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/f9495bb7-f355-431a-91c5-7a82fc3f84a8/call-ldsc/inputs/-261022183/ieu-b-5099.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5099/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Feb  3 03:43:02 2023
Reading summary statistics from /data/cromwell-executions/qc/f9495bb7-f355-431a-91c5-7a82fc3f84a8/call-ldsc/inputs/-261022183/ieu-b-5099.vcf.gz ...
Read summary statistics for 7588838 SNPs.
Dropped 26714 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, 1214037 SNPs remain.
After merging with regression SNP LD, 1214037 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2974 (0.0091)
Lambda GC: 1.7809
Mean Chi^2: 2.1114
Intercept: 1.0698 (0.0108)
Ratio: 0.0628 (0.0098)
Analysis finished at Fri Feb  3 03:44:49 2023
Total time elapsed: 1.0m:46.36s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9693,
    "inflation_factor": 1.6505,
    "mean_EFFECT": 0.0016,
    "n": 175799,
    "n_snps": 7588946,
    "n_clumped_hits": 217,
    "n_p_sig": 21790,
    "n_mono": 0,
    "n_ns": 0,
    "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": 75202,
    "n_est": 174806.5405,
    "ratio_se_n": 0.9972,
    "mean_diff": -0.001,
    "ratio_diff": 13.7975,
    "sd_y_est1": 2.2838,
    "sd_y_est2": 2.2774,
    "r2_sum1": 0.2895,
    "r2_sum2": 0.0555,
    "r2_sum3": 0.0558,
    "r2_sum4": 0.0555,
    "ldsc_nsnp_merge_refpanel_ld": 1214037,
    "ldsc_nsnp_merge_regression_ld": 1214037,
    "ldsc_observed_scale_h2_beta": 0.2974,
    "ldsc_observed_scale_h2_se": 0.0091,
    "ldsc_intercept_beta": 1.0698,
    "ldsc_intercept_se": 0.0108,
    "ldsc_lambda_gc": 1.7809,
    "ldsc_mean_chisq": 2.1114,
    "ldsc_ratio": 0.0628
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
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 75 0.9999901 3 58 0 7584007 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 8.668124e+00 5.770671e+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 7.867553e+07 5.646020e+07 8.28000e+02 3.217146e+07 6.913254e+07 1.146072e+08 2.492223e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.621600e-03 2.198990e-02 -5.28897e-01 -9.702800e-03 9.004000e-04 1.210290e-02 3.035000e-01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.533990e-02 9.907300e-03 6.20000e-03 8.400000e-03 1.110000e-02 1.850000e-02 1.273000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.192938e-01 3.080377e-01 0.00000e+00 1.327000e-01 3.861998e-01 6.846002e-01 1.000000e+00 ▇▅▅▃▃
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.193093e-01 3.080423e-01 0.00000e+00 1.325625e-01 3.861551e-01 6.845972e-01 1.000000e+00 ▇▅▅▃▃
numeric AF 0 1.0000000 NA NA NA NA NA 2.596234e-01 2.552765e-01 1.10000e-02 5.100000e-02 1.610000e-01 4.050000e-01 9.887000e-01 ▇▂▂▁▁
numeric AF_reference 75202 0.9900906 NA NA NA NA NA 2.574915e-01 2.525476e-01 0.00000e+00 5.051920e-02 1.685300e-01 4.019570e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.736953e+05 4.706873e+03 1.49468e+05 1.757990e+05 1.757990e+05 1.757990e+05 1.757990e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G -0.0052959 0.0155 0.7326001 0.7325961 0.122 0.1417730 161405
1 706368 rs55727773 A G 0.0028039 0.0146 0.8477000 0.8477030 0.470 0.2751600 161405
1 714596 rs149887893 T C 0.0447986 0.0373 0.2297000 0.2297377 0.031 NA 161405
1 715265 rs12184267 C T 0.0473956 0.0378 0.2098998 0.2098959 0.031 0.0275559 161405
1 715367 rs12184277 A G 0.0447045 0.0375 0.2332002 0.2332142 0.032 0.0281550 161405
1 717485 rs12184279 C A 0.0430954 0.0380 0.2568000 0.2567570 0.031 NA 161405
1 717587 rs144155419 G A 0.0361973 0.0563 0.5203002 0.5202656 0.016 0.0045927 161405
1 720381 rs116801199 G T 0.0430015 0.0346 0.2139001 0.2139349 0.033 0.0359425 161405
1 721290 rs12565286 G C 0.0440982 0.0344 0.1999001 0.1998692 0.033 0.0371406 161405
