Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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-11358/UKB-b-11358_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11358/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11358/UKB-b-11358_data.vcf.gz ...
Read summary statistics for 9851866 SNPs.
Dropped 14738 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, 1289166 SNPs remain.
After merging with regression SNP LD, 1289166 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0256 (0.0018)
Lambda GC: 1.2679
Mean Chi^2: 1.3137
Intercept: 1.0827 (0.0074)
Ratio: 0.2635 (0.0236)
Analysis finished at Thu Oct 17 14:42:09 2019
Total time elapsed: 1.0m:51.5s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.1999,
    "mean_EFFECT": -0.0004,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 9,
    "n_p_sig": 682,
    "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": 184849,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NA",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1289166,
    "ldsc_nsnp_merge_regression_ld": 1289166,
    "ldsc_observed_scale_h2_beta": 0.0256,
    "ldsc_observed_scale_h2_se": 0.0018,
    "ldsc_intercept_beta": 1.0827,
    "ldsc_intercept_se": 0.0074,
    "ldsc_lambda_gc": 1.2679,
    "ldsc_mean_chisq": 1.3137,
    "ldsc_ratio": 0.2636
}
 

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 TRUE
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 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 9837196 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 9851866 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 8.622825e+00 5.748290e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 <U+2587><U+2585><U+2583><U+2582><U+2582>
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.886027e+07 5.628334e+07 828.0000000 3.259061e+07 6.948835e+07 1.145912e+08 2.492385e+08 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -4.225000e-04 1.065890e-02 -0.2013710 -3.471900e-03 -1.132000e-04 3.123400e-03 2.443460e-01 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 7.226300e-03 6.843800e-03 0.0020218 2.474800e-03 4.149800e-03 9.575700e-03 1.068650e-01 <U+2587><U+2581><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.687210e-01 2.970751e-01 0.0000000 2.000000e-01 4.600002e-01 7.300002e-01 1.000000e+00 <U+2587><U+2586><U+2586><U+2586><U+2586>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.687201e-01 2.970492e-01 0.0000000 2.035446e-01 4.578009e-01 7.259173e-01 1.000000e+00 <U+2587><U+2586><U+2586><U+2586><U+2586>
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035071e-01 2.568647e-01 0.0009710 1.316800e-02 7.791000e-02 3.164510e-01 9.990260e-01 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric AF_reference 184849 0.9812372 NA NA NA NA NA NA NA 2.068392e-01 2.482924e-01 0.0000000 1.198080e-02 9.984030e-02 3.202880e-01 1.000000e+00 <U+2587><U+2582><U+2581><U+2581><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0007881 0.0037173 0.8300000 0.8320936 0.623729 0.7821490 NA
1 54676 rs2462492 C T 0.0033035 0.0036839 0.3700002 0.3698573 0.400487 NA NA
1 86028 rs114608975 T C -0.0022722 0.0058903 0.6999999 0.6996840 0.103541 0.0277556 NA
1 91536 rs6702460 G T -0.0014239 0.0036277 0.6899999 0.6946864 0.456885 0.4207270 NA
1 234313 rs8179466 C T -0.0039113 0.0071551 0.5800000 0.5846198 0.074497 NA NA
1 534192 rs6680723 C T -0.0012957 0.0041426 0.7499995 0.7544610 0.241021 NA NA
1 546697 rs12025928 A G 0.0053451 0.0051687 0.2999998 0.3010705 0.913488 NA NA
1 693731 rs12238997 A G -0.0005997 0.0034724 0.8600001 0.8628939 0.116370 0.1417730 NA
1 705882 rs72631875 G A 0.0011270 0.0050902 0.8200001 0.8247766 0.067243 0.0315495 NA
1 706368 rs55727773 A G 0.0008178 0.0025727 0.7499995 0.7505709 0.515615 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0004335 0.0053950 0.9400001 0.9359613 0.042037 0.0473243 NA
22 51219766 rs182321900 C T 0.0032918 0.0251046 0.9000000 0.8956761 0.001945 NA NA
22 51220146 rs868950473 C T 0.0033292 0.0248647 0.8900000 0.8934875 0.001994 NA NA
22 51221190 rs369304721 G A -0.0040729 0.0053874 0.4500005 0.4496453 0.049796 NA NA
22 51221731 rs115055839 T C -0.0038967 0.0040299 0.3300000 0.3335704 0.073327 0.0625000 NA
22 51222100 rs114553188 G T -0.0002774 0.0047474 0.9500000 0.9534112 0.054452 0.0880591 NA
22 51223637 rs375798137 G A 0.0000880 0.0047704 0.9900000 0.9852791 0.054082 0.0788738 NA
22 51229805 rs9616985 T C -0.0042215 0.0040446 0.2999998 0.2965987 0.073160 0.0730831 NA
22 51232488 rs376461333 A G -0.0103170 0.0095231 0.2800000 0.2786451 0.020056 NA NA
