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-57/ieu-a-57.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-57/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 11:21:57 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-57/ieu-a-57.vcf.gz ...
Read summary statistics for 2465731 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, 1153188 SNPs remain.
After merging with regression SNP LD, 1153188 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1445 (0.0098)
Lambda GC: 1.0346
Mean Chi^2: 1.11
Intercept: 0.8724 (0.0071)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:22:28 2020
Total time elapsed: 30.4s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9167,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0.0001,
    "n": 117340,
    "n_snps": 2465731,
    "n_clumped_hits": 42,
    "n_p_sig": 903,
    "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": 8918,
    "n_miss_AF_reference": 21052,
    "n_est": 113061.2644,
    "ratio_se_n": 0.9816,
    "mean_diff": 0,
    "ratio_diff": 3.1847,
    "sd_y_est1": 1.3545,
    "sd_y_est2": 1.3295,
    "r2_sum1": 0.0225,
    "r2_sum2": 0.0123,
    "r2_sum3": 0.0127,
    "r2_sum4": 0.0175,
    "ldsc_nsnp_merge_refpanel_ld": 1153188,
    "ldsc_nsnp_merge_regression_ld": 1153188,
    "ldsc_observed_scale_h2_beta": 0.1445,
    "ldsc_observed_scale_h2_se": 0.0098,
    "ldsc_intercept_beta": 0.8724,
    "ldsc_intercept_se": 0.0071,
    "ldsc_lambda_gc": 1.0346,
    "ldsc_mean_chisq": 1.11,
    "ldsc_ratio": -1.16
}

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 2465731 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 8.585873e+00 5.656931e+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 7.885250e+07 5.563946e+07 11523.0000 3.271598e+07 7.028922e+07 1.143162e+08 2.49219e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.458000e-04 1.061480e-02 -0.2100 -5.300000e-03 0.000000e+00 5.100000e-03 1.90000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.929500e-03 5.952000e-03 0.0045 5.800000e-03 6.800000e-03 9.400000e-03 9.10000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.943467e-01 2.918622e-01 0.0000 2.399999e-01 4.899999e-01 7.499995e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.943696e-01 2.916528e-01 0.0000 2.410310e-01 4.938422e-01 7.474270e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 8918 0.9963832 NA NA NA NA NA 3.573313e-01 2.750582e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.91700e-01 ▇▅▃▂▂
numeric AF_reference 21052 0.9914622 NA NA NA NA NA 3.606562e-01 2.561602e-01 0.0000 1.451680e-01 2.983230e-01 5.451280e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 8.478844e+04 8.106840e+03 50002.0000 8.309900e+04 8.674900e+04 8.691400e+04 1.17340e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 785050 rs2905062 G A -0.0004 0.0094 0.9599999 0.9660577 NA 0.626997 61774
1 990380 rs3121561 C T -0.0071 0.0096 0.4600002 0.4595529 0.26670 0.343450 65758
1 998501 rs3813193 G C -0.0071 0.0097 0.4600002 0.4641937 0.15000 0.206669 62136
1 1003629 rs4075116 C T -0.0062 0.0072 0.3900004 0.3891769 0.73730 0.720647 84085
1 1005806 rs3934834 C T -0.0084 0.0089 0.3500000 0.3452615 0.11670 0.223442 68628
1 1017170 rs3766193 C G 0.0033 0.0065 0.6100002 0.6116691 0.56670 0.575479 84890
1 1017197 rs3766192 C T 0.0027 0.0062 0.6600001 0.6632112 0.57630 0.511182 85266
1 1017587 rs3766191 C T -0.0097 0.0091 0.2900000 0.2864534 0.09649 0.171126 68566
1 1018562 rs9442371 C T 0.0021 0.0061 0.7300002 0.7306490 0.59170 0.530152 85321
1 1018704 rs9442372 A G 0.0027 0.0061 0.6600001 0.6580385 0.60170 0.611022 85325
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C -0.0250 0.0130 0.0490004 0.0544704 0.1500 0.1563500 65946
22 51217134 rs117417021 A G -0.0003 0.0096 0.9699999 0.9750702 0.4417 0.2671730 57629
22 51222100 rs114553188 G T -0.0120 0.0160 0.4400003 0.4532547 0.0667 0.0880591 70061
22 51223637 rs375798137 G A -0.0120 0.0160 0.4400003 0.4532547 0.0667 0.0788738 70060
22 51229805 rs9616985 T C -0.0320 0.0180 0.0810009 0.0754404 0.0917 0.0730831 57744
23 35921591 rs2204667 C G 0.0031 0.0074 0.6800001 0.6752754 0.1667 NA 86848
23 51666786 rs14115 A G 0.0059 0.0120 0.6300007 0.6229550 0.0250 NA 80480
23 70163799 rs1626496 A C -0.0049 0.0110 0.6499995 0.6559913 0.0750 NA 86778
23 91415872 rs6562597 G A 0.0100 0.0210 0.6200004 0.6339387 0.0083 0.0021192 76432
23 118495837 rs12882977 G A -0.0017 0.0054 0.7499995 0.7529023 0.5167 0.2307280 86796

