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-1015/ieu-a-1015.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-1015/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 10:11:32 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1015/ieu-a-1015.vcf.gz ...
Read summary statistics for 2175178 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, 1030327 SNPs remain.
After merging with regression SNP LD, 1030327 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0776 (0.0498)
Lambda GC: 1.039
Mean Chi^2: 1.0408
Intercept: 1.0248 (0.0084)
Ratio: 0.6067 (0.2065)
Analysis finished at Tue Feb  4 10:12:04 2020
Total time elapsed: 31.97s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8608,
    "inflation_factor": 1.0393,
    "mean_EFFECT": 0.0001,
    "n": 10112,
    "n_snps": 2175178,
    "n_clumped_hits": 3,
    "n_p_sig": 63,
    "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": 16626,
    "n_est": 10572.2818,
    "ratio_se_n": 1.0225,
    "mean_diff": 4.8626e-07,
    "ratio_diff": 0.5603,
    "sd_y_est1": 0.9635,
    "sd_y_est2": 0.9852,
    "r2_sum1": 0.0135,
    "r2_sum2": 0.0146,
    "r2_sum3": 0.0139,
    "r2_sum4": 0.0139,
    "ldsc_nsnp_merge_refpanel_ld": 1030327,
    "ldsc_nsnp_merge_regression_ld": 1030327,
    "ldsc_observed_scale_h2_beta": 0.0776,
    "ldsc_observed_scale_h2_se": 0.0498,
    "ldsc_intercept_beta": 1.0248,
    "ldsc_intercept_se": 0.0084,
    "ldsc_lambda_gc": 1.039,
    "ldsc_mean_chisq": 1.0408,
    "ldsc_ratio": 0.6078
}

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 TRUE
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 2175178 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 8.573430e+00 5.656026e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.905215e+07 5.566824e+07 2.5452e+04 3.291431e+07 7.044340e+07 1.145345e+08 2.492107e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 8.990000e-05 2.297540e-02 -2.5600e-01 -1.200000e-02 0.000000e+00 1.300000e-02 2.430000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.037230e-02 9.705400e-03 1.2000e-02 1.400000e-02 1.600000e-02 2.200000e-02 8.500000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.938654e-01 2.905478e-01 0.0000e+00 2.407997e-01 4.916998e-01 7.452003e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.944522e-01 2.907842e-01 0.0000e+00 2.410310e-01 4.917677e-01 7.388827e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.925027e-01 2.753957e-01 1.0100e-02 1.532000e-01 3.413000e-01 6.039000e-01 9.899000e-01 ▇▆▅▃▃
numeric AF_reference 16626 0.9923565 NA NA NA NA NA 3.783561e-01 2.369435e-01 1.9970e-04 1.797120e-01 3.312700e-01 5.529150e-01 1.000000e+00 ▇▇▆▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.011200e+04 0.000000e+00 1.0112e+04 1.011200e+04 1.011200e+04 1.011200e+04 1.011200e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A 0.012 0.024 0.6043006 0.6170751 0.8720 0.718251 10112
1 990380 rs3121561 C T -0.012 0.021 0.5607006 0.5677092 0.1715 0.343450 10112
1 990417 rs2465136 T C -0.012 0.020 0.5601999 0.5485062 0.1714 0.383986 10112
1 998501 rs3813193 G C -0.012 0.027 0.6616998 0.6567213 0.1024 0.206669 10112
1 1003629 rs4075116 C T 0.001 0.025 0.9671000 0.9680931 0.9158 0.720647 10112
1 1005806 rs3934834 C T -0.023 0.023 0.3021997 0.3173105 0.1016 0.223442 10112
1 1017170 rs3766193 C G 0.014 0.018 0.4312002 0.4367000 0.8115 0.575479 10112
1 1017197 rs3766192 C T 0.018 0.019 0.3588996 0.3434511 0.8243 0.511182 10112
