0.00109447:0.419579:0.839076:114422:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763122 ES:SE:LP:AF:SS:ID   -0.0011457:0.000877479:0.717453:0.763122:114422:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105233 ES:SE:LP:AF:SS:ID   0.000885996:0.00121333:0.332307:0.105233:114422:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00774894   ES:SE:LP:AF:SS:ID   0.000868267:0.00447707:0.0725136:0.00774894:114422:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.12991  ES:SE:LP:AF:SS:ID   0.000970171:0.00111491:0.415437:0.12991:114422:rs762168062