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-22601_41133206/ukb-d-22601_41133206.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-22601_41133206/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 14:49:01 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_41133206/ukb-d-22601_41133206.vcf.gz ...
Read summary statistics for 11949597 SNPs.
Dropped 10396 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, 1282988 SNPs remain.
After merging with regression SNP LD, 1282988 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0048 (0.0049)
Lambda GC: 0.9906
Mean Chi^2: 0.9955
Intercept: 1.004 (0.0061)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 14:50:45 2019
Total time elapsed: 1.0m:44.09s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9489,
    "inflation_factor": 0.9937,
    "mean_EFFECT": -2.3082e-06,
    "n": 89866,
    "n_snps": 11949597,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1182301,
    "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": 278493,
    "n_est": 90065.1233,
    "ratio_se_n": 1.0011,
    "mean_diff": -8.0456e-06,
    "ratio_diff": 158.8849,
    "sd_y_est1": 0.2238,
    "sd_y_est2": 0.224,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1282988,
    "ldsc_nsnp_merge_regression_ld": 1282988,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.004,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 0.9906,
    "ldsc_mean_chisq": 0.9955,
    "ldsc_ratio": -0.8889
}

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 11939821 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 53261 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32120 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.069441e+00 6.184578e+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 7.888926e+07 5.598004e+07 3.02000e+02 3.269494e+07 6.991385e+07 1.147513e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.300000e-06 4.067500e-03 -4.12142e-02 -1.404900e-03 -1.300000e-05 1.371600e-03 5.175950e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.159300e-03 2.595700e-03 8.72700e-04 1.212200e-03 1.915800e-03 4.350700e-03 1.618210e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.010824e-01 2.882123e-01 1.00000e-07 2.517352e-01 5.013454e-01 7.505334e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.010806e-01 2.882134e-01 1.00000e-07 2.517310e-01 5.013423e-01 7.505334e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.155471e-01 2.595421e-01 2.63270e-03 1.572640e-02 9.367860e-02 3.429740e-01 9.973670e-01 ▇▂▁▁▁
numeric AF_reference 278493 0.9766944 NA NA NA NA NA 2.168366e-01 2.509982e-01 0.00000e+00 1.238020e-02 1.132190e-01 3.448480e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 8.986600e+04 0.000000e+00 8.98660e+04 8.986600e+04 8.986600e+04 8.986600e+04 8.986600e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0029947 0.0018437 0.1043249 0.1043211 0.1114870 0.1894970 89866
1 693731 rs12238997 A G -0.0018898 0.0017465 0.2792319 0.2792310 0.1164980 0.1417730 89866
1 707522 rs371890604 G C -0.0026506 0.0019635 0.1770362 0.1770331 0.0978285 0.1293930 89866
1 717587 rs144155419 G A -0.0018654 0.0046769 0.6899983 0.6899983 0.0158090 0.0045926 89866
1 730087 rs148120343 T C -0.0040264 0.0024218 0.0964007 0.0963965 0.0569661 0.0127796 89866
1 731718 rs142557973 T C -0.0024918 0.0016574 0.1327159 0.1327134 0.1223780 0.1543530 89866
1 732032 rs61770163 A C -0.0021643 0.0017669 0.2206119 0.2206070 0.1220530 0.1555510 89866
1 734349 rs141242758 T C -0.0024698 0.0016586 0.1364690 0.1364668 0.1216170 0.1525560 89866
1 740284 rs61770167 C T 0.0032322 0.0075794 0.6697874 0.6697865 0.0057975 0.0023962 89866
1 749963 rs529266287 T TAA 0.0025665 0.0016318 0.1157721 0.1157687 0.8689590 0.7641770 89866
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0002918 0.0019399 0.8804159 0.8804165 0.0553576 0.0309934 89866
23 154923374 rs111332691 T A -0.0023685 0.0021119 0.2620813 0.2620765 0.0449113 0.0116556 89866
23 154925045 rs509981 C T 0.0006422 0.0010185 0.5283394 0.5283389 0.2444280 0.3634440 89866
23 154925895 rs538470 C T 0.0009458 0.0010415 0.3637944 0.3637918 0.2408760 0.3634440 89866
23 154927581 rs644138 G A 0.0005857 0.0009581 0.5409972 0.5409954 0.3001910 0.4635760 89866
23 154929412 rs557132 C T 0.0006539 0.0010189 0.5209955 0.5209950 0.2442750 0.3568210 89866
23 154929637 rs35185538 CT C 0.0001364 0.0010639 0.8979551 0.8979546 0.2286930 0.3011920 89866
23 154929952 rs4012982 CAA C 0.0004195 0.0010722 0.6956471 0.6956456 0.2381980 0.3165560 89866
23 154930230 rs781880 A G 0.0005706 0.0010185 0.5753419 0.5753410 0.2447120 0.3618540 89866
23 154930487 rs781879 T A -0.0023510 0.0034550 0.4962186 0.4962162 0.0196791 0.1263580 89866