1 1017587 rs3766191 C T -0.027 0.023 0.2416000 0.2404299 0.0991 0.171126 10112
1 1018562 rs9442371 C T 0.015 0.017 0.3964003 0.3775860 0.8135 0.530152 10112
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51158017 rs6010065 G C 0.002 0.014 0.9076000 0.8864030 0.4546 0.5475240 10112
22 51162059 rs10451 G A -0.001 0.014 0.9292999 0.9430567 0.3874 0.3865810 10112
22 51163138 rs715586 C T 0.011 0.027 0.6869008 0.6837088 0.0668 0.0902556 10112
22 51165664 rs8137951 G A -0.001 0.014 0.9248000 0.9430567 0.3887 0.4063500 10112
22 51171497 rs2301584 G A 0.021 0.018 0.2492000 0.2433450 0.2365 0.2533950 10112
22 51171693 rs756638 G A -0.028 0.022 0.1905000 0.2031148 0.1104 0.3049120 10112
22 51175626 rs3810648 A G -0.110 0.064 0.0866204 0.0856599 0.0101 0.1084270 10112
22 51178090 rs2285395 G A -0.104 0.064 0.1065999 0.1041626 0.0101 0.0666933 10112
23 51666786 rs14115 A G 0.011 0.029 0.7131995 0.7044574 0.0565 NA 10112
23 118495837 rs12882977 G A -0.010 0.021 0.6437007 0.6339387 0.1137 0.2307280 10112

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.872    ES:SE:LP:AF:SS:ID   0.012:0.024:0.218747:0.872:10112:rs3094315
1   990380  rs3121561   C   T   .   PASS    AF=0.1715   ES:SE:LP:AF:SS:ID   -0.012:0.021:0.251269:0.1715:10112:rs3121561
1   990417  rs2465136   T   C   .   PASS    AF=0.1714   ES:SE:LP:AF:SS:ID   -0.012:0.02:0.251657:0.1714:10112:rs2465136
1   998501  rs3813193   G   C   .   PASS    AF=0.1024   ES:SE:LP:AF:SS:ID   -0.012:0.027:0.179339:0.1024:10112:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.9158   ES:SE:LP:AF:SS:ID   0.001:0.025:0.0145286:0.9158:10112:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1016   ES:SE:LP:AF:SS:ID   -0.023:0.023:0.519706:0.1016:10112:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.8115   ES:SE:LP:AF:SS:ID   0.014:0.018:0.365321:0.8115:10112:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.8243   ES:SE:LP:AF:SS:ID   0.018:0.019:0.445027:0.8243:10112:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.0991   ES:SE:LP:AF:SS:ID   -0.027:0.023:0.616903:0.0991:10112:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.8135   ES:SE:LP:AF:SS:ID   0.015:0.017:0.401866:0.8135:10112:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.8134   ES:SE:LP:AF:SS:ID   0.015:0.017:0.401976:0.8134:10112:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.0946   ES:SE:LP:AF:SS:ID   -0.016:0.026:0.264002:0.0946:10112:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.9143   ES:SE:LP:AF:SS:ID   -0.004:0.025:0.0594337:0.9143:10112:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.087    ES:SE:LP:AF:SS:ID   -0.015:0.026:0.260744:0.087:10112:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.8967   ES:SE:LP:AF:SS:ID   0.012:0.023:0.219539:0.8967:10112:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.8017   ES:SE:LP:AF:SS:ID   0.013:0.018:0.344189:0.8017:10112:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.902    ES:SE:LP:AF:SS:ID   -0.017:0.026:0.300422:0.902:10112:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1751   ES:SE:LP:AF:SS:ID   -0.007:0.018:0.151318:0.1751:10112:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1758   ES:SE:LP:AF:SS:ID   -0.007:0.018:0.150458:0.1758:10112:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.978    ES:SE:LP:AF:SS:ID   -0.032:0.05:0.288361:0.978:10112:rs9651273
1   1033999 rs4970353   C   T   .   PASS    AF=0.9784   ES:SE:LP:AF:SS:ID   -0.037:0.051:0.333295:0.9784:10112:rs4970353
