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-20113_100/ukb-d-20113_100.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-20113_100/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 15:01:01 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20113_100/ukb-d-20113_100.vcf.gz ...
Read summary statistics for 9755774 SNPs.
Dropped 7421 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, 1275809 SNPs remain.
After merging with regression SNP LD, 1275809 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0822 (0.1302)
Lambda GC: 1.0135
Mean Chi^2: 1.009
Intercept: 1.0044 (0.0061)
Ratio: 0.4866 (0.6709)
Analysis finished at Mon Nov 25 15:02:29 2019
Total time elapsed: 1.0m:27.96s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9403,
    "inflation_factor": 1.0131,
    "mean_EFFECT": -0.0001,
    "n": 2906,
    "n_snps": 9755774,
    "n_clumped_hits": 0,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1067316,
    "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": 193953,
    "n_est": 2918.49,
    "ratio_se_n": 1.0021,
    "mean_diff": -0.0001,
    "ratio_diff": 19.6736,
    "sd_y_est1": 0.4975,
    "sd_y_est2": 0.4985,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1275809,
    "ldsc_nsnp_merge_regression_ld": 1275809,
    "ldsc_observed_scale_h2_beta": 0.0822,
    "ldsc_observed_scale_h2_se": 0.1302,
    "ldsc_intercept_beta": 1.0044,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 1.0135,
    "ldsc_mean_chisq": 1.009,
    "ldsc_ratio": 0.4889
}

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 9748900 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 47313 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29803 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.079256e+00 6.176256e+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 7.873178e+07 5.609491e+07 302.0000000 3.244903e+07 6.961644e+07 1.147345e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -7.260000e-05 2.994360e-02 -0.2892990 -1.433150e-02 -1.262000e-04 1.413610e-02 2.975570e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.579870e-02 1.491780e-02 0.0106750 1.430970e-02 1.916360e-02 3.310500e-02 8.547540e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.978646e-01 2.890885e-01 0.0000000 2.470501e-01 4.972090e-01 7.477389e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.978091e-01 2.891217e-01 0.0000000 2.469538e-01 4.971545e-01 7.477159e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.603617e-01 2.629619e-01 0.0094699 4.300160e-02 1.577740e-01 4.145040e-01 9.905300e-01 ▇▂▂▁▁
numeric AF_reference 193953 0.9801192 NA NA NA NA NA 2.598289e-01 2.537538e-01 0.0000000 4.852240e-02 1.729230e-01 4.101440e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.906000e+03 0.000000e+00 2906.0000000 2.906000e+03 2.906000e+03 2.906000e+03 2.906000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0086905 0.0231702 0.7076329 0.7076061 0.1111720 0.1894970 2906
1 693731 rs12238997 A G -0.0040485 0.0215716 0.8511410 0.8511282 0.1160680 0.1417730 2906
1 707522 rs371890604 G C -0.0178187 0.0239304 0.4565707 0.4565104 0.0980237 0.1293930 2906
1 717587 rs144155419 G A -0.0044515 0.0579232 0.9387471 0.9387413 0.0161674 0.0045926 2906
1 730087 rs148120343 T C -0.0093235 0.0296201 0.7529602 0.7529378 0.0576893 0.0127796 2906
1 731718 rs142557973 T C -0.0098290 0.0204769 0.6312596 0.6312240 0.1223740 0.1543530 2906
1 732032 rs61770163 A C -0.0091309 0.0218148 0.6755663 0.6755358 0.1219650 0.1555510 2906
1 734349 rs141242758 T C -0.0084516 0.0204834 0.6799234 0.6798926 0.1215630 0.1525560 2906
1 749963 rs529266287 T TAA 0.0062421 0.0201487 0.7567336 0.7567103 0.8703350 0.7641770 2906
1 751343 rs28544273 T A -0.0079131 0.0198965 0.6908695 0.6908405 0.1241430 0.2426120 2906
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0244484 0.0223725 0.2745788 0.2744869 0.0623281 0.0309934 2906
23 154923374 rs111332691 T A 0.0239078 0.0263599 0.3644962 0.3644194 0.0443909 0.0116556 2906
23 154925045 rs509981 C T 0.0018299 0.0127307 0.8857140 0.8857040 0.2412490 0.3634440 2906
23 154925895 rs538470 C T 0.0023253 0.0130228 0.8583010 0.8582881 0.2369750 0.3634440 2906
23 154927581 rs644138 G A -0.0053969 0.0118464 0.6487300 0.6486971 0.3037750 0.4635760 2906
23 154929412 rs557132 C T 0.0023116 0.0127407 0.8560369 0.8560242 0.2409490 0.3568210 2906
23 154929637 rs35185538 CT C 0.0154051 0.0132661 0.2456422 0.2455451 0.2270290 0.3011920 2906
23 154929952 rs4012982 CAA C 0.0033690 0.0133657 0.8010090 0.8009911 0.2344250 0.3165560 2906
23 154930230 rs781880 A G 0.0034832 0.0127468 0.7846699 0.7846504 0.2405400 0.3618540 2906
23 154930487 rs781879 T A 0.0578339 0.0457901 0.2066831 0.2065813 0.0193886 0.1263580 2906

