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-89/ieu-a-89.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-89/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 20:41:46 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-89/ieu-a-89.vcf.gz ...
Read summary statistics for 2546513 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, 1173862 SNPs remain.
After merging with regression SNP LD, 1173862 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3191 (0.0141)
Lambda GC: 1.984
Mean Chi^2: 2.9134
Intercept: 1.2983 (0.0164)
Ratio: 0.1559 (0.0086)
Analysis finished at Tue Feb  4 20:42:10 2020
Total time elapsed: 23.75s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9188,
    "inflation_factor": 1.92,
    "mean_EFFECT": -0.0004,
    "n": 253280,
    "n_snps": 2546513,
    "n_clumped_hits": 386,
    "n_p_sig": 26596,
    "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": 6441,
    "n_miss_AF_reference": 22999,
    "n_est": 249013.6194,
    "ratio_se_n": 0.9915,
    "mean_diff": 0.0001,
    "ratio_diff": 1.4266,
    "sd_y_est1": 1.0688,
    "sd_y_est2": 1.0598,
    "r2_sum1": 0.1345,
    "r2_sum2": 0.1178,
    "r2_sum3": 0.1198,
    "r2_sum4": 0.1186,
    "ldsc_nsnp_merge_refpanel_ld": 1173862,
    "ldsc_nsnp_merge_regression_ld": 1173862,
    "ldsc_observed_scale_h2_beta": 0.3191,
    "ldsc_observed_scale_h2_se": 0.0141,
    "ldsc_intercept_beta": 1.2983,
    "ldsc_intercept_se": 0.0164,
    "ldsc_lambda_gc": 1.984,
    "ldsc_mean_chisq": 2.9134,
    "ldsc_ratio": 0.1559
}

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 2546513 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 8.598360e+00 5.666255e+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 7.879899e+07 5.567987e+07 11523.0000 3.263536e+07 7.018317e+07 1.142489e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -3.719000e-04 9.946400e-03 -0.4300 -4.300000e-03 -1.000000e-04 3.900000e-03 3.50000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.383300e-03 5.657300e-03 0.0029 3.100000e-03 3.700000e-03 5.300000e-03 2.50000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 3.930106e-01 3.116795e-01 0.0000 9.800090e-02 3.500000e-01 6.600001e-01 1.00000e+00 ▇▅▃▃▃
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 3.929515e-01 3.117364e-01 0.0000 9.767120e-02 3.475285e-01 6.599371e-01 1.00000e+00 ▇▃▃▃▃
numeric AF 6441 0.9974707 NA NA NA NA NA 3.549411e-01 2.785707e-01 0.0040 1.130000e-01 2.860000e-01 5.580000e-01 9.92000e-01 ▇▅▃▂▂
numeric AF_reference 22999 0.9909684 NA NA NA NA NA 3.593200e-01 2.580339e-01 0.0000 1.421730e-01 2.959270e-01 5.451280e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.391236e+05 3.323750e+04 50003.0000 2.412180e+05 2.516400e+05 2.530860e+05 2.53280e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0071 0.0140 0.6100002 0.6120546 0.068 0.0371406 87868
1 723819 rs11804171 T A -0.0089 0.0140 0.5199996 0.5249627 0.037 0.1345850 88951
1 723891 rs2977670 G C 0.0052 0.0150 0.7300002 0.7288418 0.929 0.7799520 68243
1 750235 rs12138618 G A -0.0070 0.0160 0.6700003 0.6617488 0.058 NA 62564
1 752566 rs3094315 G A 0.0041 0.0053 0.4400003 0.4391763 0.845 0.7182510 138910
1 753541 rs2073813 G A -0.0034 0.0083 0.6800001 0.6820711 0.125 0.3019170 69852
1 754192 rs3131968 A G 0.0082 0.0074 0.2700001 0.2678151 0.875 0.6785140 98741
1 768448 rs12562034 G A -0.0053 0.0088 0.5500004 0.5469926 0.092 0.1918930 88015
1 775659 rs2905035 A G 0.0022 0.0060 0.7099994 0.7138677 0.875 0.7450080 148267
1 777122 rs2980319 A T 0.0027 0.0060 0.6499995 0.6527104 0.875 0.7472040 148975
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51217134 rs117417021 A G 0.0051 0.0057 0.3700002 0.3709278 0.442 0.2671730 129026
22 51222100 rs114553188 G T 0.0140 0.0086 0.0949992 0.1035446 0.067 0.0880591 201104
22 51223637 rs375798137 G A 0.0140 0.0086 0.1100001 0.1035446 0.067 0.0788738 202089
22 51229805 rs9616985 T C -0.0080 0.0110 0.4600002 0.4670589 0.092 0.0730831 128177
23 35921591 rs2204667 C G -0.0011 0.0040 0.7899998 0.7833162 0.167 NA 253074
23 51666786 rs14115 A G 0.0140 0.0067 0.0389996 0.0366580 0.025 NA 240463
23 70163799 rs1626496 A C -0.0150 0.0057 0.0080000 0.0084989 0.075 NA 251135
23 74963352 rs1053838 T G 0.0130 0.0390 0.7400005 0.7388827 0.991 NA 101301
23 91415872 rs6562597 G A 0.0180 0.0110 0.0929994 0.1017635 0.008 0.0021192 227262
23 118495837 rs12882977 G A -0.0040 0.0029 0.1700000 0.1677991 0.509 0.2307280 253176

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.068    ES:SE:LP:AF:SS:ID   -0.0071:0.014:0.21467:0.068:87868:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.037    ES:SE:LP:AF:SS:ID   -0.0089:0.014:0.283997:0.037:88951:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.929    ES:SE:LP:AF:SS:ID   0.0052:0.015:0.136677:0.929:68243:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.058    ES:SE:LP:AF:SS:ID   -0.007:0.016:0.173925:0.058:62564:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.845    ES:SE:LP:AF:SS:ID   0.0041:0.0053:0.356547:0.845:138910:rs3094315