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   -0.00299469:0.00184373:0.981612:0.111487:89866:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116498 ES:SE:LP:AF:SS:ID   -0.00188983:0.00174653:0.554035:0.116498:89866:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978285    ES:SE:LP:AF:SS:ID   -0.00265058:0.00196347:0.751938:0.0978285:89866:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015809 ES:SE:LP:AF:SS:ID   -0.00186542:0.00467691:0.161152:0.015809:89866:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569661    ES:SE:LP:AF:SS:ID   -0.00402642:0.00242179:1.01592:0.0569661:89866:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122378 ES:SE:LP:AF:SS:ID   -0.00249182:0.00165736:0.877077:0.122378:89866:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122053 ES:SE:LP:AF:SS:ID   -0.00216434:0.00176693:0.656371:0.122053:89866:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121617 ES:SE:LP:AF:SS:ID   -0.00246977:0.00165859:0.864966:0.121617:89866:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00579754   ES:SE:LP:AF:SS:ID   0.00323218:0.00757943:0.174063:0.00579754:89866:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.868959 ES:SE:LP:AF:SS:ID   0.00256647:0.0016318:0.936396:0.868959:89866:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123678 ES:SE:LP:AF:SS:ID   -0.00240062:0.0016177:0.860688:0.123678:89866:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143191 ES:SE:LP:AF:SS:ID   -0.00221658:0.00160162:0.77892:0.143191:89866:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123813 ES:SE:LP:AF:SS:ID   -0.00241873:0.00161536:0.871888:0.123813:89866:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869927 ES:SE:LP:AF:SS:ID   0.00262756:0.00157394:1.0221:0.869927:89866:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87461  ES:SE:LP:AF:SS:ID   0.00239031:0.0015996:0.869351:0.87461:89866:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12951  ES:SE:LP:AF:SS:ID   -0.00279462:0.00157875:1.11517:0.12951:89866:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0357365    ES:SE:LP:AF:SS:ID   0.000481147:0.00288838:0.0616299:0.0357365:89866:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869574 ES:SE:LP:AF:SS:ID   0.00267242:0.00157255:1.04942:0.869574:89866:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869652 ES:SE:LP:AF:SS:ID   0.00269014:0.00157325:1.05907:0.869652:89866:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86957  ES:SE:LP:AF:SS:ID   0.00267615:0.00157249:1.05166:0.86957:89866:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00528163   ES:SE:LP:AF:SS:ID   -0.0147039:0.00789017:1.20491:0.00528163:89866:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00524722   ES:SE:LP:AF:SS:ID   -0.0147467:0.00790985:1.20568:0.00524722:89866:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0056565    ES:SE:LP:AF:SS:ID   -0.0121811:0.00774603:0.936194:0.0056565:89866:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869566 ES:SE:LP:AF:SS:ID   0.00263827:0.00156937:1.0327:0.869566:89866:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126879 ES:SE:LP:AF:SS:ID   -0.0025746:0.00160208:0.966371:0.126879:89866:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869094 ES:SE:LP:AF:SS:ID   0.00255582:0.0015653:0.989213:0.869094:89866:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868498 ES:SE:LP:AF:SS:ID   0.00255021:0.00156435:0.986906:0.868498:89866:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869245 ES:SE:LP:AF:SS:ID   0.00263839:0.00156673:1.03534:0.869245:89866:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869251 ES:SE:LP:AF:SS:ID   0.00263862:0.00156684:1.03538:0.869251:89866:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869252 ES:SE:LP:AF:SS:ID   0.00264034:0.00156685:1.03637:0.869252:89866:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869724 ES:SE:LP:AF:SS:ID   0.00266294:0.00157102:1.04542:0.869724:89866:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991203    ES:SE:LP:AF:SS:ID   -0.00238495:0.00182893:0.716174:0.0991203:89866:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00649047   ES:SE:LP:AF:SS:ID   -0.0123056:0.00705854:1.09005:0.00649047:89866:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873732 ES:SE:LP:AF:SS:ID   0.00251861:0.00159436:0.942418:0.873732:89866:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863116 ES:SE:LP:AF:SS:ID   0.00260485:0.00156382:1.01874:0.863116:89866:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868511 ES:SE:LP:AF:SS:ID   0.00285843:0.00157943:1.15284:0.868511:89866:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86539  ES:SE:LP:AF:SS:ID   0.00261355:0.00157967:1.00864:0.86539:89866:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0994301    ES:SE:LP:AF:SS:ID   -0.00260425:0.00189167:0.773117:0.0994301:89866:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870696 ES:SE:LP:AF:SS:ID   0.00250575:0.00159785:0.93242:0.870696:89866:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870695 ES:SE:LP:AF:SS:ID   0.00250579:0.00159784:0.932442:0.870695:89866:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870693 ES:SE:LP:AF:SS:ID   0.00250597:0.00159785:0.932539:0.870693:89866:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871061 ES:SE:LP:AF:SS:ID   0.00257241:0.0015986:0.968252:0.871061:89866:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126484 ES:SE:LP:AF:SS:ID   -0.00280135:0.00160021:1.09682:0.126484:89866:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106022 ES:SE:LP:AF:SS:ID   -0.00248212:0.00173957:0.813538:0.106022:89866:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854451 ES:SE:LP:AF:SS:ID   0.00238857:0.00156345:0.897649:0.854451:89866:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839008 ES:SE:LP:AF:SS:ID   -0.000205966:0.00154454:0.0487033:0.839008:89866:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.76317  ES:SE:LP:AF:SS:ID   0.00115373:0.0012418:0.452411:0.76317:89866:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.10519  ES:SE:LP:AF:SS:ID   0.00114705:0.00171139:0.298688:0.10519:89866:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00773441   ES:SE:LP:AF:SS:ID   0.00144509:0.0063404:0.0863392:0.00773441:89866:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129876 ES:SE:LP:AF:SS:ID   -0.00290287:0.0015778:1.18179:0.129876:89866:rs762168062