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/2da58da4-3465-4f3f-8e26-37fd0cbe633f/call-ldsc/inputs/562856188/ieu-b-31.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-31/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Aug 21 01:27:59 2020
Reading summary statistics from /data/cromwell-executions/qc/2da58da4-3465-4f3f-8e26-37fd0cbe633f/call-ldsc/inputs/562856188/ieu-b-31.vcf.gz ...
Read summary statistics for 26946663 SNPs.
Dropped 127474 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1220779 SNPs remain.
After merging with regression SNP LD, 1220779 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2294 (0.0251)
Lambda GC: 1.7479
Mean Chi^2: 3.5529
Intercept: 1.3499 (0.031)
Ratio: 0.137 (0.0121)
Analysis finished at Fri Aug 21 01:33:42 2020
Total time elapsed: 5.0m:43.36s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9666,
    "inflation_factor": 1.1894,
    "mean_EFFECT": -0.0015,
    "n": 521594,
    "n_snps": 26946895,
    "n_clumped_hits": 510,
    "n_p_sig": 110952,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 50372,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 2124828,
    "n_est": 382636.9335,
    "ratio_se_n": 0.8565,
    "mean_diff": 0.0008,
    "ratio_diff": 1.2565,
    "sd_y_est1": 1.3057,
    "sd_y_est2": 1.1184,
    "r2_sum1": 0.1511,
    "r2_sum2": 0.0886,
    "r2_sum3": 0.1208,
    "r2_sum4": 0.1595,
    "ldsc_nsnp_merge_refpanel_ld": 1220779,
    "ldsc_nsnp_merge_regression_ld": 1220779,
    "ldsc_observed_scale_h2_beta": 0.2294,
    "ldsc_observed_scale_h2_se": 0.0251,
    "ldsc_intercept_beta": 1.3499,
    "ldsc_intercept_se": 0.031,
    "ldsc_lambda_gc": 1.7479,
    "ldsc_mean_chisq": 3.5529,
    "ldsc_ratio": 0.1371
}

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 TRUE
n_p_sig TRUE
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 47 0.9999983 3 64 0 26945091 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.653443e+00 5.782457e+00 1.000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.898078e+07 5.624809e+07 56.000000 3.283316e+07 6.963389e+07 1.148532e+08 2.492398e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.503200e-03 1.712029e-01 -93.661600 -2.284200e-02 -9.300000e-05 2.126400e-02 4.105960e+01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.386600e-02 1.460227e-01 0.000462 6.815000e-03 4.620900e-02 1.174750e-01 7.430190e+01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.700682e-01 2.991976e-01 0.000000 2.036601e-01 4.619745e-01 7.297330e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.700679e-01 2.991988e-01 0.000000 2.036802e-01 4.619640e-01 7.297219e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 7.885060e-02 1.926031e-01 0.000025 1.660000e-04 7.900000e-04 2.301000e-02 9.999750e-01 ▇▁▁▁▁
