Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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 /data/cromwell-executions/qc/307fc3d0-4dac-4244-a187-3341d2da1754/call-ldsc/inputs/-2071042851/bbj-a-160.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/bbj-a-160/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Jan 21 19:50:34 2022
Reading summary statistics from /data/cromwell-executions/qc/307fc3d0-4dac-4244-a187-3341d2da1754/call-ldsc/inputs/-2071042851/bbj-a-160.vcf.gz ...
Read summary statistics for 8872069 SNPs.
Dropped 96061 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1071230 SNPs remain.
After merging with regression SNP LD, 1071230 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0243 (0.0053)
Lambda GC: 1.0196
Mean Chi^2: 1.0351
Intercept: 0.9878 (0.0081)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Fri Jan 21 19:52:20 2022
Total time elapsed: 1.0m:46.15s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.911,
    "inflation_factor": 1.014,
    "mean_EFFECT": -0.0009,
    "n": "-Inf",
    "n_snps": 8872152,
    "n_clumped_hits": 12,
    "n_p_sig": 441,
    "n_mono": 0,
    "n_ns": 822038,
    "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": 17303,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1071230,
    "ldsc_nsnp_merge_regression_ld": 1071230,
    "ldsc_observed_scale_h2_beta": 0.0243,
    "ldsc_observed_scale_h2_se": 0.0053,
    "ldsc_intercept_beta": 0.9878,
    "ldsc_intercept_se": 0.0081,
    "ldsc_lambda_gc": 1.0196,
    "ldsc_mean_chisq": 1.0351,
    "ldsc_ratio": -0.3476
}
 

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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 4 0.9999995 3 12 0 8870975 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 99 0 37224 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 23996 0 NA NA NA NA NA NA NA NA NA NA
logical N 8872152 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.838036e+00 6.011729e+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 NA NA 7.946180e+07 5.554818e+07 7914.0000000 3.374429e+07 7.079028e+07 1.147656e+08 2.492139e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -8.990000e-04 1.318202e-01 -3.6282200 -2.483430e-02 -3.209000e-04 2.399190e-02 6.444410e+00 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 7.229030e-02 1.142172e-01 0.0196819 2.227550e-02 3.037560e-02 6.633630e-02 5.165310e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.971827e-01 2.892748e-01 0.0000000 2.467954e-01 4.970230e-01 7.473826e-01 9.999999e-01 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.971827e-01 2.892748e-01 0.0000000 2.467952e-01 4.970232e-01 7.473825e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.647065e-01 2.772434e-01 0.0000525 2.786860e-02 1.604160e-01 4.375052e-01 9.999480e-01 ▇▂▂▁▁
numeric AF_reference 17303 0.9980497 NA NA NA NA NA NA NA 2.525843e-01 2.494078e-01 0.0001997 3.833870e-02 1.739220e-01 4.057510e-01 9.998000e-01 ▇▃▂▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 751343 rs28544273 T A -0.0618361 0.0313462 0.0485322 0.0485317 0.140848 0.242612 NA
1 751756 rs143225517 T C -0.0616366 0.0312230 0.0483727 0.0483730 0.140194 0.242212 NA
1 752566 rs3094315 G A 0.0518330 0.0270498 0.0553388 0.0553388 0.842147 0.718251 NA
1 752894 rs3131971 T C 0.0587491 0.0299330 0.0496833 0.0496826 0.855854 0.753195 NA
1 753405 rs3115860 C A 0.0608501 0.0307161 0.0475861 0.0475858 0.856567 0.751797 NA
1 753425 rs3131970 T C 0.0602671 0.0304586 0.0478542 0.0478547 0.855256 0.749002 NA
1 755890 rs3115858 A T 0.0619717 0.0311571 0.0467003 0.0467004 0.855710 0.751398 NA
