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-22617_2131/ukb-d-22617_2131.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-22617_2131/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 15:02:49 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_2131/ukb-d-22617_2131.vcf.gz ...
Read summary statistics for 10330770 SNPs.
Dropped 8151 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, 1280058 SNPs remain.
After merging with regression SNP LD, 1280058 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.008 (0.0046)
Lambda GC: 1.0201
Mean Chi^2: 1.0168
Intercept: 1.0026 (0.0059)
Ratio: 0.1573 (0.3516)
Analysis finished at Mon Nov 25 15:04:31 2019
Total time elapsed: 1.0m:41.81s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9432,
    "inflation_factor": 1.0231,
    "mean_EFFECT": -5.0873e-06,
    "n": 91149,
    "n_snps": 10330770,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1102512,
    "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": 203249,
    "n_est": 91195.0896,
    "ratio_se_n": 1.0003,
    "mean_diff": -0,
    "ratio_diff": 46.3023,
    "sd_y_est1": 0.1412,
    "sd_y_est2": 0.1412,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1280058,
    "ldsc_nsnp_merge_regression_ld": 1280058,
    "ldsc_observed_scale_h2_beta": 0.008,
    "ldsc_observed_scale_h2_se": 0.0046,
    "ldsc_intercept_beta": 1.0026,
    "ldsc_intercept_se": 0.0059,
    "ldsc_lambda_gc": 1.0201,
    "ldsc_mean_chisq": 1.0168,
    "ldsc_ratio": 0.1548
}

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 10323181 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 49232 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30561 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.077381e+00 6.178013e+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 7.877878e+07 5.605914e+07 3.02000e+02 3.253980e+07 6.969975e+07 1.147270e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.100000e-06 1.733400e-03 -1.61988e-02 -7.758000e-04 -1.170000e-05 7.501000e-04 2.059460e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.447700e-03 9.364000e-04 5.46400e-04 7.331000e-04 1.020300e-03 1.892000e-03 5.386200e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.965091e-01 2.895728e-01 1.00000e-07 2.453421e-01 4.950989e-01 7.472622e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.965074e-01 2.895739e-01 1.00000e-07 2.453388e-01 4.950969e-01 7.472609e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.471096e-01 2.627918e-01 6.70960e-03 3.318150e-02 1.385520e-01 3.951278e-01 9.932900e-01 ▇▂▂▁▁
numeric AF_reference 203249 0.9803259 NA NA NA NA NA 2.469217e-01 2.536896e-01 0.00000e+00 3.554310e-02 1.551520e-01 3.917730e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 9.114900e+04 0.000000e+00 9.11490e+04 9.114900e+04 9.114900e+04 9.114900e+04 9.114900e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0015422 0.0011558 0.1820992 0.1820963 0.1114870 0.1894970 91149
1 693731 rs12238997 A G -0.0014320 0.0010946 0.1907959 0.1907937 0.1164590 0.1417730 91149
1 707522 rs371890604 G C -0.0015808 0.0012301 0.1987719 0.1987691 0.0978765 0.1293930 91149
1 717587 rs144155419 G A -0.0028473 0.0029323 0.3315439 0.3315403 0.0157837 0.0045926 91149
1 730087 rs148120343 T C -0.0025972 0.0015172 0.0869261 0.0869205 0.0569973 0.0127796 91149
1 731718 rs142557973 T C -0.0013993 0.0010387 0.1779418 0.1779386 0.1223590 0.1543530 91149
1 732032 rs61770163 A C -0.0019056 0.0011075 0.0853297 0.0853265 0.1220470 0.1555510 91149
1 734349 rs141242758 T C -0.0013341 0.0010395 0.1993669 0.1993645 0.1215880 0.1525560 91149
1 749963 rs529266287 T TAA 0.0014097 0.0010225 0.1680119 0.1680090 0.8689170 0.7641770 91149
1 751343 rs28544273 T A -0.0014899 0.0010138 0.1416492 0.1416438 0.1236990 0.2426120 91149
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0005468 0.0012160 0.6529471 0.6529462 0.0552869 0.0309934 91149
23 154923374 rs111332691 T A -0.0003072 0.0013233 0.8164521 0.8164513 0.0448387 0.0116556 91149
23 154925045 rs509981 C T 0.0006023 0.0006377 0.3449110 0.3449095 0.2444670 0.3634440 91149
23 154925895 rs538470 C T 0.0007706 0.0006520 0.2372471 0.2372438 0.2409490 0.3634440 91149
23 154927581 rs644138 G A 0.0006361 0.0005998 0.2889389 0.2889357 0.3001640 0.4635760 91149
23 154929412 rs557132 C T 0.0006116 0.0006379 0.3376696 0.3376675 0.2443160 0.3568210 91149
23 154929637 rs35185538 CT C 0.0005773 0.0006661 0.3861117 0.3861095 0.2286640 0.3011920 91149
23 154929952 rs4012982 CAA C 0.0006862 0.0006714 0.3067743 0.3067708 0.2382530 0.3165560 91149
23 154930230 rs781880 A G 0.0006455 0.0006377 0.3113931 0.3113906 0.2447660 0.3618540 91149
23 154930487 rs781879 T A 0.0027130 0.0021627 0.2096829 0.2096792 0.0196632 0.1263580 91149

