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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-44/ieu-a-44.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/ieu-a-import/processed/ieu-a-44/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 11:38:47 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-44/ieu-a-44.vcf.gz ...
Read summary statistics for 545856 SNPs.
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, 515329 SNPs remain.
After merging with regression SNP LD, 515329 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1101 (0.0242)
Lambda GC: 1.0512
Mean Chi^2: 1.0756
Intercept: 1.0238 (0.0074)
Ratio: 0.3151 (0.0982)
Analysis finished at Wed Feb  5 11:39:00 2020
Total time elapsed: 12.98s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9229,
    "inflation_factor": 1.0676,
    "mean_EFFECT": -0.0033,
    "n": 26475,
    "n_snps": 545856,
    "n_clumped_hits": 8,
    "n_p_sig": 106,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 14,
    "n_miss_AF_reference": 3379,
    "n_est": 26007.527,
    "ratio_se_n": 0.9911,
    "mean_diff": 0.0032,
    "ratio_diff": 2.4021,
    "sd_y_est1": 2.3501,
    "sd_y_est2": 2.3293,
    "r2_sum1": 0.0751,
    "r2_sum2": 0.0136,
    "r2_sum3": 0.0138,
    "r2_sum4": 0.013,
    "ldsc_nsnp_merge_refpanel_ld": 515329,
    "ldsc_nsnp_merge_regression_ld": 515329,
    "ldsc_observed_scale_h2_beta": 0.1101,
    "ldsc_observed_scale_h2_se": 0.0242,
    "ldsc_intercept_beta": 1.0238,
    "ldsc_intercept_se": 0.0074,
    "ldsc_lambda_gc": 1.0512,
    "ldsc_mean_chisq": 1.0756,
    "ldsc_ratio": 0.3148
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
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 30 0 545856 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 8.785925e+00 5.780551e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 <U+2587><U+2585><U+2585><U+2582><U+2582>
numeric POS 0 1.0000000 NA NA NA NA NA 7.790047e+07 5.661917e+07 1.88560e+04 3.102369e+07 6.850725e+07 1.142756e+08 2.492107e+08 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA -3.253800e-03 9.652910e-02 -1.83254e+01 -1.980260e-02 0.000000e+00 1.980260e-02 4.350530e+00 <U+2581><U+2581><U+2581><U+2581><U+2587>
numeric SE 0 1.0000000 NA NA NA NA NA 3.428280e-02 5.993490e-02 1.81214e-02 2.110780e-02 2.400690e-02 3.112240e-02 2.509160e+00 <U+2587><U+2581><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.892211e-01 2.916967e-01 0.00000e+00 2.339898e-01 4.858598e-01 7.420625e-01 1.000000e+00 <U+2587><U+2587><U+2587><U+2587><U+2587>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.922950e-01 2.991932e-01 0.00000e+00 2.358187e-01 4.861669e-01 7.156888e-01 1.000000e+00 <U+2587><U+2587><U+2585><U+2587><U+2586>
numeric AF 14 0.9999744 NA NA NA NA NA 3.704999e-01 2.574224e-01 1.58000e-04 1.501830e-01 3.140620e-01 5.591397e-01 9.998420e-01 <U+2587><U+2586><U+2585><U+2583><U+2582>