1 756604 rs3131962 A G 0.0617065 0.0310743 0.0470587 0.0470586 0.853791 0.748003 NA
1 757734 rs4951929 C T 0.0623550 0.0313677 0.0468263 0.0468258 0.853211 0.748203 NA
1 757936 rs4951862 C A 0.0624730 0.0313707 0.0464323 0.0464321 0.853828 0.748802 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154789496 rs5940513 A G -0.0090115 0.0257963 0.7268403 0.7268402 0.7799050 0.6378810 NA
23 154803410 rs368676291 T C -0.0106544 0.0269448 0.6925370 0.6925360 0.7587920 0.5353640 NA
23 154803411 rs373288103 G A -0.0106365 0.0269528 0.6931129 0.6931128 0.7587980 0.5353640 NA
23 154803415 rs112167337 A C -0.0108697 0.0270279 0.6875622 0.6875619 0.7571190 0.5345700 NA
23 154803793 rs5940526 T A -0.0106061 0.0270694 0.6951956 0.6951976 0.7566730 0.5311260 NA
23 154804301 rs5940397 G A -0.0095652 0.0273845 0.7268688 0.7268692 0.7724110 0.6442380 NA
23 154805102 rs12834147 G C -0.0096639 0.0274965 0.7252454 0.7252446 0.7678120 0.6360260 NA
23 154805911 rs2890132 G A -0.0099928 0.0275617 0.7169321 0.7169317 0.7693250 0.6378810 NA
23 154812754 rs183018361 G T 0.1729140 0.2988040 0.5628012 0.5628004 0.0013019 0.0230464 NA
23 154821956 rs5940536 G A 0.1409040 0.2778030 0.6120093 0.6120086 0.0012706 0.0389404 NA

bcf preview

1   751343  rs28544273  T   A   .   PASS    AF=0.140848 ES:SE:LP:AF:ID  -0.0618361:0.0313462:1.31397:0.140848:rs28544273
1   751756  rs28527770  T   C   .   PASS    AF=0.140194 ES:SE:LP:AF:ID  -0.0616366:0.031223:1.3154:0.140194:rs28527770
1   752566  rs3094315   G   A   .   PASS    AF=0.842147 ES:SE:LP:AF:ID  0.051833:0.0270498:1.25697:0.842147:rs3094315
1   752894  rs3131971   T   C   .   PASS    AF=0.855854 ES:SE:LP:AF:ID  0.0587491:0.029933:1.30379:0.855854:rs3131971
1   753405  rs3115860   C   A   .   PASS    AF=0.856567 ES:SE:LP:AF:ID  0.0608501:0.0307161:1.32252:0.856567:rs3115860
1   753425  rs1431026348    T   C   .   PASS    AF=0.855256 ES:SE:LP:AF:ID  0.0602671:0.0304586:1.32008:0.855256:rs1431026348
1   755890  rs1280367067    A   T   .   PASS    AF=0.85571  ES:SE:LP:AF:ID  0.0619717:0.0311571:1.33068:0.85571:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.853791 ES:SE:LP:AF:ID  0.0617065:0.0310743:1.32736:0.853791:rs3131962
1   757734  rs1557551770    C   T   .   PASS    AF=0.853211 ES:SE:LP:AF:ID  0.062355:0.0313677:1.32951:0.853211:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.853828 ES:SE:LP:AF:ID  0.062473:0.0313707:1.33318:0.853828:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.848637 ES:SE:LP:AF:ID  0.0604825:0.0304582:1.32734:0.848637:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.854402 ES:SE:LP:AF:ID  0.0636201:0.0319052:1.33585:0.854402:rs3131954
1   759837  rs3115851   T   A   .   PASS    AF=0.854024 ES:SE:LP:AF:ID  0.064853:0.032349:1.34693:0.854024:rs3115851
1   760912  rs1048488   C   T   .   PASS    AF=0.842422 ES:SE:LP:AF:ID  0.0607806:0.0307497:1.318:0.842422:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.841786 ES:SE:LP:AF:ID  0.0607185:0.0307786:1.31405:0.841786:rs3115850
1   761752  rs1057213   C   T   .   PASS    AF=0.850518 ES:SE:LP:AF:ID  0.0656542:0.0326752:1.35158:0.850518:rs1057213
1   845635  rs117086422 C   T   .   PASS    AF=0.134869 ES:SE:LP:AF:ID  -0.0301747:0.0318639:0.46389:0.134869:rs117086422
1   846078  rs778265812 C   T   .   PASS    AF=0.134139 ES:SE:LP:AF:ID  -0.0290904:0.0313879:0.450963:0.134139:rs778265812
1   846808  rs4475691   C   T   .   PASS    AF=0.142046 ES:SE:LP:AF:ID  -0.024034:0.0285629:0.39783:0.142046:rs4475691
1   846864  rs1269142199    G   C   .   PASS    AF=0.139955 ES:SE:LP:AF:ID  -0.0252653:0.0292245:0.411953:0.139955:rs1269142199