22 51237063 rs3896457 T C 0.0057045 0.0024756 0.0210000 0.0212050 0.297930 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623729 ES:SE:LP:AF:ID  -0.000788136:0.00371732:0.0809219:0.623729:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400487 ES:SE:LP:AF:ID  0.00330353:0.00368393:0.431798:0.400487:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103541 ES:SE:LP:AF:ID  -0.00227217:0.00589031:0.154902:0.103541:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456885 ES:SE:LP:AF:ID  -0.00142388:0.00362769:0.161151:0.456885:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074497 ES:SE:LP:AF:ID  -0.00391134:0.00715512:0.236572:0.074497:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.241021 ES:SE:LP:AF:ID  -0.00129566:0.00414263:0.124939:0.241021:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913488 ES:SE:LP:AF:ID  0.00534512:0.00516866:0.522879:0.913488:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.11637  ES:SE:LP:AF:ID  -0.000599661:0.00347244:0.0655015:0.11637:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067243 ES:SE:LP:AF:ID  0.00112701:0.00509025:0.0861861:0.067243:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515615 ES:SE:LP:AF:ID  0.000817827:0.0025727:0.124939:0.515615:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032992 ES:SE:LP:AF:ID  -0.00506883:0.00648694:0.366532:0.032992:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.03662  ES:SE:LP:AF:ID  -0.00492835:0.00589107:0.39794:0.03662:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.03673  ES:SE:LP:AF:ID  -0.00474004:0.00586926:0.376751:0.03673:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036432 ES:SE:LP:AF:ID  -0.00489214:0.00591141:0.387216:0.036432:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016384 ES:SE:LP:AF:ID  0.00325008:0.00910856:0.142668:0.016384:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036971 ES:SE:LP:AF:ID  -0.00548202:0.00584577:0.455932:0.036971:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037067 ES:SE:LP:AF:ID  -0.00512403:0.0058259:0.420216:0.037067:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101173 ES:SE:LP:AF:ID  0.00361815:0.00424368:0.408935:0.101173:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959121 ES:SE:LP:AF:ID  0.00545593:0.00562:0.481486:0.959121:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031416 ES:SE:LP:AF:ID  0.0092509:0.0102154:0.431798:0.031416:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053262 ES:SE:LP:AF:ID  -0.00220998:0.0081104:0.102373:0.053262:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036589 ES:SE:LP:AF:ID  -0.00530659:0.00586335:0.431798:0.036589:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036908 ES:SE:LP:AF:ID  -0.00431067:0.00580966:0.337242:0.036908:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843201 ES:SE:LP:AF:ID  0.00106781:0.00300949:0.142668:0.843201:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055961 ES:SE:LP:AF:ID  -0.00142045:0.00487074:0.113509:0.055961:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122345 ES:SE:LP:AF:ID  -0.000414936:0.00329418:0.0457575:0.122345:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025715 ES:SE:LP:AF:ID  -0.0125459:0.00810252:0.920819:0.025715:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121586 ES:SE:LP:AF:ID  -0.000222219:0.00329559:0.0222764:0.121586:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132412 ES:SE:LP:AF:ID  -0.00160938:0.00324693:0.207608:0.132412:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.01112  ES:SE:LP:AF:ID  -0.00902046:0.0118163:0.346787:0.01112:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005715 ES:SE:LP:AF:ID  0.0132782:0.0152157:0.420216:0.005715:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002251 ES:SE:LP:AF:ID  0.025369:0.0257504:0.49485:0.002251:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001017 ES:SE:LP:AF:ID  -0.0157053:0.0423571:0.148742:0.001017:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036817 ES:SE:LP:AF:ID  -0.00442557:0.00575162:0.356547:0.036817:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838933 ES:SE:LP:AF:ID  0.000887838:0.00291476:0.119186:0.838933:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838567 ES:SE:LP:AF:ID  0.000695979:0.00291165:0.091515:0.838567:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869758 ES:SE:LP:AF:ID  -0.000146573:0.00312438:0.0177288:0.869758:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129896 ES:SE:LP:AF:ID  -0.000200683:0.00313074:0.0222764:0.129896:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037325 ES:SE:LP:AF:ID  -0.00373673:0.00565418:0.29243:0.037325:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037572 ES:SE:LP:AF:ID  -0.00366983:0.00561816:0.29243:0.037572:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869106 ES:SE:LP:AF:ID  -0.000271494:0.0031183:0.0315171:0.869106:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869202 ES:SE:LP:AF:ID  -0.000323094:0.00311951:0.0362122:0.869202:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037528 ES:SE:LP:AF:ID  -0.00353331:0.00564266:0.275724:0.037528:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869109 ES:SE:LP:AF:ID  -0.000219729:0.00311825:0.0268721:0.869109:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005117 ES:SE:LP:AF:ID  0.00442023:0.0160165:0.107905:0.005117:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005083 ES:SE:LP:AF:ID  0.00464565:0.0160588:0.113509:0.005083:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838017 ES:SE:LP:AF:ID  0.000799621:0.00290355:0.107905:0.838017:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037542 ES:SE:LP:AF:ID  -0.00354:0.00565063:0.275724:0.037542:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838646 ES:SE:LP:AF:ID  0.000784345:0.00291171:0.102373:0.838646:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013768 ES:SE:LP:AF:ID  -0.00203044:0.0101648:0.0757207:0.013768:rs181660517