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   -0.00154215:0.00115575:0.739692:0.111487:91149:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116459 ES:SE:LP:AF:SS:ID   -0.00143202:0.00109462:0.719431:0.116459:91149:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978765    ES:SE:LP:AF:SS:ID   -0.00158076:0.0012301:0.701645:0.0978765:91149:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157837    ES:SE:LP:AF:SS:ID   -0.00284731:0.0029323:0.479459:0.0157837:91149:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569973    ES:SE:LP:AF:SS:ID   -0.00259725:0.0015172:1.06085:0.0569973:91149:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122359 ES:SE:LP:AF:SS:ID   -0.00139929:0.00103872:0.749722:0.122359:91149:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122047 ES:SE:LP:AF:SS:ID   -0.00190558:0.00110752:1.0689:0.122047:91149:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121588 ES:SE:LP:AF:SS:ID   -0.00133407:0.00103951:0.700347:0.121588:91149:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868917 ES:SE:LP:AF:SS:ID   0.00140969:0.00102253:0.77466:0.868917:91149:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123699 ES:SE:LP:AF:SS:ID   -0.00148992:0.00101376:0.848786:0.123699:91149:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143202 ES:SE:LP:AF:SS:ID   -0.00149876:0.00100363:0.868535:0.143202:91149:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123834 ES:SE:LP:AF:SS:ID   -0.00146703:0.0010123:0.83185:0.123834:91149:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869892 ES:SE:LP:AF:SS:ID   0.00149902:0.000986383:0.890806:0.869892:91149:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874553 ES:SE:LP:AF:SS:ID   0.00144862:0.00100238:0.828534:0.874553:91149:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129529 ES:SE:LP:AF:SS:ID   -0.0014428:0.000989479:0.839216:0.129529:91149:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358205    ES:SE:LP:AF:SS:ID   -0.000547086:0.0018077:0.117952:0.0358205:91149:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869539 ES:SE:LP:AF:SS:ID   0.00148388:0.000985559:0.878877:0.869539:91149:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869616 ES:SE:LP:AF:SS:ID   0.0014676:0.00098599:0.864438:0.869616:91149:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869535 ES:SE:LP:AF:SS:ID   0.00148403:0.000985518:0.879054:0.869535:91149:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.86952  ES:SE:LP:AF:SS:ID   0.00141634:0.000983489:0.824381:0.86952:91149:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126911 ES:SE:LP:AF:SS:ID   -0.0013464:0.00100397:0.744971:0.126911:91149:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86905  ES:SE:LP:AF:SS:ID   0.00136342:0.000980943:0.783673:0.86905:91149:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868436 ES:SE:LP:AF:SS:ID   0.00140029:0.000980321:0.814801:0.868436:91149:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869199 ES:SE:LP:AF:SS:ID   0.00137177:0.000981832:0.789494:0.869199:91149:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869205 ES:SE:LP:AF:SS:ID   0.00137074:0.000981896:0.788572:0.869205:91149:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869207 ES:SE:LP:AF:SS:ID   0.00137135:0.000981905:0.789066:0.869207:91149:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869687 ES:SE:LP:AF:SS:ID   0.00140548:0.000984532:0.814112:0.869687:91149:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991787    ES:SE:LP:AF:SS:ID   -0.00106889:0.00114576:0.454855:0.0991787:91149:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873682 ES:SE:LP:AF:SS:ID   0.00134198:0.000999114:0.746609:0.873682:91149:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863058 ES:SE:LP:AF:SS:ID   0.00154345:0.000980047:0.938212:0.863058:91149:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868472 ES:SE:LP:AF:SS:ID   0.00133515:0.000989774:0.751152:0.868472:91149:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865369 ES:SE:LP:AF:SS:ID   0.00145001:0.000989959:0.844661:0.865369:91149:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995228    ES:SE:LP:AF:SS:ID   -0.00108639:0.0011848:0.44469:0.0995228:91149:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   0.00149931:0.00100124:0.872002:0.870657:91149:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   0.00149931:0.00100123:0.871998:0.870657:91149:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870654 ES:SE:LP:AF:SS:ID   0.00149968:0.00100124:0.872306:0.870654:91149:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871019 ES:SE:LP:AF:SS:ID   0.00150108:0.0010017:0.872898:0.871019:91149:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126515 ES:SE:LP:AF:SS:ID   -0.00127006:0.00100282:0.687526:0.126515:91149:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106037 ES:SE:LP:AF:SS:ID   -0.000667576:0.00109008:0.267391:0.106037:91149:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85438  ES:SE:LP:AF:SS:ID   0.00113801:0.000979679:0.610136:0.85438:91149:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839153 ES:SE:LP:AF:SS:ID   -0.000657768:0.00096797:0.303817:0.839153:91149:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763195 ES:SE:LP:AF:SS:ID   0.000700772:0.000778297:0.434254:0.763195:91149:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105092 ES:SE:LP:AF:SS:ID   0.000397926:0.00107251:0.148363:0.105092:91149:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00772317   ES:SE:LP:AF:SS:ID   0.00135965:0.003974:0.135342:0.00772317:91149:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129904 ES:SE:LP:AF:SS:ID   -0.00127645:0.000988814:0.706098:0.129904:91149:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129636 ES:SE:LP:AF:SS:ID   -0.00124005:0.000987514:0.679405:0.129636:91149:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104365 ES:SE:LP:AF:SS:ID   0.000307048:0.00108083:0.109945:0.104365:91149:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00906976   ES:SE:LP:AF:SS:ID   -0.00645674:0.00379991:1.0492:0.00906976:91149:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00773917   ES:SE:LP:AF:SS:ID   0.00136445:0.00399058:0.135243:0.00773917:91149:rs112563271
1   770886  rs371458725 G   A   .   PASS    AF=0.103379 ES:SE:LP:AF:SS:ID   0.000235448:0.00109018:0.0814402:0.103379:91149:rs371458725