numeric AF_reference 3379 0.9938097 NA NA NA NA NA 3.709171e-01 2.458042e-01 1.99700e-04 1.647360e-01 3.164940e-01 5.497200e-01 1.000000e+00 <U+2587><U+2587><U+2585><U+2583><U+2582>
numeric N 0 1.0000000 NA NA NA NA NA 2.647500e+04 0.000000e+00 2.64750e+04 2.647500e+04 2.647500e+04 2.647500e+04 2.647500e+04 <U+2581><U+2581><U+2587><U+2581><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A -0.0392207 0.0289475 0.1841399 0.1754524 0.787508 0.7182510 26475
1 753405 rs3115860 C A 0.0080322 0.0385307 0.8411499 0.8348686 0.803500 0.7517970 26475
1 761147 rs3115850 T C 0.2876820 0.3108600 0.3538303 0.3547375 0.795385 0.7334270 26475
1 768448 rs12562034 G A -0.0099503 0.0329866 0.7006498 0.7629207 0.097894 0.1918930 26475
1 776546 rs12124819 A G -0.0304592 0.0407453 0.4589295 0.4547309 0.247549 0.0756789 26475
1 846808 rs4475691 C T 0.0099503 0.0303449 0.8000601 0.7429814 0.161820 0.2547920 26475
1 900505 rs28705211 G C -0.0198026 0.0271403 0.3847202 0.4656114 0.274934 0.1687300 26475
1 918384 rs13303118 G T -0.0294288 0.0241138 0.2110401 0.2223083 0.561250 0.4926120 26475
1 928836 rs9777703 C T -0.0060181 0.0606527 0.9271000 0.9209622 0.969854 0.8901760 26475
1 943468 rs3121567 T C -0.0295588 0.0624824 0.6806001 0.6361604 0.972290 0.8937700 26475
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51147015 rs2040487 A G 0.0000000 0.0193583 0.8730900 1.0000000 0.410438 0.4556710 26475
22 51150473 rs5770820 G A 0.0020020 0.0249950 0.9208600 0.9361609 0.283027 0.2462060 26475
22 51151350 rs6009951 C T 0.0099503 0.0226347 0.5237705 0.6602231 0.467838 0.5559110 26475
22 51151724 rs6010061 C T 0.0000000 0.0201535 0.9602099 1.0000000 0.463927 0.6098240 26475
22 51163138 rs715586 C T 0.0000000 0.0282182 0.8856899 1.0000000 0.148804 0.0902556 26475
22 51165664 rs8137951 G A -0.0392207 0.0214249 0.1051499 0.0671583 0.348639 0.4063500 26475
22 51171693 rs756638 G A -0.0487902 0.0219841 0.0405948 0.0264636 0.260221 0.3049120 26475
22 51175626 rs3810648 A G -0.0294288 0.0410305 0.4780298 0.4732248 0.084078 0.1084270 26475
22 51178090 rs2285395 G A -0.0198026 0.0443138 0.6853099 0.6549674 0.079961 0.0666933 26475
23 51666786 rs14115 A G 0.0582689 0.0418507 0.1651000 0.1638303 0.070076 NA 26475

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.787508 ES:SE:LP:AF:SS:ID   -0.0392207:0.0289475:0.734852:0.787508:26475:rs3094315
1   753405  rs3115860   C   A   .   PASS    AF=0.8035   ES:SE:LP:AF:SS:ID   0.00803217:0.0385307:0.0751266:0.8035:26475:rs3115860
1   761147  rs3115850   T   C   .   PASS    AF=0.795385 ES:SE:LP:AF:SS:ID   0.287682:0.31086:0.451205:0.795385:26475:rs3115850
1   768448  rs12562034  G   A   .   PASS    AF=0.097894 ES:SE:LP:AF:SS:ID   -0.00995033:0.0329866:0.154499:0.097894:26475:rs12562034
1   776546  rs12124819  A   G   .   PASS    AF=0.247549 ES:SE:LP:AF:SS:ID   -0.0304592:0.0407453:0.338254:0.247549:26475:rs12124819
