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-4700_irnt/ukb-d-4700_irnt.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-4700_irnt/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 15:00:27 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-4700_irnt/ukb-d-4700_irnt.vcf.gz ...
Read summary statistics for 13420581 SNPs.
Dropped 12473 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, 1283473 SNPs remain.
After merging with regression SNP LD, 1283473 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0188 (0.0897)
Lambda GC: 1.0055
Mean Chi^2: 1.003
Intercept: 1.0011 (0.0064)
Ratio: 0.3779 (2.1266)
Analysis finished at Mon Nov 25 15:02:30 2019
Total time elapsed: 2.0m:3.6s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9518,
    "inflation_factor": 1.0065,
    "mean_EFFECT": -0.0002,
    "n": 5020,
    "n_snps": 13420581,
    "n_clumped_hits": 1,
    "n_p_sig": 7,
    "n_mono": 0,
    "n_ns": 1245481,
    "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": 529142,
    "n_est": 5066.9575,
    "ratio_se_n": 1.0047,
    "mean_diff": -0.0001,
    "ratio_diff": 6.6446,
    "sd_y_est1": 0.7217,
    "sd_y_est2": 0.7251,
    "r2_sum1": 0.0039,
    "r2_sum2": 0.0075,
    "r2_sum3": 0.0074,
    "r2_sum4": 0.0066,
    "ldsc_nsnp_merge_refpanel_ld": 1283473,
    "ldsc_nsnp_merge_regression_ld": 1283473,
    "ldsc_observed_scale_h2_beta": 0.0188,
    "ldsc_observed_scale_h2_se": 0.0897,
    "ldsc_intercept_beta": 1.0011,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0055,
    "ldsc_mean_chisq": 1.003,
    "ldsc_ratio": 0.3667
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 13408767 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 56763 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33232 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.052103e+00 6.183900e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.901377e+07 5.592346e+07 302.0000000 3.290921e+07 7.010602e+07 1.148498e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.901000e-04 8.126560e-02 -1.4071800 -2.136570e-02 3.004000e-04 2.239890e-02 1.008840e+00 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.866740e-02 5.630510e-02 0.0118827 1.715100e-02 3.108500e-02 8.360980e-02 3.612100e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.994791e-01 2.887752e-01 0.0000000 2.495669e-01 4.986204e-01 7.499097e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.994472e-01 2.887943e-01 0.0000000 2.495122e-01 4.985891e-01 7.498966e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.930548e-01 2.549504e-01 0.0010003 8.029100e-03 6.285330e-02 2.998460e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 529142 0.9605723 NA NA NA NA NA 1.980611e-01 2.474894e-01 0.0000000 5.990400e-03 8.666130e-02 3.115020e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 5.020000e+03 0.000000e+00 5020.0000000 5.020000e+03 5.020000e+03 5.020000e+03 5.020000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0127908 0.0253125 0.6133594 0.6133372 0.1115960 0.1894970 5020
1 693731 rs12238997 A G 0.0019797 0.0238542 0.9338609 0.9338575 0.1172020 0.1417730 5020
1 707522 rs371890604 G C 0.0119345 0.0266696 0.6545367 0.6545180 0.0974822 0.1293930 5020
1 717587 rs144155419 G A 0.0166571 0.0643906 0.7958870 0.7958757 0.0155925 0.0045926 5020
1 723329 rs189787166 A T -0.1771540 0.2504310 0.4793536 0.4793201 0.0010737 0.0003994 5020
1 730087 rs148120343 T C 0.0264125 0.0323985 0.4149751 0.4149359 0.0593727 0.0127796 5020
1 731718 rs142557973 T C 0.0006626 0.0226205 0.9766321 0.9766310 0.1228810 0.1543530 5020
1 732032 rs61770163 A C 0.0122424 0.0240288 0.6104302 0.6104098 0.1222960 0.1555510 5020
1 734349 rs141242758 T C 0.0038206 0.0226563 0.8660909 0.8660843 0.1220810 0.1525560 5020
1 740284 rs61770167 C T 0.0474157 0.1010930 0.6390679 0.6390478 0.0060015 0.0023962 5020
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0101450 0.0268187 0.7052385 0.7052220 0.0526131 0.0309934 5020
23 154923374 rs111332691 T A -0.0118714 0.0277136 0.6684086 0.6683890 0.0462151 0.0116556 5020
23 154925045 rs509981 C T 0.0160857 0.0142370 0.2585931 0.2585387 0.2350770 0.3634440 5020
23 154925895 rs538470 C T 0.0170438 0.0145296 0.2408358 0.2407798 0.2322600 0.3634440 5020
23 154927581 rs644138 G A 0.0167919 0.0132887 0.2064249 0.2063656 0.2879850 0.4635760 5020
23 154929412 rs557132 C T 0.0160631 0.0142410 0.2593982 0.2593421 0.2349160 0.3568210 5020
23 154929637 rs35185538 CT C 0.0092139 0.0148527 0.5350545 0.5350262 0.2205000 0.3011920 5020
23 154929952 rs4012982 CAA C 0.0176298 0.0149950 0.2397668 0.2397100 0.2280610 0.3165560 5020
23 154930230 rs781880 A G 0.0167182 0.0142444 0.2405830 0.2405279 0.2353320 0.3618540 5020
23 154930487 rs781879 T A 0.0391285 0.0523517 0.4548477 0.4548125 0.0161995 0.1263580 5020

