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/9d1074a4-cf96-4fe5-adb1-b50732ce3a40/call-ldsc/inputs/562856160/ieu-b-24.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-24/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Aug 20 16:15:27 2020
Reading summary statistics from /data/cromwell-executions/qc/9d1074a4-cf96-4fe5-adb1-b50732ce3a40/call-ldsc/inputs/562856160/ieu-b-24.vcf.gz ...
Read summary statistics for 11894715 SNPs.
Dropped 36930 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, 1209998 SNPs remain.
After merging with regression SNP LD, 1209998 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0472 (0.0029)
Lambda GC: 1.1915
Mean Chi^2: 1.2166
Intercept: 0.9806 (0.007)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Aug 20 16:18:37 2020
Total time elapsed: 3.0m:9.43s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9643,
    "inflation_factor": 1.1016,
    "mean_EFFECT": 0.0002,
    "n": 262993,
    "n_snps": 11894777,
    "n_clumped_hits": 7,
    "n_p_sig": 441,
    "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": 240535,
    "n_est": 253202.0552,
    "ratio_se_n": 0.9812,
    "mean_diff": -0,
    "ratio_diff": 1.0204,
    "sd_y_est1": 1.0245,
    "sd_y_est2": 1.0053,
    "r2_sum1": 0.0011,
    "r2_sum2": 0.001,
    "r2_sum3": 0.001,
    "r2_sum4": 0.0011,
    "ldsc_nsnp_merge_refpanel_ld": 1209998,
    "ldsc_nsnp_merge_regression_ld": 1209998,
    "ldsc_observed_scale_h2_beta": 0.0472,
    "ldsc_observed_scale_h2_se": 0.0029,
    "ldsc_intercept_beta": 0.9806,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.1915,
    "ldsc_mean_chisq": 1.2166,
    "ldsc_ratio": -0.0896
}

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 8 0.9999993 3 23 0 11894403 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 8.649471e+00 5.764387e+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 7.882128e+07 5.629250e+07 1.73000e+02 3.255613e+07 6.940006e+07 1.145546e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.684000e-04 1.908040e-02 -2.10091e-01 -5.140800e-03 3.120000e-05 5.265000e-03 2.086160e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.379790e-02 1.294780e-02 2.75770e-03 3.529100e-03 7.718700e-03 2.124390e-02 9.159840e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.842959e-01 2.931536e-01 0.00000e+00 2.270001e-01 4.790005e-01 7.379994e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.842965e-01 2.931534e-01 0.00000e+00 2.269302e-01 4.786226e-01 7.378792e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.687451e-01 2.458353e-01 1.00000e-03 5.300000e-03 3.750000e-02 2.430000e-01 9.990000e-01 ▇▁▁▁▁
numeric AF_reference 240535 0.9797781 NA NA NA NA NA 1.740482e-01 2.400981e-01 0.00000e+00 4.193300e-03 5.670930e-02 2.555910e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.268342e+05 4.352861e+04 2.66640e+04 2.008230e+05 2.511160e+05 2.591560e+05 2.629930e+05 ▁▁▂▂▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 54676 rs2462492 C T 0.0031095 0.0034853 0.3720001 0.3722917 0.37200 NA 55484
1 55326 rs3107975 T C 0.0323410 0.0149178 0.0302002 0.0301627 0.00910 0.0459265 76554
1 79137 rs143777184 A T -0.0529327 0.0377130 0.1610000 0.1604480 0.00220 0.0413339 64434
1 86028 rs114608975 T C 0.0007444 0.0047175 0.8750001 0.8746164 0.09160 0.0277556 80336
1 91536 rs6702460 G T 0.0049012 0.0030455 0.1080001 0.1075408 0.44700 0.4207270 81944
1 234313 rs8179466 C T -0.0046658 0.0060335 0.4390005 0.4393420 0.07500 NA 59111
1 526736 rs28863004 C G -0.0116174 0.0121917 0.3409997 0.3406437 0.00945 0.1317890 89403
1 533198 rs78497331 C T -0.0111514 0.0237749 0.6390002 0.6390404 0.00405 0.0814696 68422
1 534192 rs6680723 C T 0.0068783 0.0042095 0.1020000 0.1022562 0.23600 NA 61541
1 544584 rs576404767 C T 0.0176181 0.0344858 0.6089996 0.6094352 0.00228 0.0003994 103195