1   846808  rs4475691   C   T   .   PASS    AF=0.16182  ES:SE:LP:AF:SS:ID   0.00995033:0.0303449:0.0968774:0.16182:26475:rs4475691
1   900505  rs28705211  G   C   .   PASS    AF=0.274934 ES:SE:LP:AF:SS:ID   -0.0198026:0.0271403:0.414855:0.274934:26475:rs28705211
1   918384  rs13303118  G   T   .   PASS    AF=0.56125  ES:SE:LP:AF:SS:ID   -0.0294288:0.0241138:0.675635:0.56125:26475:rs13303118
1   928836  rs9777703   C   T   .   PASS    AF=0.969854 ES:SE:LP:AF:SS:ID   -0.00601807:0.0606527:0.0328734:0.969854:26475:rs9777703
1   943468  rs3121567   T   C   .   PASS    AF=0.97229  ES:SE:LP:AF:SS:ID   -0.0295588:0.0624824:0.167108:0.97229:26475:rs3121567
1   1005806 rs3934834   C   T   .   PASS    AF=0.1907   ES:SE:LP:AF:SS:ID   0.00995033:0.0295406:0.122513:0.1907:26475:rs3934834
1   1018704 rs9442372   A   G   .   PASS    AF=0.512897 ES:SE:LP:AF:SS:ID   -0.0110609:0.0206255:0.224914:0.512897:26475:rs9442372
1   1021415 rs3737728   A   G   .   PASS    AF=0.687483 ES:SE:LP:AF:SS:ID   0.0198026:0.021847:0.324946:0.687483:26475:rs3737728
1   1030565 rs6687776   C   T   .   PASS    AF=0.188492 ES:SE:LP:AF:SS:ID   -0.0120726:0.0266053:0.184236:0.188492:26475:rs6687776
1   1031540 rs9651273   A   G   .   PASS    AF=0.727756 ES:SE:LP:AF:SS:ID   -0.00904074:0.023359:0.163644:0.727756:26475:rs9651273
1   1048955 rs4970405   A   G   .   PASS    AF=0.072365 ES:SE:LP:AF:SS:ID   0.00995033:0.0329866:0.142873:0.072365:26475:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.135668 ES:SE:LP:AF:SS:ID   0.00995033:0.027413:0.0868487:0.135668:26475:rs12726255
1   1061166 rs11807848  T   C   .   PASS    AF=0.411766 ES:SE:LP:AF:SS:ID   0.0222456:0.0211078:0.532718:0.411766:26475:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.5426   ES:SE:LP:AF:SS:ID   -0.0392207:0.0206554:1.13336:0.5426:26475:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.148726 ES:SE:LP:AF:SS:ID   0:0.0279495:0.0329765:0.148726:26475:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.057128 ES:SE:LP:AF:SS:ID   0.0682788:0.0395347:1.07212:0.057128:26475:rs12145826
1   1087683 rs9442380   T   C   .   PASS    AF=0.923089 ES:SE:LP:AF:SS:ID   -0.0487902:0.0386853:0.640278:0.923089:26475:rs9442380
1   1090557 rs7553429   A   C   .   PASS    AF=0.067158 ES:SE:LP:AF:SS:ID   -0.0661398:0.0675742:0.500272:0.067158:26475:rs7553429
1   1099342 rs9660710   A   C   .   PASS    AF=0.925188 ES:SE:LP:AF:SS:ID   -0.0377019:0.0391607:0.470801:0.925188:26475:rs9660710
1   1106473 rs4970420   G   A   .   PASS    AF=0.244842 ES:SE:LP:AF:SS:ID   0.0345914:0.0265999:0.748703:0.244842:26475:rs4970420
1   1119858 rs1320565   C   T   .   PASS    AF=0.104873 ES:SE:LP:AF:SS:ID   0:0.0381459:0.0107727:0.104873:26475:rs1320565
1   1121794 rs11260549  G   A   .   PASS    AF=0.129174 ES:SE:LP:AF:SS:ID   0.0387408:0.0299529:0.695186:0.129174:26475:rs11260549
1   1135242 rs9729550   A   C   .   PASS    AF=0.308446 ES:SE:LP:AF:SS:ID   0.00995033:0.0226347:0.276438:0.308446:26475:rs9729550