1 722670 rs116030099 T C 0.0724954 0.0320 0.0234801 0.0234832 0.095 0.0413339 161405
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154915619 rs571421 G A -0.0335025 0.0077 0.0000128 0.0000136 0.264 0.3565560 163862
23 154915975 rs672932 G A -0.0317990 0.0077 0.0000360 0.0000363 0.266 0.3637090 163862
23 154916845 rs669237 G T -0.0308977 0.0077 0.0000654 0.0000600 0.275 0.4166890 163862
23 154918242 rs73562846 C T -0.0419957 0.0109 0.0001263 0.0001168 0.131 0.0691391 163862
23 154918266 rs642043 C T -0.0305971 0.0077 0.0000682 0.0000708 0.326 0.4786750 163862
23 154918383 rs641588 G T -0.0335025 0.0077 0.0000133 0.0000136 0.263 0.3565560 163862
23 154925045 rs509981 C T -0.0347009 0.0077 0.0000063 0.0000066 0.266 0.3634440 163862
23 154927199 rs645904 C T -0.0369007 0.0108 0.0006525 0.0006338 0.174 0.3674170 163862
23 154927581 rs644138 G A -0.0305001 0.0078 0.0000877 0.0000922 0.324 0.4635760 163862
23 154929412 rs557132 C T -0.0343048 0.0078 0.0000108 0.0000109 0.264 0.3568210 163862

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.122    ES:SE:LP:AF:SS:SI:NC:ID -0.00529595:0.0155:0.135133:0.122:161405:0.567:67390:rs12238997
1   706368  rs963699400 A   G   .   PASS    AF=0.47 ES:SE:LP:AF:SS:SI:NC:ID 0.00280393:0.0146:0.0717578:0.47:161405:0.289:67390:rs963699400
1   714596  rs149887893 T   C   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0447986:0.0373:0.638839:0.031:161405:0.422:67390:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0473956:0.0378:0.677988:0.031:161405:0.418:67390:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.032    ES:SE:LP:AF:SS:SI:NC:ID 0.0447045:0.0375:0.632271:0.032:161405:0.42:67390:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0430954:0.038:0.590405:0.031:161405:0.418:67390:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016    ES:SE:LP:AF:SS:SI:NC:ID 0.0361973:0.0563:0.283746:0.016:161405:0.332:67390:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.033    ES:SE:LP:AF:SS:SI:NC:ID 0.0430015:0.0346:0.669789:0.033:161405:0.457:67390:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.033    ES:SE:LP:AF:SS:SI:NC:ID 0.0440982:0.0344:0.699187:0.033:161405:0.462:67390:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.095    ES:SE:LP:AF:SS:SI:NC:ID 0.0724954:0.032:1.6293:0.095:161405:0.261:67390:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.9327   ES:SE:LP:AF:SS:SI:NC:ID 0.00589736:0.0236:0.0954467:0.9327:161405:0.41:67390:rs2977670
1   726794  rs28454925  C   G   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0440041:0.0373:0.623241:0.031:161405:0.429:67390:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0435967:0.0374:0.613144:0.031:161405:0.428:67390:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.814    ES:SE:LP:AF:SS:SI:NC:ID 0.00399798:0.012:0.131356:0.814:161405:0.66:67390:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.051    ES:SE:LP:AF:SS:SI:NC:ID -0.0195967:0.026:0.345823:0.051:161405:0.446:67390:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.13 ES:SE:LP:AF:SS:SI:NC:ID -9.9995e-05:0.0139:0.00248256:0.13:161405:0.677:67390:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.021    ES:SE:LP:AF:SS:SI:NC:ID -0.0226026:0.0728:0.121363:0.021:161405:0.244:67390:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.128    ES:SE:LP:AF:SS:SI:NC:ID 0.00140098:0.0138:0.0366372:0.128:161405:0.684:67390:rs141242758
1   736289  rs1254887344    T   A   .   PASS    AF=0.133    ES:SE:LP:AF:SS:SI:NC:ID 0.00490199:0.014:0.138944:0.133:161405:0.656:67390:rs1254887344
1   752478  rs146277091 G   A   .   PASS    AF=0.032    ES:SE:LP:AF:SS:SI:NC:ID 0.0613011:0.035:1.09925:0.032:175799:0.461:74776:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID -0.00299551:0.0109:0.105241:0.821:175799:0.806:74776:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.798    ES:SE:LP:AF:SS:SI:NC:ID 0.00160128:0.0106:0.055468:0.798:175799:0.769:74776:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.846    ES:SE:LP:AF:SS:SI:NC:ID 0.00290421:0.0117:0.09442:0.846:175799:0.789:74776:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.175    ES:SE:LP:AF:SS:SI:NC:ID -0.00539542:0.0112:0.200866:0.175:175799:0.744:74776:rs1388595942