1   753541  rs2073813   G   A   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   -0.0034:0.0083:0.167491:0.125:69852:rs2073813
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.0082:0.0074:0.568636:0.875:98741:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.092    ES:SE:LP:AF:SS:ID   -0.0053:0.0088:0.259637:0.092:88015:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.0022:0.006:0.148742:0.875:148267:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.0027:0.006:0.187087:0.875:148975:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   -0.0003:0.0063:0.0177288:0.125:136071:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.866    ES:SE:LP:AF:SS:ID   0.0001:0.0063:0.00436481:0.866:136490:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.856    ES:SE:LP:AF:SS:ID   0.0009:0.0063:0.05061:0.856:137157:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.873    ES:SE:LP:AF:SS:ID   0.001:0.0062:0.0555173:0.873:137045:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   0.0061:0.01:0.251812:0.9:83792:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.108    ES:SE:LP:AF:SS:ID   -0.0052:0.011:0.207608:0.108:80738:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.167    ES:SE:LP:AF:SS:ID   0.0046:0.0067:0.309804:0.167:107660:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   0.01:0.0069:0.853872:0.425:91664:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.267    ES:SE:LP:AF:SS:ID   0.0083:0.0053:0.958607:0.267:177574:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0032:0.0053:0.267606:0.15:177361:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.737    ES:SE:LP:AF:SS:ID   -0.0081:0.0038:1.49485:0.737:240455:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.119    ES:SE:LP:AF:SS:ID   -0.0003:0.0049:0.0177288:0.119:190854:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.569    ES:SE:LP:AF:SS:ID   -0.0047:0.0036:0.721246:0.569:235188:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.576    ES:SE:LP:AF:SS:ID   -0.004:0.0034:0.619789:0.576:240151:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.096    ES:SE:LP:AF:SS:ID   -0.0008:0.0051:0.0604807:0.096:192529:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.592    ES:SE:LP:AF:SS:ID   -0.0048:0.0033:0.853872:0.592:244542:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.602    ES:SE:LP:AF:SS:ID   -0.0048:0.0033:0.853872:0.602:244492:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0005:0.0051:0.0315171:0.127:192335:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   -0.0066:0.0035:1.20761:0.717:245346:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.113    ES:SE:LP:AF:SS:ID   -0.0001:0.0052:0.00877392:0.113:189321:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   -0.0064:0.0037:1.09691:0.725:242759:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.567    ES:SE:LP:AF:SS:ID   -0.0058:0.0036:0.958607:0.567:218338:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.947    ES:SE:LP:AF:SS:ID   -0.011:0.015:0.318759:0.947:88751:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.01:0.0039:2.02687:0.6:188044:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.0008:0.0046:0.0655015:0.083:199778:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.086    ES:SE:LP:AF:SS:ID   0.0028:0.0049:0.244125:0.086:182307:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.658    ES:SE:LP:AF:SS:ID   -0.006:0.004:0.886057:0.658:188012:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.012:0.0055:1.46852:0.05:216903:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0072:0.005:0.823909:0.075:208715:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.0068:0.005:0.744727:0.067:214967:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.052    ES:SE:LP:AF:SS:ID   0.012:0.0054:1.61979:0.052:218446:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.0059:0.0049:0.638272:0.067:215007:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.014:0.0056:1.79588:0.05:213174:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.398    ES:SE:LP:AF:SS:ID   -0.0005:0.0047:0.0409586:0.398:158896:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.017    ES:SE:LP:AF:SS:ID   -0.0093:0.011:0.408935:0.017:178448:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.058    ES:SE:LP:AF:SS:ID   0.012:0.0056:1.48149:0.058:217457:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.055    ES:SE:LP:AF:SS:ID   0.012:0.0056:1.4437:0.055:218259:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.014:0.0057:1.85387:0.05:213008:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.412    ES:SE:LP:AF:SS:ID   0.006:0.0039:0.886057:0.412:183898:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.017    ES:SE:LP:AF:SS:ID   -0.0084:0.012:0.327902:0.017:166002:rs9659914