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_1152/ukb-d-22617_1152.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_1152/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 15:31:42 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22617_1152/ukb-d-22617_1152.vcf.gz ...
Read summary statistics for 9483744 SNPs.
Dropped 7025 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, 1272900 SNPs remain.
After merging with regression SNP LD, 1272900 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0057 (0.0044)
Lambda GC: 1.0059
Mean Chi^2: 1.0098
Intercept: 0.9995 (0.0058)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 15:33:18 2019
Total time elapsed: 1.0m:36.07s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9388,
    "inflation_factor": 1.0044,
    "mean_EFFECT": 2.6467e-06,
    "n": 91149,
    "n_snps": 9483744,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1049553,
    "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": 189852,
    "n_est": 91121.8225,
    "ratio_se_n": 0.9999,
    "mean_diff": 0,
    "ratio_diff": 60.6648,
    "sd_y_est1": 0.1106,
    "sd_y_est2": 0.1106,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1272900,
    "ldsc_nsnp_merge_regression_ld": 1272900,
    "ldsc_observed_scale_h2_beta": 0.0057,
    "ldsc_observed_scale_h2_se": 0.0044,
    "ldsc_intercept_beta": 0.9995,
    "ldsc_intercept_se": 0.0058,
    "ldsc_lambda_gc": 1.0059,
    "ldsc_mean_chisq": 1.0098,
    "ldsc_ratio": -0.051
}

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 9477257 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 46341 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29396 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.080640e+00 6.174066e+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 7.870147e+07 5.611057e+07 3.02000e+02 3.241426e+07 6.957035e+07 1.147250e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.600000e-06 1.114300e-03 -9.65870e-03 -5.539000e-04 -5.200000e-06 5.447000e-04 1.259090e-02 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 9.782000e-04 5.334000e-04 4.28000e-04 5.651000e-04 7.440000e-04 1.242700e-03 3.057700e-03 ▇▂▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.993120e-01 2.888966e-01 1.00000e-07 2.489299e-01 4.990614e-01 7.496957e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.993102e-01 2.888976e-01 1.00000e-07 2.489276e-01 4.990596e-01 7.496945e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.669297e-01 2.627094e-01 1.11508e-02 4.845400e-02 1.669930e-01 4.241522e-01 9.888490e-01 ▇▂▂▁▁
numeric AF_reference 189852 0.9799813 NA NA NA NA NA 2.662883e-01 2.535050e-01 0.00000e+00 5.551120e-02 1.817090e-01 4.189300e-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 0.0002015 0.0009054 0.8238651 0.8238639 0.1114870 0.1894970 91149
1 693731 rs12238997 A G 0.0003844 0.0008575 0.6539145 0.6539142 0.1164590 0.1417730 91149
1 707522 rs371890604 G C 0.0006749 0.0009636 0.4836954 0.4836944 0.0978765 0.1293930 91149
1 717587 rs144155419 G A -0.0019967 0.0022971 0.3847273 0.3847245 0.0157837 0.0045926 91149
1 730087 rs148120343 T C 0.0001788 0.0011885 0.8804309 0.8804307 0.0569973 0.0127796 91149
1 731718 rs142557973 T C 0.0004449 0.0008137 0.5845316 0.5845299 0.1223590 0.1543530 91149
1 732032 rs61770163 A C 0.0001417 0.0008676 0.8702479 0.8702478 0.1220470 0.1555510 91149
1 734349 rs141242758 T C 0.0004699 0.0008143 0.5639077 0.5639073 0.1215880 0.1525560 91149
1 749963 rs529266287 T TAA -0.0002908 0.0008010 0.7165789 0.7165775 0.8689170 0.7641770 91149
1 751343 rs28544273 T A 0.0003034 0.0007942 0.7024283 0.7024278 0.1236990 0.2426120 91149
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0019819 0.0009525 0.0374628 0.0374594 0.0552869 0.0309934 91149
23 154923374 rs111332691 T A 0.0002233 0.0010366 0.8294360 0.8294359 0.0448387 0.0116556 91149
23 154925045 rs509981 C T 0.0002050 0.0004996 0.6815677 0.6815660 0.2444670 0.3634440 91149
23 154925895 rs538470 C T 0.0003051 0.0005107 0.5502512 0.5502486 0.2409490 0.3634440 91149
23 154927581 rs644138 G A 0.0006636 0.0004699 0.1578429 0.1578399 0.3001640 0.4635760 91149
23 154929412 rs557132 C T 0.0001810 0.0004997 0.7172706 0.7172701 0.2443160 0.3568210 91149
23 154929637 rs35185538 CT C 0.0001418 0.0005218 0.7857764 0.7857773 0.2286640 0.3011920 91149
23 154929952 rs4012982 CAA C 0.0005140 0.0005259 0.3284437 0.3284424 0.2382530 0.3165560 91149
23 154930230 rs781880 A G 0.0002798 0.0004995 0.5754532 0.5754520 0.2447660 0.3618540 91149
23 154930487 rs781879 T A -0.0026411 0.0016942 0.1190189 0.1190162 0.0196632 0.1263580 91149

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111487 ES:SE:LP:AF:SS:ID   0.000201518:0.000905381:0.0841439:0.111487:91149:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116459 ES:SE:LP:AF:SS:ID   0.000384439:0.000857489:0.184479:0.116459:91149:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0978765    ES:SE:LP:AF:SS:ID   0.000674892:0.000963618:0.315428:0.0978765:91149:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157837    ES:SE:LP:AF:SS:ID   -0.00199666:0.00229706:0.414847:0.0157837:91149:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0569973    ES:SE:LP:AF:SS:ID   0.000178784:0.00118854:0.0553047:0.0569973:91149:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122359 ES:SE:LP:AF:SS:ID   0.000444917:0.000813704:0.233192:0.122359:91149:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122047 ES:SE:LP:AF:SS:ID   0.000141717:0.0008676:0.060357:0.122047:91149:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121588 