1   1036959 rs11579015  T   C   .   PASS    AF=0.202    ES:SE:LP:AF:SS:ID   -0.003:0.017:0.0680847:0.202:10112:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.2022   ES:SE:LP:AF:SS:ID   -0.003:0.017:0.0672726:0.2022:10112:rs6671356
1   1041700 rs6604968   A   G   .   PASS    AF=0.2026   ES:SE:LP:AF:SS:ID   -0.003:0.017:0.0661585:0.2026:10112:rs6604968
1   1046164 rs6666280   C   T   .   PASS    AF=0.2029   ES:SE:LP:AF:SS:ID   -0.003:0.017:0.0654006:0.2029:10112:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1721   ES:SE:LP:AF:SS:ID   0.002:0.018:0.0371573:0.1721:10112:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.2039   ES:SE:LP:AF:SS:ID   -0.003:0.017:0.0638886:0.2039:10112:rs12726255
1   1052946 rs12755848  G   T   .   PASS    AF=0.1887   ES:SE:LP:AF:SS:ID   -0.006:0.018:0.13324:0.1887:10112:rs12755848
1   1060608 rs17160824  G   A   .   PASS    AF=0.1984   ES:SE:LP:AF:SS:ID   -0.001:0.017:0.0254423:0.1984:10112:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.2021   ES:SE:LP:AF:SS:ID   -0.002:0.017:0.0327797:0.2021:10112:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.2224   ES:SE:LP:AF:SS:ID   0.001:0.016:0.0327797:0.2224:10112:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.2221   ES:SE:LP:AF:SS:ID   0.002:0.016:0.0358819:0.2221:10112:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.5416   ES:SE:LP:AF:SS:ID   0.004:0.014:0.10408:0.5416:10112:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.5726   ES:SE:LP:AF:SS:ID   0.002:0.014:0.0641402:0.5726:10112:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.4104   ES:SE:LP:AF:SS:ID   0.002:0.014:0.0444566:0.4104:10112:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.5971   ES:SE:LP:AF:SS:ID   0:0.016:0.000608438:0.5971:10112:rs10907182
1   1077064 rs4970357   C   A   .   PASS    AF=0.6082   ES:SE:LP:AF:SS:ID   -0.003:0.016:0.0696114:0.6082:10112:rs4970357
1   1080925 rs1539637   G   C   .   PASS    AF=0.5865   ES:SE:LP:AF:SS:ID   -0.001:0.015:0.0271494:0.5865:10112:rs1539637
1   1087683 rs9442380   T   C   .   PASS    AF=0.6067   ES:SE:LP:AF:SS:ID   -0.008:0.014:0.263763:0.6067:10112:rs9442380
1   1094738 rs4970362   A   G   .   PASS    AF=0.5757   ES:SE:LP:AF:SS:ID   0.003:0.014:0.0744816:0.5757:10112:rs4970362
1   1097335 rs9442385   T   G   .   PASS    AF=0.6131   ES:SE:LP:AF:SS:ID   0.005:0.014:0.147886:0.6131:10112:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.6051   ES:SE:LP:AF:SS:ID   0.005:0.014:0.139662:0.6051:10112:rs9660710
1   1110019 rs11260542  A   G   .   PASS    AF=0.1465   ES:SE:LP:AF:SS:ID   0.018:0.023:0.359817:0.1465:10112:rs11260542
1   1113121 rs12092254  G   A   .   PASS    AF=0.1467   ES:SE:LP:AF:SS:ID   0.017:0.022:0.374996:0.1467:10112:rs12092254
1   1119858 rs1320565   C   T   .   PASS    AF=0.2158   ES:SE:LP:AF:SS:ID   0.023:0.017:0.791559:0.2158:10112:rs1320565
1   1121014 rs3813204   G   A   .   PASS    AF=0.5461   ES:SE:LP:AF:SS:ID   -0.012:0.015:0.393511:0.5461:10112:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.5683   ES:SE:LP:AF:SS:ID   -0.011:0.014:0.363412:0.5683:10112:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.8876   ES:SE:LP:AF:SS:ID   -0.004:0.022:0.0681355:0.8876:10112:rs6684820
1   1125553 rs10907174  A   T   .   PASS    AF=0.7278   ES:SE:LP:AF:SS:ID   -0.014:0.016:0.43866:0.7278:10112:rs10907174
1   1129672 rs11260554  G   T   .   PASS    AF=0.5801   ES:SE:LP:AF:SS:ID   -0.009:0.014:0.295078:0.5801:10112:rs11260554