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-28/ieu-a-28.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-28/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 08:48:27 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-28/ieu-a-28.vcf.gz ...
Read summary statistics for 2446860 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, 1153812 SNPs remain.
After merging with regression SNP LD, 1153812 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2186 (0.045)
Lambda GC: 1.0381
Mean Chi^2: 1.0386
Intercept: 0.9926 (0.0066)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 08:48:56 2020
Total time elapsed: 29.44s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9263,
    "inflation_factor": 1.0465,
    "mean_EFFECT": -0.0007,
    "n": 10768.4,
    "n_snps": 2446860,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 21017,
    "n_est": 10493.9482,
    "ratio_se_n": 0.9872,
    "mean_diff": 0.0001,
    "ratio_diff": 1.7418,
    "sd_y_est1": 1.0725,
    "sd_y_est2": 1.0587,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1153812,
    "ldsc_nsnp_merge_regression_ld": 1153812,
    "ldsc_observed_scale_h2_beta": 0.2186,
    "ldsc_observed_scale_h2_se": 0.045,
    "ldsc_intercept_beta": 0.9926,
    "ldsc_intercept_se": 0.0066,
    "ldsc_lambda_gc": 1.0381,
    "ldsc_mean_chisq": 1.0386,
    "ldsc_ratio": -0.1917
}
 

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 2446860 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 8.595880e+00 5.662759e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.880672e+07 5.568129e+07 1.1523e+04 3.262746e+07 7.020600e+07 1.143215e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -6.581000e-04 2.566660e-02 -3.5490e-01 -1.390000e-02 -4.000000e-04 1.310000e-02 3.48100e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.234210e-02 1.182060e-02 1.3800e-02 1.520000e-02 1.770000e-02 2.420000e-02 1.83100e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.930246e-01 2.902622e-01 3.0000e-06 2.399999e-01 4.901997e-01 7.443994e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.930234e-01 2.902654e-01 3.0000e-07 2.400494e-01 4.902429e-01 7.441521e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.603043e-01 2.696754e-01 1.0200e-02 1.271000e-01 2.957000e-01 5.567000e-01 9.89800e-01 ▇▅▃▂▂
numeric AF_reference 21017 0.9914106 NA NA NA NA NA 3.622544e-01 2.552845e-01 0.0000e+00 1.477640e-01 3.007190e-01 5.463260e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.050286e+04 9.951179e+02 2.1490e+03 1.071570e+04 1.075990e+04 1.076690e+04 1.07684e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.1378 0.0574 0.0163900 0.0163639 0.0758 0.0371406 4376
1 723819 rs11804171 T A -0.1373 0.0572 0.0163900 0.0163794 0.0757 0.1345850 4376
1 723891 rs2977670 G C 0.1389 0.0568 0.0145301 0.0144683 0.9242 0.7799520 4376
1 752566 rs3094315 G A 0.0462 0.0251 0.0653702 0.0656747 0.8241 0.7182510 4731
1 754192 rs3131968 A G 0.0378 0.0345 0.2737001 0.2732310 0.8779 0.6785140 4726
1 775659 rs2905035 A G 0.0394 0.0342 0.2501002 0.2493018 0.8777 0.7450080 4726
1 777122 rs2980319 A T 0.0394 0.0343 0.2505002 0.2506846 0.8776 0.7472040 4726
1 779322 rs4040617 A G -0.0377 0.0350 0.2823001 0.2814164 0.1225 0.2264380 4726
1 780785 rs2977612 T A 0.0383 0.0351 0.2759002 0.2751989 0.8776 0.6693290 4726
1 785050 rs2905062 G A 0.0384 0.0351 0.2741997 0.2739475 0.8776 0.6269970 4726
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C -0.0153 0.0293 0.6023002 0.6015420 0.1438 0.1563500 10696.2
22 51217134 rs117417021 A G -0.0113 0.0217 0.6044996 0.6025498 0.4382 0.2671730 10408.9
22 51222100 rs114553188 G T -0.0048 0.0398 0.9036000 0.9040055 0.0552 0.0880591 10407.6
22 51223637 rs375798137 G A -0.0046 0.0399 0.9079000 0.9082167 0.0551 0.0788738 10406.2
22 51229805 rs9616985 T C -0.0246 0.0399 0.5374004 0.5375373 0.0975 0.0730831 6480.0
23 35921591 rs2204667 C G -0.0109 0.0198 0.5818004 0.5819730 0.1576 NA 10761.9
23 51666786 rs14115 A G 0.0065 0.0316 0.8366001 0.8370282 0.0554 NA 10765.8
23 70163799 rs1626496 A C -0.0126 0.0291 0.6657007 0.6650223 0.0709 NA 10748.8
23 91415872 rs6562597 G A 0.0446 0.0523 0.3935999 0.3937855 0.0233 0.0021192 6476.0
23 118495837 rs12882977 G A 0.0055 0.0145 0.7037007 0.7044574 0.4748 0.2307280 10730.6

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0758   ES:SE:LP:AF:SS:ID   -0.1378:0.0574:1.78542:0.0758:4376:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.0757   ES:SE:LP:AF:SS:ID   -0.1373:0.0572:1.78542:0.0757:4376:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.9242   ES:SE:LP:AF:SS:ID   0.1389:0.0568:1.83773:0.9242:4376:rs2977670
1   752566  rs3094315   G   A   .   PASS    AF=0.8241   ES:SE:LP:AF:SS:ID   0.0462:0.0251:1.18462:0.8241:4731:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8779   ES:SE:LP:AF:SS:ID   0.0378:0.0345:0.562725:0.8779:4726:rs3131968
