Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std 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-785/ieu-a-785.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-785/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 11:18:30 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-785/ieu-a-785.vcf.gz ...
Read summary statistics for 2476524 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, 1159137 SNPs remain.
After merging with regression SNP LD, 1159137 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1635 (0.0084)
Lambda GC: 1.0421
Mean Chi^2: 1.1332
Intercept: 0.8072 (0.0068)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:18:59 2020
Total time elapsed: 29.18s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9169,
    "inflation_factor": 1.0446,
    "mean_EFFECT": 0.0001,
    "n": 152893,
    "n_snps": 2476524,
    "n_clumped_hits": 30,
    "n_p_sig": 836,
    "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": 11859,
    "n_miss_AF_reference": 21191,
    "n_est": 155740.7083,
    "ratio_se_n": 1.0093,
    "mean_diff": -0,
    "ratio_diff": 11.0542,
    "sd_y_est1": 1.3923,
    "sd_y_est2": 1.4052,
    "r2_sum1": 0.0155,
    "r2_sum2": 0.008,
    "r2_sum3": 0.0078,
    "r2_sum4": 0.0123,
    "ldsc_nsnp_merge_refpanel_ld": 1159137,
    "ldsc_nsnp_merge_regression_ld": 1159137,
    "ldsc_observed_scale_h2_beta": 0.1635,
    "ldsc_observed_scale_h2_se": 0.0084,
    "ldsc_intercept_beta": 0.8072,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.0421,
    "ldsc_mean_chisq": 1.1332,
    "ldsc_ratio": -1.4474
}

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 42 0 2476524 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 8.589901e+00 5.658608e+00 1.0000 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.884560e+07 5.566381e+07 11523.0000 3.268817e+07 7.027495e+07 1.143323e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.422000e-04 9.767500e-03 -0.1954 -4.800000e-03 1.000000e-04 4.900000e-03 2.04400e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.286300e-03 5.575000e-03 0.0040 5.300000e-03 6.200000e-03 8.700000e-03 8.40000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.915145e-01 2.925487e-01 0.0000 2.366999e-01 4.906005e-01 7.440001e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.915137e-01 2.925505e-01 0.0000 2.366771e-01 4.905673e-01 7.440229e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 11859 0.9952114 NA NA NA NA NA 3.568859e-01 2.753567e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.91700e-01 ▇▅▃▂▂
numeric AF_reference 21191 0.9914432 NA NA NA NA NA 3.603152e-01 2.563056e-01 0.0000 1.447680e-01 2.977240e-01 5.447280e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.025234e+05 1.206757e+04 50000.7000 1.005120e+05 1.044250e+05 1.045900e+05 1.52893e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C 0.0051 0.0187 0.7858000 0.7850629 0.0678 0.0371406 54354.0
1 752566 rs3094315 G A -0.0122 0.0084 0.1464000 0.1463957 0.8448 0.7182510 66360.8
1 775659 rs2905035 A G -0.0113 0.0095 0.2342998 0.2342533 0.8750 0.7450080 70540.8
1 777122 rs2980319 A T -0.0117 0.0095 0.2181002 0.2181064 0.8750 0.7472040 71011.8
1 779322 rs4040617 A G 0.0134 0.0100 0.1802001 0.1802453 0.1250 0.2264380 65595.3
1 780785 rs2977612 T A -0.0119 0.0101 0.2386998 0.2387098 0.8661 0.6693290 65191.5
1 785050 rs2905062 G A -0.0099 0.0078 0.2057998 0.2043588 NA 0.6269970 93030.6
1 785989 rs2980300 T C -0.0108 0.0098 0.2704002 0.2704439 0.8729 0.6269970 65613.7
1 798959 rs11240777 G A 0.0133 0.0106 0.2095999 0.2095815 0.1667 0.4099440 52296.0
1 990380 rs3121561 C T 0.0103 0.0088 0.2417998 0.2418181 0.2667 0.3434500 69565.0
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C -0.0093 0.0120 0.4382995 0.4383397 0.1500 0.1563500 70597.5
22 51217134 rs117417021 A G 0.0033 0.0093 0.7226999 0.7227104 0.4417 0.2671730 55791.0
22 51222100 rs114553188 G T -0.0166 0.0146 0.2555001 0.2555440 0.0667 0.0880591 84159.0
22 51223637 rs375798137 G A -0.0168 0.0147 0.2530999 0.2530979 0.0667 0.0788738 84158.3
22 51229805 rs9616985 T C 0.0220 0.0172 0.2009000 0.2008725 0.0917 0.0730831 57392.0
23 35921591 rs2204667 C G -0.0038 0.0069 0.5818004 0.5818225 0.1667 NA 104559.0
23 51666786 rs14115 A G 0.0078 0.0113 0.4899999 0.4900272 0.0250 NA 98944.7
23 70163799 rs1626496 A C -0.0036 0.0098 0.7133998 0.7133602 0.0750 NA 104537.0
23 91415872 rs6562597 G A -0.0166 0.0191 0.3847999 0.3847870 0.0083 0.0021192 92657.7
23 118495837 rs12882977 G A -0.0010 0.0050 0.8415000 0.8414806 0.5167 0.2307280 104599.0

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   0.0051:0.0187:0.104688:0.0678:54354:rs12565286