1   754063  rs12184312  G   T   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0697038:0.0364:1.25735:0.031:175799:0.436:74776:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0758017:0.0358:1.46623:0.031:175799:0.441:74776:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.82 ES:SE:LP:AF:SS:SI:NC:ID 0.00729656:0.0111:0.291154:0.82:175799:0.751:74776:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.82 ES:SE:LP:AF:SS:SI:NC:ID 0.00739729:0.0111:0.296279:0.82:175799:0.751:74776:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0708947:0.0354:1.34602:0.031:175799:0.439:74776:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.822    ES:SE:LP:AF:SS:SI:NC:ID 0.00670241:0.0112:0.259795:0.822:175799:0.754:74776:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.799    ES:SE:LP:AF:SS:SI:NC:ID 0.00190181:0.0105:0.0651482:0.799:175799:0.759:74776:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.071496:0.0355:1.35823:0.031:175799:0.439:74776:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.799    ES:SE:LP:AF:SS:SI:NC:ID 0.00150113:0.0106:0.0517827:0.799:175799:0.759:74776:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.837    ES:SE:LP:AF:SS:SI:NC:ID -0.00410158:0.0117:0.139123:0.837:161405:0.788:67390:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.846    ES:SE:LP:AF:SS:SI:NC:ID 0.00240288:0.0116:0.0777418:0.846:175799:0.782:74776:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.844    ES:SE:LP:AF:SS:SI:NC:ID 0.00280393:0.0116:0.0909256:0.844:175799:0.783:74776:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.813    ES:SE:LP:AF:SS:SI:NC:ID 0.00910129:0.0111:0.387004:0.813:175799:0.751:74776:rs3115853
1   757734  rs1557551770    C   T   .   PASS    AF=0.845    ES:SE:LP:AF:SS:SI:NC:ID 0.00250313:0.0116:0.0814979:0.845:175799:0.784:74776:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.845    ES:SE:LP:AF:SS:SI:NC:ID 0.00250313:0.0116:0.0809219:0.845:175799:0.784:74776:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.845    ES:SE:LP:AF:SS:SI:NC:ID 0.00160128:0.0116:0.0505612:0.845:175799:0.784:74776:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.845    ES:SE:LP:AF:SS:SI:NC:ID 0.0031951:0.0116:0.106682:0.845:175799:0.783:74776:rs3131954
1   759036  rs114525117 G   A   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0717001:0.0356:1.35625:0.031:175799:0.419:74776:rs114525117
1   760912  rs1048488   C   T   .   PASS    AF=0.823    ES:SE:LP:AF:SS:SI:NC:ID -0.00390238:0.011:0.139542:0.823:175799:0.788:74776:rs1048488
1   760998  rs148828841 C   A   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0717968:0.036:1.33847:0.031:175799:0.415:74776:rs148828841
1   761147  rs3115850   T   C   .   PASS    AF=0.823    ES:SE:LP:AF:SS:SI:NC:ID -0.00380276:0.011:0.135786:0.823:175799:0.787:74776:rs3115850
1   761606  rs377377186 G   A   .   PASS    AF=0.031    ES:SE:LP:AF:SS:SI:NC:ID 0.0499048:0.0394:0.687611:0.031:161405:0.388:67390:rs377377186
1   761732  rs2286139   C   T   .   PASS    AF=0.808    ES:SE:LP:AF:SS:SI:NC:ID 0.00769957:0.0111:0.310514:0.808:175799:0.752:74776:rs2286139
1   761881  rs374493323 A   C   .   PASS    AF=0.029    ES:SE:LP:AF:SS:SI:NC:ID 0.0795953:0.0387:1.40187:0.029:175799:0.418:74776:rs374493323
1   763394  rs3115847   G   A   .   PASS    AF=0.678    ES:SE:LP:AF:SS:SI:NC:ID 0.00940408:0.0124:0.346209:0.678:175799:0.395:74776:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.112    ES:SE:LP:AF:SS:SI:NC:ID 0.00180162:0.0142:0.0452752:0.112:165729:0.718:68624:rs61768174