numeric AF_reference 2124828 0.9211476 NA NA NA NA NA 8.966970e-02 1.921881e-01 0.000000 1.397800e-03 7.388200e-03 5.291530e-02 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.391926e+05 1.250756e+05 396.000000 4.392470e+05 4.634550e+05 5.201190e+05 5.215940e+05 ▁▁▁▂▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 16141 rs529651976 C T 0.427499 0.216687 0.0485255 0.0485084 0.000511 0.0025958 35253
1 49298 rs200943160 T C 0.003358 0.011295 0.7662421 0.7662377 0.823742 0.7821490 35253
1 54353 rs140052487 C A 0.084058 0.101643 0.4082432 0.4082413 0.001815 0.0089856 35253
1 54564 rs558796213 G T 0.089614 0.112446 0.4254818 0.4254792 0.000141 0.0041933 403994
1 54591 rs561234294 A G 0.021401 0.120776 0.8593399 0.8593546 0.001552 0.0035942 35253
1 54712 rs552304420 T C 0.045321 0.044239 0.3055991 0.3056190 0.010379 0.0109824 35253
1 54815 rs568686875 T C 0.201867 0.187680 0.2820928 0.2821100 0.000481 0.0019968 35253
1 55326 rs3107975 T C -0.010242 0.033275 0.7582405 0.7582356 0.019596 0.0459265 35253
1 55351 rs531766459 T A -0.004365 0.059198 0.9412010 0.9412208 0.000503 0.0007987 403994
1 55405 rs372455836 C T 0.049055 0.056330 0.3838301 0.3838359 0.006824 0.0075879 35253
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51237137 rs534739169 A C -0.028764 0.087717 0.7429815 0.7429735 0.000213 0.0001997 439247
22 51237410 rs530437591 G A -0.026768 0.057426 0.6411417 0.6411222 0.000353 0.0017971 439247
22 51237486 rs149820726 G C 0.134882 0.159779 0.3985704 0.3985697 0.000539 0.0025958 35253
22 51238275 rs202031343 C T 0.206938 0.103855 0.0463255 0.0463089 0.001276 0.0009984 35253
22 51238307 rs577028785 A G 0.060542 0.238760 0.7998250 0.7998290 0.000241 0.0015974 35253
22 51238349 rs546389903 T C -0.244042 0.284104 0.3903462 0.3903470 0.000170 0.0013978 35253
22 51238660 rs569936315 A G -0.095505 0.151423 0.5282457 0.5282258 0.000066 0.0167732 439247
22 51239586 rs535432390 T G -0.034566 0.021053 0.1006060 0.1006198 0.002957 0.0001997 462485
22 51239678 rs573137567 G T 0.040117 0.086834 0.6441085 0.6440839 0.001830 0.0233626 35253
22 51244163 rs199560686 A G 0.272460 0.204812 0.1834028 0.1834217 0.000053 0.0077875 439247

bcf preview

1   16141   rs529651976 C   T   .   PASS    AF=0.000511 ES:SE:LP:AF:SS:ID   0.427499:0.216687:1.31403:0.000511:35253:rs529651976
1   49298   rs10399793  T   C   .   PASS    AF=0.823742 ES:SE:LP:AF:SS:ID   0.003358:0.011295:0.115634:0.823742:35253:rs10399793
1   54353   rs140052487 C   A   .   PASS    AF=0.001815 ES:SE:LP:AF:SS:ID   0.084058:0.101643:0.389081:0.001815:35253:rs140052487
1   54564   rs558796213 G   T   .   PASS    AF=0.000141 ES:SE:LP:AF:SS:ID   0.089614:0.112446:0.371119:0.000141:403994:rs558796213
1   54591   rs561234294 A   G   .   PASS    AF=0.001552 ES:SE:LP:AF:SS:ID   0.021401:0.120776:0.065835:0.001552:35253:rs561234294
1   54712   rs573184866 T   C   .   PASS    AF=0.010379 ES:SE:LP:AF:SS:ID   0.045321:0.044239:0.514848:0.010379:35253:rs573184866
