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-1095/ieu-a-1095.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-1095/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 11:10:39 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1095/ieu-a-1095.vcf.gz ...
Read summary statistics for 2427702 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, 1147603 SNPs remain.
After merging with regression SNP LD, 1147603 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1246 (0.0097)
Lambda GC: 1.2545
Mean Chi^2: 1.4382
Intercept: 0.983 (0.01)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:11:08 2020
Total time elapsed: 28.78s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9158,
    "inflation_factor": 1.3107,
    "mean_EFFECT": -0,
    "n": 182416,
    "n_snps": 2427702,
    "n_clumped_hits": 68,
    "n_p_sig": 2460,
    "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": 0,
    "n_miss_AF_reference": 20692,
    "n_est": 171588.1838,
    "ratio_se_n": 0.9699,
    "mean_diff": 3.8822e-06,
    "ratio_diff": 3.6291,
    "sd_y_est1": 1.8189,
    "sd_y_est2": 1.7641,
    "r2_sum1": 0.0546,
    "r2_sum2": 0.0165,
    "r2_sum3": 0.0175,
    "r2_sum4": 0.0311,
    "ldsc_nsnp_merge_refpanel_ld": 1147603,
    "ldsc_nsnp_merge_regression_ld": 1147603,
    "ldsc_observed_scale_h2_beta": 0.1246,
    "ldsc_observed_scale_h2_se": 0.0097,
    "ldsc_intercept_beta": 0.983,
    "ldsc_intercept_se": 0.01,
    "ldsc_lambda_gc": 1.2545,
    "ldsc_mean_chisq": 1.4382,
    "ldsc_ratio": -0.0388
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique FALSE
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 0 1.0000000 3 42 0 2427702 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 8.595797e+00 5.662339e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.879647e+07 5.567566e+07 1.15230e+04 3.261901e+07 7.019811e+07 1.143065e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.140000e-05 1.161300e-02 -1.70000e-01 -6.100000e-03 1.000000e-04 6.200000e-03 1.70000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 9.170800e-03 5.075300e-03 2.07740e-03 6.149200e-03 7.269600e-03 9.944200e-03 7.97864e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.585064e-01 2.988150e-01 0.00000e+00 1.900002e-01 4.400003e-01 7.199992e-01 1.00000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.585000e-01 2.988036e-01 0.00000e+00 1.900000e-01 4.400014e-01 7.199998e-01 9.90000e-01 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 3.602106e-01 2.728016e-01 1.00000e-02 1.200000e-01 2.900000e-01 5.600000e-01 9.90000e-01 ▇▅▃▃▂
numeric AF_reference 20692 0.9914767 NA NA NA NA NA 3.627693e-01 2.549926e-01 1.99700e-04 1.485620e-01 3.013180e-01 5.469250e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.824160e+05 0.000000e+00 1.82416e+05 1.824160e+05 1.824160e+05 1.824160e+05 1.82416e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A -0.0028 0.0123053 0.8200001 0.8200006 0.82 0.718251 182416
1 754192 rs3131968 A G -0.0014 0.0159372 0.9299999 0.9300000 0.86 0.678514 182416
1 768448 rs12562034 G A -0.0330 0.0176821 0.0619998 0.0620002 0.10 0.191893 182416
1 775659 rs2905035 A G -0.0120 0.0136690 0.3800004 0.3799986 0.86 0.745008 182416
1 777122 rs2980319 A T -0.0130 0.0139099 0.3500000 0.3500016 0.86 0.747204 182416
1 779322 rs4040617 A G 0.0120 0.0152054 0.4299995 0.4299990 0.14 0.226438 182416
1 780785 rs2977612 T A -0.0110 0.0145615 0.4500005 0.4499990 0.86 0.669329 182416
1 785050 rs2905062 G A -0.0120 0.0152054 0.4299995 0.4299990 0.86 0.626997 182416
1 785989 rs2980300 T C -0.0140 0.0152944 0.3599996 0.3599986 0.86 0.626997 182416
1 798026 rs4951864 C T 0.0260 0.0211980 0.2200002 0.2199990 0.90 0.894169 182416
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C -0.0049 0.0093440 0.5999997 0.5999999 0.39 0.3724040 182416
22 51216564 rs9616970 T C -0.0012 0.0119482 0.9199999 0.9200001 0.15 0.1563500 182416
22 51217134 rs117417021 A G -0.0082 0.0093405 0.3800004 0.3799999 0.44 0.2671730 182416
22 51223637 rs375798137 G A -0.0018 0.0159238 0.9100000 0.9100002 0.07 0.0788738 182416
22 51229805 rs9616985 T C 0.0062 0.0212057 0.7700005 0.7700005 0.09 0.0730831 182416
23 35921591 rs2204667 C G -0.0110 0.0082043 0.1800002 0.1799999 0.17 NA 182416
23 51666786 rs14115 A G 0.0080 0.0133833 0.5500004 0.5500002 0.02 NA 182416
23 70163799 rs1626496 A C -0.0012 0.0106158 0.9100000 0.9099996 0.07 NA 182416
23 91415872 rs6562597 G A 0.0210 0.0224698 0.3500000 0.3500008 0.01 0.0021192 182416
23 118495837 rs12882977 G A -0.0022 0.0057095 0.6999999 0.6999998 0.52 0.2307280 182416