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111172 ES:SE:LP:AF:SS:ID   -0.00869052:0.0231702:0.150192:0.111172:2906:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116068 ES:SE:LP:AF:SS:ID   -0.00404854:0.0215716:0.0699985:0.116068:2906:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0980237    ES:SE:LP:AF:SS:ID   -0.0178187:0.0239304:0.340492:0.0980237:2906:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0161674    ES:SE:LP:AF:SS:ID   -0.00445151:0.0579232:0.0274514:0.0161674:2906:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0576893    ES:SE:LP:AF:SS:ID   -0.00932346:0.0296201:0.123228:0.0576893:2906:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122374 ES:SE:LP:AF:SS:ID   -0.00982901:0.0204769:0.199792:0.122374:2906:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121965 ES:SE:LP:AF:SS:ID   -0.00913086:0.0218148:0.170332:0.121965:2906:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121563 ES:SE:LP:AF:SS:ID   -0.00845165:0.0204834:0.16754:0.121563:2906:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.870335 ES:SE:LP:AF:SS:ID   0.00624214:0.0201487:0.121057:0.870335:2906:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.124143 ES:SE:LP:AF:SS:ID   -0.00791313:0.0198965:0.160604:0.124143:2906:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.144138 ES:SE:LP:AF:SS:ID   -0.0155119:0.0196805:0.365874:0.144138:2906:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124249 ES:SE:LP:AF:SS:ID   -0.007822:0.0198658:0.158766:0.124249:2906:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   0.0140205:0.0193704:0.328605:0.870459:2906:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873999 ES:SE:LP:AF:SS:ID   0.00715093:0.0196593:0.14504:0.873999:2906:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128905 ES:SE:LP:AF:SS:ID   -0.0126311:0.0194373:0.287479:0.128905:2906:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0352719    ES:SE:LP:AF:SS:ID   -0.0132571:0.0359248:0.147436:0.0352719:2906:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870125 ES:SE:LP:AF:SS:ID   0.013389:0.019364:0.310382:0.870125:2906:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870468 ES:SE:LP:AF:SS:ID   0.0134484:0.0194093:0.311191:0.870468:2906:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870284 ES:SE:LP:AF:SS:ID   0.0141583:0.0193703:0.332658:0.870284:2906:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.869891 ES:SE:LP:AF:SS:ID   0.0139853:0.0193029:0.329006:0.869891:2906:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126799 ES:SE:LP:AF:SS:ID   -0.011486:0.01969:0.252037:0.126799:2906:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86958  ES:SE:LP:AF:SS:ID   0.0145811:0.0192484:0.347946:0.86958:2906:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868956 ES:SE:LP:AF:SS:ID   0.0130079:0.0192361:0.301939:0.868956:2906:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869689 ES:SE:LP:AF:SS:ID   0.0141641:0.0192782:0.334823:0.869689:2906:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869718 ES:SE:LP:AF:SS:ID   0.0140778:0.0192831:0.332162:0.869718:2906:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.86973  ES:SE:LP:AF:SS:ID   0.0140602:0.0192832:0.331637:0.86973:2906:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869985 ES:SE:LP:AF:SS:ID   0.0137912:0.019322:0.322909:0.869985:2906:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0984312    ES:SE:LP:AF:SS:ID   -0.0135086:0.0224271:0.262013:0.0984312:2906:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873799 ES:SE:LP:AF:SS:ID   0.00847692:0.0196233:0.176665:0.873799:2906:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862638 ES:SE:LP:AF:SS:ID   0.0107179:0.0192305:0.238568:0.862638:2906:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.867936 ES:SE:LP:AF:SS:ID   0.0140862:0.019433:0.329201:0.867936:2906:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865277 ES:SE:LP:AF:SS:ID   0.0114837:0.0193995:0.256549:0.865277:2906:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0981553    ES:SE:LP:AF:SS:ID   -0.0151656:0.0236935:0.282185:0.0981553:2906:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87099  ES:SE:LP:AF:SS:ID   0.00800583:0.0196898:0.164733:0.87099:2906:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870988 ES:SE:LP:AF:SS:ID   0.00801184:0.0196896:0.164877:0.870988:2906:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870986 ES:SE:LP:AF:SS:ID   0.00800611:0.0196897:0.16474:0.870986:2906:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871237 ES:SE:LP:AF:SS:ID   0.00833772:0.0196864:0.172668:0.871237:2906:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126611 ES:SE:LP:AF:SS:ID   -0.0105371:0.0196822:0.227356:0.126611:2906:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105187 ES:SE:LP:AF:SS:ID   -0.0105363:0.0214587:0.20519:0.105187:2906:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854691 ES:SE:LP:AF:SS:ID   0.0083336:0.0193069:0.176502:0.854691:2906:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.833478 ES:SE:LP:AF:SS:ID   0.00282788:0.0189138:0.0549462:0.833478:2906:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.757857 ES:SE:LP:AF:SS:ID   0.0100798:0.0151423:0.296132:0.757857:2906:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.110289 ES:SE:LP:AF:SS:ID   -0.00437129:0.0210046:0.0782319:0.110289:2906:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.130107 ES:SE:LP:AF:SS:ID   -0.0145092:0.0193894:0.342621:0.130107:2906:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129238 ES:SE:LP:AF:SS:ID   -0.0126346:0.0194065:0.288135:0.129238:2906:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.109766 ES:SE:LP:AF:SS:ID   -0.00572615:0.0211072:0.104474:0.109766:2906:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.109059 ES:SE:LP:AF:SS:ID   -0.006744:0.0212525:0.124349:0.109059:2906:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.827462 ES:SE:LP:AF:SS:ID   0.0103424:0.018936:0.232853:0.827462:2906:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.869403 ES:SE:LP:AF:SS:ID   0.0140886:0.0193195:0.331694:0.869403:2906:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129256 ES:SE:LP:AF:SS:ID   -0.0140256:0.0194093:0.32793:0.129256:2906:rs59066358