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51226692 rs150189434 G A -0.0136816 0.0348640 0.6950003 0.6947422 0.00379 0.0155751 164409
22 51227766 rs186062720 T C 0.0186728 0.0282468 0.5090003 0.5085745 0.00225 0.0005990 136100
22 51229805 rs9616985 T C -0.0057930 0.0054257 0.2850001 0.2856524 0.07640 0.0730831 223460
22 51230673 rs555680442 G C 0.0389029 0.0302858 0.2000000 0.1989579 0.00174 0.0017971 136837
22 51232488 rs376461333 A G -0.0080579 0.0098078 0.4110002 0.4113134 0.01910 NA 131356
22 51234048 rs141330630 T C -0.0258823 0.0379149 0.4949998 0.4948331 0.00196 0.0095847 124603
22 51234159 rs8138356 T A -0.0262951 0.0460538 0.5679996 0.5680235 0.00209 0.0215655 95924
22 51237063 rs3896457 T C -0.0002245 0.0029976 0.9400001 0.9402943 0.28600 0.2050720 200189
22 51239586 rs535432390 T G 0.0258015 0.0312201 0.4089997 0.4085553 0.00243 0.0001997 114119
23 91532627 rs879949883 G A 0.0012392 0.0033853 0.7149999 0.7143199 0.21900 NA 253449

bcf preview

1   54676   rs2462492   C   T   .   PASS    AF=0.372    ES:SE:LP:AF:SS:ID   0.00310951:0.00348526:0.429457:0.372:55484:rs2462492
1   55326   rs3107975   T   C   .   PASS    AF=0.0091   ES:SE:LP:AF:SS:ID   0.032341:0.0149178:1.51999:0.0091:76554:rs3107975
1   79137   rs143777184 A   T   .   PASS    AF=0.0022   ES:SE:LP:AF:SS:ID   -0.0529327:0.037713:0.793174:0.0022:64434:rs143777184
1   86028   rs114608975 T   C   .   PASS    AF=0.0916   ES:SE:LP:AF:SS:ID   0.000744408:0.00471749:0.0579919:0.0916:80336:rs114608975
1   91536   rs1251109649    G   T   .   PASS    AF=0.447    ES:SE:LP:AF:SS:ID   0.00490123:0.00304548:0.966576:0.447:81944:rs1251109649
1   234313  rs8179466   C   T   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   -0.00466575:0.00603352:0.357535:0.075:59111:rs8179466
1   526736  rs28863004  C   G   .   PASS    AF=0.00945  ES:SE:LP:AF:SS:ID   -0.0116174:0.0121917:0.467246:0.00945:89403:rs28863004
1   533198  rs1557498752    C   T   .   PASS    AF=0.00405  ES:SE:LP:AF:SS:ID   -0.0111514:0.0237749:0.194499:0.00405:68422:rs1557498752
1   534192  rs6680723   C   T   .   PASS    AF=0.236    ES:SE:LP:AF:SS:ID   0.00687831:0.00420946:0.9914:0.236:61541:rs6680723
1   544584  rs576404767 C   T   .   PASS    AF=0.00228  ES:SE:LP:AF:SS:ID   0.0176181:0.0344858:0.215383:0.00228:103195:rs576404767
1   546697  rs12025928  A   G   .   PASS    AF=0.917    ES:SE:LP:AF:SS:ID   0.00895702:0.00590608:0.886057:0.917:87386:rs12025928
1   565130  rs371431021 G   A   .   PASS    AF=0.0043   ES:SE:LP:AF:SS:ID   -0.00809044:0.0193954:0.170053:0.0043:79936:rs371431021
1   565196  rs139723294 T   C   .   PASS    AF=0.00185  ES:SE:LP:AF:SS:ID   -0.0427127:0.0213831:1.33913:0.00185:84071:rs139723294
1   565469  rs554127336 C   T   .   PASS    AF=0.0028   ES:SE:LP:AF:SS:ID   0.0257841:0.0295764:0.416801:0.0028:98219:rs554127336
1   566792  rs9283152   T   C   .   PASS    AF=0.00499  ES:SE:LP:AF:SS:ID   -0.00208005:0.0225879:0.0329203:0.00499:80671:rs9283152
1   566875  rs2185539   C   T   .   PASS    AF=0.00211  ES:SE:LP:AF:SS:ID   0.0102218:0.0318499:0.126098:0.00211:67063:rs2185539
1   567006  rs565235853 G   T   .   PASS    AF=0.00179  ES:SE:LP:AF:SS:ID   -0.0238167:0.031139:0.352617:0.00179:121250:rs565235853
1   567540  rs146275198 A   G   .   PASS    AF=0.00156  ES:SE:LP:AF:SS:ID   0.00120346:0.0417224:0.0101054:0.00156:66636:rs146275198
1   567726  rs560688216 T   C   .   PASS    AF=0.00325  ES:SE:LP:AF:SS:ID   -0.00821785:0.0325859:0.0963675:0.00325:69451:rs560688216
1   567867  rs2000096   A   G   .   PASS    AF=0.0121   ES:SE:LP:AF:SS:ID   -0.00494688:0.016582:0.116339:0.0121:74267:rs2000096
1   568201  rs4098611   T   C   .   PASS    AF=0.00182  ES:SE:LP:AF:SS:ID   -0.0193458:0.0282187:0.307153:0.00182:58490:rs4098611