1   1152631 rs11721 C   A   .   PASS    AF=0.103082 ES:SE:LP:AF:SS:ID   0.00702462:0.0377002:0.0678308:0.103082:26475:rs11721
1   1156131 rs2887286   T   C   .   PASS    AF=0.183115 ES:SE:LP:AF:SS:ID   0.0171462:0.0276966:0.275446:0.183115:26475:rs2887286
1   1158277 rs3813199   G   A   .   PASS    AF=0.126591 ES:SE:LP:AF:SS:ID   0.0253178:0.0332245:0.351123:0.126591:26475:rs3813199
1   1162435 rs3766186   C   A   .   PASS    AF=0.125399 ES:SE:LP:AF:SS:ID   0.0171462:0.0337173:0.207167:0.125399:26475:rs3766186
1   1163804 rs7515488   C   T   .   PASS    AF=0.184783 ES:SE:LP:AF:SS:ID   0.0198026:0.0292507:0.294547:0.184783:26475:rs7515488
1   1176597 rs6675798   T   C   .   PASS    AF=0.114719 ES:SE:LP:AF:SS:ID   0.0544562:0.0334155:0.968955:0.114719:26475:rs6675798
1   1192515 rs7524470   A   G   .   PASS    AF=0.032107 ES:SE:LP:AF:SS:ID   0.00995033:0.0538116:0.055315:0.032107:26475:rs7524470
1   1194804 rs11804831  T   C   .   PASS    AF=0.246218 ES:SE:LP:AF:SS:ID   0.0283995:0.0249398:0.594005:0.246218:26475:rs11804831
1   1210963 rs6689813   T   C   .   PASS    AF=0.076454 ES:SE:LP:AF:SS:ID   0.0704225:0.0553959:0.697864:0.076454:26475:rs6689813
1   1211292 rs6685064   C   T   .   PASS    AF=0.110548 ES:SE:LP:AF:SS:ID   0.00995033:0.0391292:0.0955063:0.110548:26475:rs6685064
1   1220136 rs2144440   A   G   .   PASS    AF=0.065515 ES:SE:LP:AF:SS:ID   0.0861777:0.0561415:0.939793:0.065515:26475:rs2144440
1   1239935 rs12410087  A   C   .   PASS    AF=0.128739 ES:SE:LP:AF:SS:ID   0.0392207:0.0392113:0.598014:0.128739:26475:rs12410087
1   1242084 rs3737717   A   G   .   PASS    AF=0.04602  ES:SE:LP:AF:SS:ID   0.0198026:0.292973:0.0219931:0.04602:26475:rs3737717
1   1254841 rs10907179  C   G   .   PASS    AF=0.895436 ES:SE:LP:AF:SS:ID   -0.114289:0.0821204:0.798439:0.895436:26475:rs10907179
1   1264539 rs307354    G   C   .   PASS    AF=0.922384 ES:SE:LP:AF:SS:ID   -0.00995033:0.0512928:0.101094:0.922384:26475:rs307354
1   1288583 rs3845295   C   G   .   PASS    AF=0.903153 ES:SE:LP:AF:SS:ID   -0.0110609:0.0459443:0.0860961:0.903153:26475:rs3845295
1   1305561 rs17160669  C   T   .   PASS    AF=0.163729 ES:SE:LP:AF:SS:ID   0.0487902:0.033544:0.820104:0.163729:26475:rs17160669
1   1310924 rs2765033   T   C   .   PASS    AF=0.939971 ES:SE:LP:AF:SS:ID   0.0356272:0.0625442:0.237884:0.939971:26475:rs2765033
1   1314015 rs2649588   C   T   .   PASS    AF=0.896743 ES:SE:LP:AF:SS:ID   -0.0397809:0.0391607:0.512141:0.896743:26475:rs2649588
1   1334475 rs17851391  G   C   .   PASS    AF=0.033133 ES:SE:LP:AF:SS:ID   -0.0953102:0.0735222:0.706218:0.033133:26475:rs17851391
1   1356550 rs12089560  A   G   .   PASS    AF=0.103257 ES:SE:LP:AF:SS:ID   0.0198026:0.0457828:0.203794:0.103257:26475:rs12089560
1   1366917 rs873926    G   C   .   PASS    AF=0.310425 ES:SE:LP:AF:SS:ID   0.0110609:0.0298645:0.146302:0.310425:26475:rs873926