1   775659  rs2905035   A   G   .   PASS    AF=0.8777   ES:SE:LP:AF:SS:ID   0.0394:0.0342:0.601886:0.8777:4726:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.8776   ES:SE:LP:AF:SS:ID   0.0394:0.0343:0.601192:0.8776:4726:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1225   ES:SE:LP:AF:SS:ID   -0.0377:0.035:0.549289:0.1225:4726:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8776   ES:SE:LP:AF:SS:ID   0.0383:0.0351:0.559248:0.8776:4726:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.8776   ES:SE:LP:AF:SS:ID   0.0384:0.0351:0.561933:0.8776:4726:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8763   ES:SE:LP:AF:SS:ID   0.0393:0.0352:0.579055:0.8763:4727:rs2980300
1   962210  rs3128126   A   G   .   PASS    AF=0.4506   ES:SE:LP:AF:SS:ID   0.0014:0.0236:0.0205882:0.4506:4376:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.3005   ES:SE:LP:AF:SS:ID   0.0119:0.0217:0.232993:0.3005:10406.6:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.1918   ES:SE:LP:AF:SS:ID   0.0205:0.021:0.48096:0.1918:10402.4:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7319   ES:SE:LP:AF:SS:ID   0.0181:0.0183:0.492144:0.7319:10764.7:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1754   ES:SE:LP:AF:SS:ID   0.0145:0.0203:0.323215:0.1754:10410.2:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5387   ES:SE:LP:AF:SS:ID   0.0076:0.0174:0.178618:0.5387:10404:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5444   ES:SE:LP:AF:SS:ID   0.0039:0.0161:0.0933418:0.5444:10404.7:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1676   ES:SE:LP:AF:SS:ID   0.0205:0.021:0.4832:0.1676:10407.2:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.553    ES:SE:LP:AF:SS:ID   0.0042:0.0157:0.103584:0.553:10404.5:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5529   ES:SE:LP:AF:SS:ID   0.0042:0.0157:0.103805:0.5529:10404.5:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1686   ES:SE:LP:AF:SS:ID   0.0255:0.0214:0.631899:0.1686:10405.9:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7209   ES:SE:LP:AF:SS:ID   0.0228:0.0161:0.805208:0.7209:10410.7:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1676   ES:SE:LP:AF:SS:ID   0.026:0.0216:0.642637:0.1676:10405.5:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7326   ES:SE:LP:AF:SS:ID   0.0208:0.0174:0.636012:0.7326:10405.7:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5365   ES:SE:LP:AF:SS:ID   0.0062:0.0166:0.149844:0.5365:10403.6:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.9434   ES:SE:LP:AF:SS:ID   0.0065:0.0528:0.0450343:0.9434:8661.9:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.5957   ES:SE:LP:AF:SS:ID   -0.01:0.0163:0.266241:0.5957:10403.9:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1747   ES:SE:LP:AF:SS:ID   0.003:0.0198:0.0567529:0.1747:10411:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1569   ES:SE:LP:AF:SS:ID   -0.0022:0.0229:0.0350807:0.1569:6124:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7239   ES:SE:LP:AF:SS:ID   -0.0118:0.0166:0.321027:0.7239:10410.9:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1013   ES:SE:LP:AF:SS:ID   -0.0038:0.0255:0.0545314:0.1013:10410.7:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1382   ES:SE:LP:AF:SS:ID   -0.0013:0.0227:0.0210438:0.1382:10409.7:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1303   ES:SE:LP:AF:SS:ID   -0.0007:0.0224:0.0103722:0.1303:10410.7:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1002   ES:SE:LP:AF:SS:ID   -0.0025:0.0252:0.0353633:0.1002:10410.9:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1336   ES:SE:LP:AF:SS:ID   0.0026:0.0218:0.0437835:0.1336:10410.9:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1022   ES:SE:LP:AF:SS:ID   -0.0022:0.0251:0.0317506:0.1022:10410.8:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.33 ES:SE:LP:AF:SS:ID   0.0103:0.0205:0.210067:0.33:6124:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0336   ES:SE:LP:AF:SS:ID   0.0141:0.0443:0.125228:0.0336:10410.7:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   -0.0022:0.0252:0.0315638:0.1121:10409.8:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1022   ES:SE:LP:AF:SS:ID   -0.0028:0.0253:0.0406724:0.1022:10410.6:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   -0.0038:0.0254:0.054827:0.102:10410.7:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4236   ES:SE:LP:AF:SS:ID   0.0044:0.0163:0.104799:0.4236:10405.1:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0324   ES:SE:LP:AF:SS:ID   0.0217:0.0463:0.194092:0.0324:10410.7:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5297   ES:SE:LP:AF:SS:ID   0.0017:0.016:0.0394817:0.5297:10405.2:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7138   ES:SE:LP:AF:SS:ID   0.014:0.0223:0.275724:0.7138:10401.9:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.1512   ES:SE:LP:AF:SS:ID   -0.0203:0.0211:0.475344:0.1512:10410.9:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.0774   ES:SE:LP:AF:SS:ID   -0.0048:0.0328:0.0537934:0.0774:4376:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.6122   ES:SE:LP:AF:SS:ID   -0.0025:0.0179:0.0509517:0.6122:10402.8:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6271   ES:SE:LP:AF:SS:ID   -0.0045:0.0188:0.090765:0.6271:10403.9:rs10907183