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   -0.0122:0.0084:0.834459:0.8448:66360.8:rs3094315
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0113:0.0095:0.630228:0.875:70540.8:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0117:0.0095:0.661344:0.875:71011.8:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0134:0.01:0.744245:0.125:65595.3:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   -0.0119:0.0101:0.622148:0.8661:65191.5:rs2977612
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0099:0.0078:0.686555:93030.6:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   -0.0108:0.0098:0.567993:0.8729:65613.7:rs2980300
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   0.0133:0.0106:0.678609:0.1667:52296:rs11240777
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0103:0.0088:0.616544:0.2667:69565:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0122:0.0089:0.76853:0.15:68468.5:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0011:0.0063:0.0647951:0.7373:99136.4:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   0.0104:0.0084:0.66615:0.1167:73957.6:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   -0.0053:0.006:0.423543:0.5667:97452:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   -0.0051:0.0058:0.421132:0.5763:98328.6:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.0129:0.0086:0.874194:0.09649:76755.3:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   -0.005:0.0055:0.439735:0.5917:100165:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   -0.0052:0.0055:0.462937:0.6017:100148:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.0102:0.0086:0.627825:0.1271:76660.7:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   -0.0028:0.0061:0.189633:0.7167:101431:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  0.011:0.0087:0.685922:76655.5:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   -0.0035:0.0062:0.2423:0.725:100917:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   -0.0091:0.0062:0.8471:0.5667:87821.9:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.01:0.0068:0.849551:0.6:72184.8:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0154:0.008:1.26576:0.08333:78719.7:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0194:0.0089:1.53358:0.08621:68885.7:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   -0.0034:0.0069:0.20607:0.6583:73695.6:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0203:0.0096:1.46256:0.05:87574.4:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0135:0.0087:0.918293:0.075:82931.5:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0141:0.0089:0.946537:0.06667:85776:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.0181:0.0095:1.24603:0.05172:87593.6:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0144:0.0087:1.00926:0.06667:85805.5:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0198:0.0098:1.36311:0.05:87095.1:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0023:0.0081:0.109914:0.3981:57571.6:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0126:0.019:0.294821:0.01667:69041:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.021:0.01:1.44697:0.05833:87473.7:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.0212:0.01:1.46839:0.05455:87493.3:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0213:0.01:1.47925:87019.4:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0082:0.0067:0.655608:0.4123:69854.8:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0111:0.0202:0.234555:0.01667:63020:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0031:0.0067:0.191384:0.5517:69290.5:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.0155:0.01:0.916856:0.7542:58048.5:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0158:0.0088:1.13918:0.08333:73354.4:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.0013:0.0072:0.0671712:0.675:66990.4:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.0003:0.0077:0.013721:0.6833:66538.9:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92373  ES:SE:LP:AF:SS:ID   0.0087:0.0121:0.325966:0.92373:91156.5:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.91228  ES:SE:LP:AF:SS:ID   0.0018:0.0106:0.0628835:0.91228:95455.9:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   0.0028:0.0139:0.075514:0.9661:95345.9:rs4970358
1   1094738 rs4970362   A   G   .   PASS    AF=0.6667   ES:SE:LP:AF:SS:ID   0.0072:0.0076:0.464073:0.6667:53846.6:rs4970362
1   1097335 rs9442385   T   G   .   PASS    AF=0.94167  ES:SE:LP:AF:SS:ID   0.0043:0.0103:0.169861:0.94167:100441:rs9442385