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.82 ES:SE:LP:AF:SS:ID   -0.0028:0.0123053:0.0861861:0.82:182416:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0014:0.0159372:0.0315171:0.86:182416:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.033:0.0176821:1.20761:0.1:182416:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.012:0.013669:0.420216:0.86:182416:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.013:0.0139099:0.455932:0.86:182416:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.012:0.0152054:0.366532:0.14:182416:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.011:0.0145615:0.346787:0.86:182416:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.012:0.0152054:0.366532:0.86:182416:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.014:0.0152944:0.443698:0.86:182416:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   0.026:0.021198:0.657577:0.9:182416:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.025:0.0212768:0.619789:0.1:182416:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   -0.0079:0.0146612:0.229148:0.21:182416:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.44 ES:SE:LP:AF:SS:ID   0.004:0.010381:0.154902:0.44:182416:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.28 ES:SE:LP:AF:SS:ID   0.0081:0.0092266:0.420216:0.28:182416:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.17 ES:SE:LP:AF:SS:ID   -0.0025:0.00938753:0.102373:0.17:182416:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.74 ES:SE:LP:AF:SS:ID   -0.018:0.00760901:1.74473:0.74:182416:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.16 ES:SE:LP:AF:SS:ID   0.0021:0.00922894:0.0861861:0.16:182416:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.55 ES:SE:LP:AF:SS:ID   -0.014:0.00664024:1.45593:0.55:182416:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.56 ES:SE:LP:AF:SS:ID   -0.014:0.00620257:1.61979:0.56:182416:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0014:0.00927341:0.0555173:0.15:182416:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.57 ES:SE:LP:AF:SS:ID   -0.015:0.00610435:1.85387:0.57:182416:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.57 ES:SE:LP:AF:SS:ID   -0.015:0.0061668:1.82391:0.57:182416:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0013:0.00939957:0.05061:0.15:182416:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.72 ES:SE:LP:AF:SS:ID   -0.016:0.00644182:1.88606:0.72:182416:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.003:0.00941503:0.124939:0.15:182416:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.73 ES:SE:LP:AF:SS:ID   -0.017:0.00691827:1.85387:0.73:182416:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.56 ES:SE:LP:AF:SS:ID   -0.016:0.00676356:1.74473:0.56:182416:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0027:0.00700715:0.154902:0.6:182416:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.16 ES:SE:LP:AF:SS:ID   -0.001:0.0079579:0.0457575:0.16:182416:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.16 ES:SE:LP:AF:SS:ID   -0.0056:0.0101195:0.236572:0.16:182416:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.72 ES:SE:LP:AF:SS:ID   -0.0071:0.00699354:0.508638:0.72:182416:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.011:0.0101822:0.552842:0.1:182416:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   -0.0049:0.00909368:0.229148:0.14:182416:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.13 ES:SE:LP:AF:SS:ID   -0.0061:0.00925873:0.29243:0.13:182416:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.012:0.00978371:0.657577:0.1:182416:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   -0.007:0.00906509:0.356547:0.14:182416:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.011:0.0106133:0.522879:0.1:182416:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.32 ES:SE:LP:AF:SS:ID   -0.0079:0.00919014:0.408935:0.32:182416:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.03 ES:SE:LP:AF:SS:ID   0.015:0.0198566:0.346787:0.03:182416:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.11 ES:SE:LP:AF:SS:ID   -0.012:0.0102129:0.619789:0.11:182416:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.0095:0.0103784:0.443698:0.1:182416:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.01:0.0104804:0.468521:0.1:182416:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.42 ES:SE:LP:AF:SS:ID   -0.0051:0.00705903:0.327902:0.42:182416:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.03 ES:SE:LP:AF:SS:ID   0.0057:0.0204068:0.107905:0.03:182416:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.54 ES:SE:LP:AF:SS:ID   -0.0002:0.00797801:0.00877392:0.54:182416:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.71 ES:SE:LP:AF:SS:ID   -0.0079:0.00979637:0.376751:0.71:182416:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0076:0.00903019:0.39794:0.15:182416:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   -0.013:0.0157787:0.387216:0.08:182416:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.62 ES:SE:LP:AF:SS:ID   -0.0057:0.00738157:0.356547:0.62:182416:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.63 ES:SE:LP:AF:SS:ID   -0.0038:0.00812489:0.19382:0.63:182416:rs10907183