1   54815   rs568686875 T   C   .   PASS    AF=0.000481 ES:SE:LP:AF:SS:ID   0.201867:0.18768:0.549608:0.000481:35253:rs568686875
1   55326   rs3107975   T   C   .   PASS    AF=0.019596 ES:SE:LP:AF:SS:ID   -0.010242:0.033275:0.120193:0.019596:35253:rs3107975
1   55351   rs531766459 T   A   .   PASS    AF=0.000503 ES:SE:LP:AF:SS:ID   -0.004365:0.059198:0.0263176:0.000503:403994:rs531766459
1   55405   rs372455836 C   T   .   PASS    AF=0.006824 ES:SE:LP:AF:SS:ID   0.049055:0.05633:0.415861:0.006824:35253:rs372455836
1   55416   rs193242050 G   A   .   PASS    AF=9.2e-05  ES:SE:LP:AF:SS:ID   -0.076905:0.166616:0.190838:9.2e-05:439247:rs193242050
1   55427   rs183189405 T   C   .   PASS    AF=0.002334 ES:SE:LP:AF:SS:ID   -0.089086:0.111079:0.37412:0.002334:35253:rs183189405
1   56586   rs541979596 G   A   .   PASS    AF=0.001466 ES:SE:LP:AF:SS:ID   -0.205821:0.133361:0.91101:0.001466:35253:rs541979596
1   57095   rs553759011 T   C   .   PASS    AF=3.6e-05  ES:SE:LP:AF:SS:ID   -0.001648:0.222691:0.00257298:3.6e-05:403994:rs553759011
1   57183   rs368339209 A   G   .   PASS    AF=2.8e-05  ES:SE:LP:AF:SS:ID   -0.471362:0.36358:0.710407:2.8e-05:403994:rs368339209
1   61804   rs567421057 G   A   .   PASS    AF=7.4e-05  ES:SE:LP:AF:SS:ID   -0.178631:0.161091:0.572738:7.4e-05:403994:rs567421057
1   61993   rs190553843 C   T   .   PASS    AF=9.5e-05  ES:SE:LP:AF:SS:ID   0.29185:0.159043:1.17711:9.5e-05:439247:rs190553843
1   62124   rs528478839 G   A   .   PASS    AF=0.000182 ES:SE:LP:AF:SS:ID   0.398012:0.39345:0.506238:0.000182:35253:rs528478839
1   62157   rs10399597  G   A   .   PASS    AF=0.000132 ES:SE:LP:AF:SS:ID   0.086947:0.09908:0.420002:0.000132:439247:rs10399597
1   62509   rs534313866 T   C   .   PASS    AF=0.000533 ES:SE:LP:AF:SS:ID   0.40906:0.218939:1.20956:0.000533:35253:rs534313866
1   62617   rs543126209 T   G   .   PASS    AF=8.9e-05  ES:SE:LP:AF:SS:ID   -0.045688:0.165743:0.106343:8.9e-05:439247:rs543126209
1   64670   rs545257650 A   G   .   PASS    AF=0.000146 ES:SE:LP:AF:SS:ID   -0.171667:0.117699:0.839583:0.000146:439247:rs545257650
1   64908   rs540391097 A   G   .   PASS    AF=0.000642 ES:SE:LP:AF:SS:ID   0.004577:0.05309:0.0309188:0.000642:439247:rs540391097
1   65009   rs563233355 G   A   .   PASS    AF=0.000288 ES:SE:LP:AF:SS:ID   -0.108171:0.073433:0.851635:0.000288:439247:rs563233355
1   65974   rs531923826 A   G   .   PASS    AF=0.004647 ES:SE:LP:AF:SS:ID   0.022648:0.068952:0.129262:0.004647:35253:rs531923826
1   67179   rs149952626 C   G   .   PASS    AF=0.000128 ES:SE:LP:AF:SS:ID   -0.348814:0.367752:0.464878:0.000128:35253:rs149952626
1   67223   rs78676975  C   T   .   PASS    AF=0.000469 ES:SE:LP:AF:SS:ID   0.121674:0.261517:0.192624:0.000469:35253:rs78676975
1   67224   rs566526215 G   A   .   PASS    AF=0.000161 ES:SE:LP:AF:SS:ID   -0.152394:0.123545:0.662808:0.000161:439247:rs566526215