1   568322  rs9699599   A   G   .   PASS    AF=0.00202  ES:SE:LP:AF:SS:ID   -0.0238239:0.0366738:0.28735:0.00202:71862:rs9699599
1   568800  rs375217967 G   A   .   PASS    AF=0.0148   ES:SE:LP:AF:SS:ID   -0.00483218:0.0071637:0.30103:0.0148:79149:rs375217967
1   569204  rs112660509 T   C   .   PASS    AF=0.0026   ES:SE:LP:AF:SS:ID   0.00405725:0.00605493:0.298432:0.0026:71843:rs112660509
1   569543  rs538153094 G   A   .   PASS    AF=0.00145  ES:SE:LP:AF:SS:ID   0.00509876:0.0160437:0.124939:0.00145:76641:rs538153094
1   569604  rs9645429   G   A   .   PASS    AF=0.00122  ES:SE:LP:AF:SS:ID   -0.0301103:0.0232306:0.709965:0.00122:78871:rs9645429
1   569624  rs6594035   T   C   .   PASS    AF=0.0127   ES:SE:LP:AF:SS:ID   0.0413962:0.0171593:1.7986:0.0127:53691:rs6594035
1   603515  rs190065153 C   A   .   PASS    AF=0.003    ES:SE:LP:AF:SS:ID   -0.021095:0.0434235:0.202732:0.003:76084:rs190065153
1   603516  rs182349900 C   A   .   PASS    AF=0.00303  ES:SE:LP:AF:SS:ID   0.0255499:0.0438823:0.251812:0.00303:75222:rs182349900
1   693731  rs12238997  A   G   .   PASS    AF=0.122    ES:SE:LP:AF:SS:ID   0.00228172:0.00427405:0.226214:0.122:188812:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.0671   ES:SE:LP:AF:SS:ID   -0.0036654:0.00598557:0.267606:0.0671:124366:rs72631875
1   705942  rs544671234 A   T   .   PASS    AF=0.00176  ES:SE:LP:AF:SS:ID   -0.0107012:0.0333438:0.126098:0.00176:94658:rs544671234
1   713092  rs4565649   G   A   .   PASS    AF=0.00624  ES:SE:LP:AF:SS:ID   -0.0531408:0.0343739:0.91364:0.00624:106676:rs4565649
1   713977  rs74512038  C   T   .   PASS    AF=0.00621  ES:SE:LP:AF:SS:ID   0.0709086:0.0356329:1.33255:0.00621:91546:rs74512038
1   714277  rs138660747 C   A   .   PASS    AF=0.00698  ES:SE:LP:AF:SS:ID   -0.0333047:0.0186763:1.12726:0.00698:110980:rs138660747
1   714596  rs149887893 T   C   .   PASS    AF=0.0378   ES:SE:LP:AF:SS:ID   -0.00980742:0.00971079:0.505845:0.0378:116495:rs149887893
1   715205  rs141090730 C   G   .   PASS    AF=0.00668  ES:SE:LP:AF:SS:ID   -0.0475528:0.0333755:0.812479:0.00668:106137:rs141090730
1   715265  rs12184267  C   T   .   PASS    AF=0.0408   ES:SE:LP:AF:SS:ID   -0.0113688:0.00849741:0.742321:0.0408:155585:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.0411   ES:SE:LP:AF:SS:ID   -0.0113339:0.00847135:0.742321:0.0411:156728:rs12184277
1   717474  rs141784362 C   T   .   PASS    AF=0.0061   ES:SE:LP:AF:SS:ID   -0.0539282:0.034524:0.928118:0.0061:106553:rs141784362
1   717485  rs12184279  C   A   .   PASS    AF=0.0406   ES:SE:LP:AF:SS:ID   -0.00875976:0.00935923:0.457175:0.0406:125465:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.0152   ES:SE:LP:AF:SS:ID   0.022142:0.0126577:1.09474:0.0152:152562:rs144155419
1   718336  rs188996809 T   C   .   PASS    AF=0.00157  ES:SE:LP:AF:SS:ID   3.7852e-05:0.0317647:0.000434512:0.00157:103710:rs188996809
1   720381  rs116801199 G   T   .   PASS    AF=0.0422   ES:SE:LP:AF:SS:ID   -0.0100688:0.00841998:0.634512:0.0422:158541:rs116801199
1   720583  rs551231909 G   A   .   PASS    AF=0.00548  ES:SE:LP:AF:SS:ID   -0.0356902:0.0372298:0.471083:0.00548:103570:rs551231909
1   720984  rs564367954 T   G   .   PASS    AF=0.00106  ES:SE:LP:AF:SS:ID   0.0384404:0.0503447:0.35164:0.00106:60545:rs564367954
1   721290  rs12565286  G   C   .   PASS    AF=0.0424   ES:SE:LP:AF:SS:ID   -0.00993269:0.00839465:0.625252:0.0424:158849:rs12565286
1   722559  rs150361918 T   C   .   PASS    AF=0.00713  ES:SE:LP:AF:SS:ID   -0.0423585:0.032778:0.705534:0.00713:104173:rs150361918
1   722603  rs138029171 T   C   .   PASS    AF=0.0053   ES:SE:LP:AF:SS:ID   -0.0567397:0.0368564:0.910095:0.0053:105312:rs138029171
1   722670  rs116030099 T   C   .   PASS    AF=0.0981   ES:SE:LP:AF:SS:ID   0.0058164:0.00467185:0.67162:0.0981:142629:rs116030099