bcf preview

1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0004:0.0094:0.0177288:61774:rs2905062
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0071:0.0096:0.337242:0.2667:65758:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.0071:0.0097:0.337242:0.15:62136:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   -0.0062:0.0072:0.408935:0.7373:84085:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   -0.0084:0.0089:0.455932:0.1167:68628:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0033:0.0065:0.21467:0.5667:84890:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0027:0.0062:0.180456:0.5763:85266:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   -0.0097:0.0091:0.537602:0.09649:68566:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0021:0.0061:0.136677:0.5917:85321:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0027:0.0061:0.180456:0.6017:85325:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   -0.0083:0.0093:0.431798:0.1271:68488:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   -0.0035:0.0064:0.229148:0.7167:85667:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.0083:0.0095:0.420216:66340:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   -0.0042:0.0068:0.275724:0.725:85503:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0003:0.0065:0.0177288:0.5667:80819:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0044:0.007:0.275724:0.6:69686:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0047:0.0083:0.244125:0.08333:69658:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.005:0.0089:0.236572:0.08621:65010:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   0.0011:0.0071:0.0555173:0.6583:69648:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.011:0.0099:0.585027:0.05:77007:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.006:0.0089:0.30103:0.075:71779:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0069:0.0093:0.337242:0.06667:75221:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.012:0.0099:0.657577:0.05172:74923:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0044:0.0091:0.200659:0.06667:75160:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.012:0.01:0.60206:0.05:74775:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   0.0003:0.0087:0.0132283:0.3981:55548:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.017:0.019:0.420216:0.01667:64740:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.0097:0.01:0.455932:0.05833:76933:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.011:0.01:0.522879:0.05455:76943:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.012:0.011:0.60206:74741:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0081:0.0073:0.568636:0.4123:69053:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.014:0.021:0.283997:0.01667:58348:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0025:0.0071:0.142668:0.5517:68614:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.0019:0.01:0.0705811:0.7542:57205:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   -0.0043:0.0094:0.187087:0.08333:63265:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.003:0.0075:0.161151:0.675:69104:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.0033:0.0082:0.161151:0.6833:64541:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92373  ES:SE:LP:AF:SS:ID   0.006:0.013:0.200659:0.92373:78071:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.91228  ES:SE:LP:AF:SS:ID   0.0039:0.011:0.130768:0.91228:78580:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   0.0038:0.015:0.09691:0.9661:80061:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.94167  ES:SE:LP:AF:SS:ID   0.005:0.011:0.180456:0.94167:82057:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.94068  ES:SE:LP:AF:SS:ID   0.0019:0.011:0.0655015:0.94068:85100:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.95833  ES:SE:LP:AF:SS:ID   -0.0078:0.015:0.21467:0.95833:84794:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.1441   ES:SE:LP:AF:SS:ID   -0.015:0.011:0.744727:0.1441:52720:rs4970420
1   1113121 rs12092254  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   0.0051:0.015:0.130768:0.1:56871:rs12092254
1   1119858 rs1320565   C   T   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.0007:0.013:0.0177288:0.09167:57652:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.04167  ES:SE:LP:AF:SS:ID   -0.017:0.018:0.468521:0.04167:71037:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.004:0.01:0.161151:0.1121:66416:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0039:0.0089:0.180456:0.125:75332:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0082:0.0066:0.657577:0.2667:84442:rs6684820