1   67631   rs533896527 G   C   .   PASS    AF=0.000198 ES:SE:LP:AF:SS:ID   -0.097552:0.095728:0.511224:0.000198:439247:rs533896527
1   69594   rs144967600 T   C   .   PASS    AF=0.000745 ES:SE:LP:AF:SS:ID   -0.071976:0.188989:0.152839:0.000745:35253:rs144967600
1   69610   rs376022826 C   T   .   PASS    AF=0.000222 ES:SE:LP:AF:SS:ID   0.058824:0.378144:0.0573165:0.000222:35253:rs376022826
1   70317   rs570011908 G   A   .   PASS    AF=0.000636 ES:SE:LP:AF:SS:ID   -0.009942:0.207632:0.0169179:0.000636:35253:rs570011908
1   72526   rs547237130 A   G   .   PASS    AF=0.038342 ES:SE:LP:AF:SS:ID   0.009192:0.023307:0.159069:0.038342:35253:rs547237130
1   73093   rs535508237 G   A   .   PASS    AF=0.003935 ES:SE:LP:AF:SS:ID   -0.119718:0.070362:1.05131:0.003935:35253:rs535508237
1   77763   rs557457745 G   A   .   PASS    AF=0.005364 ES:SE:LP:AF:SS:ID   0.051872:0.062805:0.388439:0.005364:35253:rs557457745
1   78942   rs372315362 C   G   .   PASS    AF=0.007964 ES:SE:LP:AF:SS:ID   -0.031058:0.049397:0.276101:0.007964:35253:rs372315362
1   79033   rs2462495   A   G   .   PASS    AF=0.998702 ES:SE:LP:AF:SS:ID   0.030693:0.046669:0.291776:0.998702:403994:rs2462495
1   79137   rs143777184 A   T   .   PASS    AF=0.001016 ES:SE:LP:AF:SS:ID   0.022565:0.042995:0.222043:0.001016:439247:rs143777184
1   79188   rs534350410 G   T   .   PASS    AF=0.001117 ES:SE:LP:AF:SS:ID   -0.018478:0.149173:0.0450844:0.001117:35253:rs534350410
1   82957   rs189774606 C   T   .   PASS    AF=0.000458 ES:SE:LP:AF:SS:ID   -0.003124:0.057022:0.0194113:0.000458:439247:rs189774606
1   82961   rs537801787 C   T   .   PASS    AF=0.000505 ES:SE:LP:AF:SS:ID   -0.245113:0.216868:0.587783:0.000505:35253:rs537801787
1   82994   rs574556077 A   G   .   PASS    AF=0.000162 ES:SE:LP:AF:SS:ID   0.282006:0.354494:0.370266:0.000162:35253:rs574556077
1   83170   rs562997564 G   T   .   PASS    AF=0.001254 ES:SE:LP:AF:SS:ID   0.21624:0.138611:0.925399:0.001254:35253:rs562997564
1   83771   rs189906733 T   G   .   PASS    AF=0.000653 ES:SE:LP:AF:SS:ID   0.008935:0.049471:0.0671951:0.000653:439247:rs189906733
1   84139   rs183605470 A   T   .   PASS    AF=0.020789 ES:SE:LP:AF:SS:ID   0.026065:0.03179:0.38482:0.020789:35253:rs183605470
1   84618   rs576633512 C   T   .   PASS    AF=0.000714 ES:SE:LP:AF:SS:ID   0.005594:0.187179:0.0104848:0.000714:35253:rs576633512
1   85622   rs185273034 A   T   .   PASS    AF=0.001252 ES:SE:LP:AF:SS:ID   0.158655:0.138316:0.599735:0.001252:35253:rs185273034
1   85892   rs147185795 A   G   .   PASS    AF=0.000451 ES:SE:LP:AF:SS:ID   0.028684:0.064577:0.182476:0.000451:439247:rs147185795
1   86028   rs114608975 T   C   .   PASS    AF=0.061284 ES:SE:LP:AF:SS:ID   -0.006518:0.018266:0.141932:0.061284:35253:rs114608975
1   86192   rs548281277 G   A   .   PASS    AF=0.034608 ES:SE:LP:AF:SS:ID   0.00243:0.024492:0.0357588:0.034608:35253:rs548281277