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111596 ES:SE:LP:AF:SS:ID   0.0127908:0.0253125:0.212285:0.111596:5020:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117202 ES:SE:LP:AF:SS:ID   0.00197972:0.0238542:0.0297178:0.117202:5020:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0974822    ES:SE:LP:AF:SS:ID   0.0119345:0.0266696:0.184066:0.0974822:5020:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0155925    ES:SE:LP:AF:SS:ID   0.0166571:0.0643906:0.0991486:0.0155925:5020:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00107374   ES:SE:LP:AF:SS:ID   -0.177154:0.250431:0.319344:0.00107374:5020:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0593727    ES:SE:LP:AF:SS:ID   0.0264125:0.0323985:0.381978:0.0593727:5020:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122881 ES:SE:LP:AF:SS:ID   0.000662619:0.0226205:0.010269:0.122881:5020:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122296 ES:SE:LP:AF:SS:ID   0.0122424:0.0240288:0.214364:0.122296:5020:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122081 ES:SE:LP:AF:SS:ID   0.00382063:0.0226563:0.0624365:0.122081:5020:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00600148   ES:SE:LP:AF:SS:ID   0.0474157:0.101093:0.194453:0.00600148:5020:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00160769   ES:SE:LP:AF:SS:ID   -0.119474:0.211145:0.242961:0.00160769:5020:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868575 ES:SE:LP:AF:SS:ID   -0.00718414:0.0222196:0.126992:0.868575:5020:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00147176   ES:SE:LP:AF:SS:ID   0.257331:0.213902:0.640123:0.00147176:5020:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123452 ES:SE:LP:AF:SS:ID   0.00841007:0.0219726:0.153712:0.123452:5020:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143455 ES:SE:LP:AF:SS:ID   0.0154396:0.0219289:0.317479:0.143455:5020:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123627 ES:SE:LP:AF:SS:ID   0.00907894:0.0219354:0.168149:0.123627:5020:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870498 ES:SE:LP:AF:SS:ID   -0.00848603:0.0214407:0.159721:0.870498:5020:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875496 ES:SE:LP:AF:SS:ID   -0.0096742:0.0217683:0.182593:0.875496:5020:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12921  ES:SE:LP:AF:SS:ID   0.0073139:0.021451:0.134807:0.12921:5020:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.037749 ES:SE:LP:AF:SS:ID   -0.0481032:0.0383546:0.678112:0.037749:5020:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869957 ES:SE:LP:AF:SS:ID   -0.00638385:0.0214037:0.116045:0.869957:5020:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870062 ES:SE:LP:AF:SS:ID   -0.00720738:0.0214117:0.132871:0.870062:5020:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86989  ES:SE:LP:AF:SS:ID   -0.00471599:0.0213984:0.0832424:0.86989:5020:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005739 ES:SE:LP:AF:SS:ID   0.155722:0.1016:0.901657:0.005739:5020:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00570659   ES:SE:LP:AF:SS:ID   0.155328:0.101884:0.894722:0.00570659:5020:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00512187   ES:SE:LP:AF:SS:ID   0.0910924:0.112279:0.379625:0.00512187:5020:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870279 ES:SE:LP:AF:SS:ID   -0.0087818:0.0213785:0.166691:0.870279:5020:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12635  ES:SE:LP:AF:SS:ID   0.010324:0.0217993:0.196672:0.12635:5020:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87002  ES:SE:LP:AF:SS:ID   -0.00856869:0.0213499:0.162297:0.87002:5020:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869361 ES:SE:LP:AF:SS:ID   -0.00491533:0.0213093:0.0874676:0.869361:5020:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870174 ES:SE:LP:AF:SS:ID   -0.00855188:0.0213621:0.161824:0.870174:5020:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870178 ES:SE:LP:AF:SS:ID   -0.00854841:0.0213637:0.161735:0.870178:5020:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870181 ES:SE:LP:AF:SS:ID   -0.00855857:0.0213634:0.161959:0.870181:5020:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870498 ES:SE:LP:AF:SS:ID   -0.00850618:0.0214102:0.160418:0.870498:5020:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0981568    ES:SE:LP:AF:SS:ID   -0.000500782:0.0249648:0.00700623:0.0981568:5020:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00535349   ES:SE:LP:AF:SS:ID   0.0570211:0.10642:0.227595:0.00535349:5020:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874624 ES:SE:LP:AF:SS:ID   -0.00969866:0.0217161:0.183643:0.874624:5020:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863361 ES:SE:LP:AF:SS:ID   -0.000802291:0.0213291:0.0132301:0.863361:5020:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868823 ES:SE:LP:AF:SS:ID   -0.0099022:0.0215099:0.190251:0.868823:5020:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866182 ES:SE:LP:AF:SS:ID   -0.00494836:0.0214987:0.0872632:0.866182:5020:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0982986    ES:SE:LP:AF:SS:ID   0.00330623:0.0258345:0.0466405:0.0982986:5020:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871328 ES:SE:LP:AF:SS:ID   -0.00548134:0.0217473:0.0963593:0.871328:5020:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871328 ES:SE:LP:AF:SS:ID   -0.00548134:0.0217473:0.0963593:0.871328:5020:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871322 ES:SE:LP:AF:SS:ID   -0.00548449:0.0217475:0.096419:0.871322:5020:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871538 ES:SE:LP:AF:SS:ID   -0.00526919:0.021758:0.0922356:0.871538:5020:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125868 ES:SE:LP:AF:SS:ID   0.0110671:0.0217469:0.214072:0.125868:5020:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105615 ES:SE:LP:AF:SS:ID   0.0010112:0.0237794:0.014986:0.105615:5020:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.856038 ES:SE:LP:AF:SS:ID   -0.00518075:0.0213069:0.0926419:0.856038:5020:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0010175    ES:SE:LP:AF:SS:ID   -0.176271:0.250208:0.317716:0.0010175:5020:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838787 ES:SE:LP:AF:SS:ID   0.0029191:0.0212224:0.0503158:0.838787:5020:rs376645387