1   847228  rs3905286   C   T   .   PASS    AF=0.146723 ES:SE:LP:AF:ID  -0.0275764:0.0301744:0.44277:0.146723:rs3905286
1   847491  rs1158719307    G   A   .   PASS    AF=0.148421 ES:SE:LP:AF:ID  -0.0276246:0.0301775:0.443724:0.148421:rs1158719307
1   848090  rs4246505   G   A   .   PASS    AF=0.135231 ES:SE:LP:AF:ID  -0.0304643:0.0312178:0.482628:0.135231:rs4246505
1   848445  rs1156895099    G   A   .   PASS    AF=0.149813 ES:SE:LP:AF:ID  -0.0287165:0.0304252:0.461863:0.149813:rs1156895099
1   848456  rs11507767  A   G   .   PASS    AF=0.150256 ES:SE:LP:AF:ID  -0.0290933:0.0305279:0.467773:0.150256:rs11507767
1   848654  rs5772026   TG  T   .   PASS    AF=0.132458 ES:SE:LP:AF:ID  -0.0305533:0.0316011:0.476744:0.132458:rs5772026
1   848738  rs3829741   C   T   .   PASS    AF=0.134758 ES:SE:LP:AF:ID  -0.0298509:0.0312774:0.468668:0.134758:rs3829741
1   849440  rs79376265  C   T   .   PASS    AF=0.144737 ES:SE:LP:AF:ID  0.0482527:0.0335949:0.821268:0.144737:rs79376265
1   849863  rs61620633  G   GACTGCCCAGCTC   .   PASS    AF=0.153138 ES:SE:LP:AF:ID  -0.0292861:0.0310401:0.461641:0.153138:rs61620633
1   850062  rs28723578  A   T   .   PASS    AF=0.150708 ES:SE:LP:AF:ID  -0.0290447:0.0307298:0.462715:0.150708:rs28723578
1   850123  rs28622257  C   T   .   PASS    AF=0.135747 ES:SE:LP:AF:ID  -0.0305208:0.0315312:0.477469:0.135747:rs28622257
1   850528  rs114889920 A   G   .   PASS    AF=0.145382 ES:SE:LP:AF:ID  0.0473804:0.0330955:0.817442:0.145382:rs114889920
1   851030  rs1284752010    G   C   .   PASS    AF=0.142079 ES:SE:LP:AF:ID  0.047943:0.0329741:0.835775:0.142079:rs1284752010
1   851190  rs28609852  G   A   .   PASS    AF=0.149116 ES:SE:LP:AF:ID  -0.0303351:0.0311986:0.480316:0.149116:rs28609852
1   851204  rs28552953  G   C   .   PASS    AF=0.15968  ES:SE:LP:AF:ID  -0.0312275:0.0314944:0.492915:0.15968:rs28552953
1   852664  rs28605311  C   T   .   PASS    AF=0.139485 ES:SE:LP:AF:ID  -0.032442:0.0319057:0.5097:0.139485:rs28605311
1   852758  rs4970462   G   C   .   PASS    AF=0.13456  ES:SE:LP:AF:ID  -0.0320822:0.0320111:0.499988:0.13456:rs4970462
1   853239  rs4970380   A   G   .   PASS    AF=0.13546  ES:SE:LP:AF:ID  -0.0321793:0.0320657:0.500863:0.13546:rs4970380
1   853488  rs77644389  G   A   .   PASS    AF=0.148017 ES:SE:LP:AF:ID  0.0453702:0.0320302:0.805112:0.148017:rs77644389
1   854168  rs79188446  C   T   .   PASS    AF=0.148635 ES:SE:LP:AF:ID  0.0449389:0.0317886:0.802839:0.148635:rs79188446
1   855635  rs77712898  CCTT    C   .   PASS    AF=0.149954 ES:SE:LP:AF:ID  0.0438838:0.0312056:0.796855:0.149954:rs77712898
1   855774  rs77595185  G   A   .   PASS    AF=0.150248 ES:SE:LP:AF:ID  0.043727:0.031129:0.795583:0.150248:rs77595185
1   856436  rs34105146  TG  T   .   PASS    AF=0.118773 ES:SE:LP:AF:ID  -0.037321:0.0358823:0.525353:0.118773:rs34105146
1   857177  rs386627408 T   C   .   PASS    AF=0.439536 ES:SE:LP:AF:ID  0.0338433:0.0217598:0.921282:0.439536:rs386627408
1   857318  rs144110716 G   GGAGT   .   PASS    AF=0.150605 ES:SE:LP:AF:ID  0.0425504:0.029925:0.809515:0.150605:rs144110716
1   857443  rs56663360  C   T   .   PASS    AF=0.174129 ES:SE:LP:AF:ID  0.0421327:0.0301081:0.791292:0.174129:rs56663360
1   858040  rs4970460   C   A   .   PASS    AF=0.151939 ES:SE:LP:AF:ID  -0.0421813:0.033141:0.692301:0.151939:rs4970460
1   858051  rs4970459   C   T   .   PASS    AF=0.153871 ES:SE:LP:AF:ID  -0.0416632:0.032836:0.6893:0.153871:rs4970459
1   858149  rs77520260  C   T   .   PASS    AF=0.150395 ES:SE:LP:AF:ID  0.0414139:0.0293671:0.800034:0.150395:rs77520260
1   858691  rs34628185  TG  T   .   PASS    AF=0.401682 ES:SE:LP:AF:ID  -0.0184053:0.0221111:0.392349:0.401682:rs34628185