ES:SE:LP:AF:SS:ID   0.000469902:0.000814321:0.248792:0.121588:91149:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868917 ES:SE:LP:AF:SS:ID   -0.0002908:0.000801021:0.144736:0.868917:91149:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123699 ES:SE:LP:AF:SS:ID   0.000303402:0.000794152:0.153398:0.123699:91149:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143202 ES:SE:LP:AF:SS:ID   0.000263082:0.000786217:0.131994:0.143202:91149:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123834 ES:SE:LP:AF:SS:ID   0.000299879:0.000793003:0.151616:0.123834:91149:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869892 ES:SE:LP:AF:SS:ID   -0.00020352:0.000772705:0.101136:0.869892:91149:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874553 ES:SE:LP:AF:SS:ID   -0.000288779:0.000785236:0.146878:0.874553:91149:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129529 ES:SE:LP:AF:SS:ID   0.000122252:0.00077513:0.0581513:0.129529:91149:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0358205    ES:SE:LP:AF:SS:ID   -0.000739283:0.00141608:0.220672:0.0358205:91149:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869539 ES:SE:LP:AF:SS:ID   -0.000238689:0.000772059:0.120789:0.869539:91149:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869616 ES:SE:LP:AF:SS:ID   -0.000245099:0.000772396:0.12436:0.869616:91149:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869535 ES:SE:LP:AF:SS:ID   -0.000241035:0.000772027:0.122122:0.869535:91149:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.86952  ES:SE:LP:AF:SS:ID   -0.000206285:0.000770437:0.102982:0.86952:91149:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126911 ES:SE:LP:AF:SS:ID   0.000193697:0.000786481:0.0939539:0.126911:91149:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86905  ES:SE:LP:AF:SS:ID   -0.000200452:0.000768442:0.100067:0.86905:91149:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868436 ES:SE:LP:AF:SS:ID   -0.000235715:0.000767955:0.119821:0.868436:91149:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869199 ES:SE:LP:AF:SS:ID   -0.000217455:0.000769139:0.109362:0.869199:91149:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869205 ES:SE:LP:AF:SS:ID   -0.000217735:0.000769189:0.10951:0.869205:91149:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869207 ES:SE:LP:AF:SS:ID   -0.00021718:0.000769195:0.1092:0.869207:91149:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869687 ES:SE:LP:AF:SS:ID   -0.0002273:0.000771254:0.114519:0.869687:91149:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991787    ES:SE:LP:AF:SS:ID   0.000874405:0.000897547:0.481549:0.0991787:91149:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873682 ES:SE:LP:AF:SS:ID   -0.000256072:0.000782676:0.128698:0.873682:91149:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863058 ES:SE:LP:AF:SS:ID   -0.000153466:0.000767742:0.0749123:0.863058:91149:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868472 ES:SE:LP:AF:SS:ID   -0.00023926:0.000775359:0.120535:0.868472:91149:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865369 ES:SE:LP:AF:SS:ID   -0.000219107:0.000775505:0.109281:0.865369:91149:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995228    ES:SE:LP:AF:SS:ID   0.000565769:0.000928132:0.265886:0.0995228:91149:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   -0.000213652:0.000784339:0.104955:0.870657:91149:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870657 ES:SE:LP:AF:SS:ID   -0.000213845:0.000784339:0.10506:0.870657:91149:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870654 ES:SE:LP:AF:SS:ID   -0.000213907:0.000784342:0.105093:0.870654:91149:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871019 ES:SE:LP:AF:SS:ID   -0.000235497:0.000784706:0.116853:0.871019:91149:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126515 ES:SE:LP:AF:SS:ID   0.000221008:0.000785579:0.108765:0.126515:91149:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106037 ES:SE:LP:AF:SS:ID   0.000734218:0.000853927:0.409053:0.106037:91149:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85438  ES:SE:LP:AF:SS:ID   -0.000525491:0.000767447:0.306697:0.85438:91149:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839153 ES:SE:LP:AF:SS:ID   0.000672682:0.00075827:0.425955:0.839153:91149:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763195 ES:SE:LP:AF:SS:ID   -0.000281316:0.000609691:0.190772:0.763195:91149:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105092 ES:SE:LP:AF:SS:ID   0.000257255:0.00084016:0.119498:0.105092:91149:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129904 ES:SE:LP:AF:SS:ID   0.000248318:0.000774606:0.125788:0.129904:91149:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129636 ES:SE:LP:AF:SS:ID   0.000121839:0.000773588:0.0580654:0.129636:91149:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104365 ES:SE:LP:AF:SS:ID   0.00037182:0.000846682:0.180092:0.104365:91149:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.103379 ES:SE:LP:AF:SS:ID   0.000399196:0.000854005:0.193694:0.103379:91149:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.829291 ES:SE:LP:AF:SS:ID   0.000274564:0.000754731:0.145078:0.829291:91149:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.869067 ES:SE:LP:AF:SS:ID   -0.000235652:0.000769858:0.119454:0.869067:91149:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129741 ES:SE:LP:AF:SS:ID   0.000150753:0.000773165:0.0729336:0.129741:91149:rs59066358