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-74/ieu-a-74.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-74/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 11:31:15 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-74/ieu-a-74.vcf.gz ...
Read summary statistics for 2465561 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, 1153429 SNPs remain.
After merging with regression SNP LD, 1153429 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1109 (0.0084)
Lambda GC: 1.0219
Mean Chi^2: 1.0688
Intercept: 0.892 (0.0072)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:31:47 2020
Total time elapsed: 32.33s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9167,
    "inflation_factor": 1,
    "mean_EFFECT": 0.0001,
    "n": 124591,
    "n_snps": 2465561,
    "n_clumped_hits": 24,
    "n_p_sig": 585,
    "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": 9232,
    "n_miss_AF_reference": 20987,
    "n_est": 120852.4358,
    "ratio_se_n": 0.9849,
    "mean_diff": -0,
    "ratio_diff": 6.7309,
    "sd_y_est1": 1.3341,
    "sd_y_est2": 1.3139,
    "r2_sum1": 0.0123,
    "r2_sum2": 0.0069,
    "r2_sum3": 0.0071,
    "r2_sum4": 0.0101,
    "ldsc_nsnp_merge_refpanel_ld": 1153429,
    "ldsc_nsnp_merge_regression_ld": 1153429,
    "ldsc_observed_scale_h2_beta": 0.1109,
    "ldsc_observed_scale_h2_se": 0.0084,
    "ldsc_intercept_beta": 0.892,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.0219,
    "ldsc_mean_chisq": 1.0688,
    "ldsc_ratio": -1.5698
}

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 2465561 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 8.585199e+00 5.656658e+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 7.885480e+07 5.563934e+07 11523.0000 3.271980e+07 7.028962e+07 1.143186e+08 2.49219e+08 ▇▇▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 9.750000e-05 1.016200e-02 -0.2000 -4.900000e-03 0.000000e+00 5.000000e-03 2.00000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.591000e-03 5.727900e-03 0.0042 5.600000e-03 6.500000e-03 9.100000e-03 8.60000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.963278e-01 2.907812e-01 0.0000 2.399999e-01 5.000000e-01 7.499995e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.962497e-01 2.906408e-01 0.0000 2.433450e-01 4.965045e-01 7.478856e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 9232 0.9962556 NA NA NA NA NA 3.573448e-01 2.750614e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.91700e-01 ▇▅▃▂▂
numeric AF_reference 20987 0.9914879 NA NA NA NA NA 3.606875e-01 2.561429e-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 8.569549e+04 9.084279e+03 50000.0000 8.391000e+04 8.749600e+04 8.755600e+04 1.24591e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 785050 rs2905062 G A 0.0062 0.0091 0.4899999 0.4956699 NA 0.626997 62914
1 990380 rs3121561 C T 0.0027 0.0092 0.7700005 0.7691566 0.26670 0.343450 66409
1 998501 rs3813193 G C 0.0072 0.0093 0.4400003 0.4388163 0.15000 0.206669 62751
1 1003629 rs4075116 C T 0.0065 0.0068 0.3400001 0.3391317 0.73730 0.720647 84643
1 1005806 rs3934834 C T 0.0085 0.0085 0.3200000 0.3173105 0.11670 0.223442 69246
1 1017170 rs3766193 C G 0.0022 0.0063 0.7300002 0.7269344 0.56670 0.575479 85528
1 1017197 rs3766192 C T 0.0022 0.0060 0.7099994 0.7138677 0.57630 0.511182 85904
1 1017587 rs3766191 C T 0.0064 0.0089 0.4700002 0.4720786 0.09649 0.171126 69163
1 1018562 rs9442371 C T 0.0017 0.0059 0.7700005 0.7732429 0.59170 0.530152 85956
1 1018704 rs9442372 A G 0.0015 0.0059 0.8000000 0.7993122 0.60170 0.611022 85944
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C 0.0220 0.0120 0.0619998 0.0667530 0.1500 0.1563500 64793
22 51217134 rs117417021 A G 0.0230 0.0093 0.0120000 0.0133940 0.4417 0.2671730 56769
22 51222100 rs114553188 G T -0.0025 0.0150 0.8700001 0.8676323 0.0667 0.0880591 69456
22 51223637 rs375798137 G A -0.0026 0.0150 0.8600001 0.8623894 0.0667 0.0788738 69455
22 51229805 rs9616985 T C 0.0380 0.0180 0.0350002 0.0347628 0.0917 0.0730831 53788
23 35921591 rs2204667 C G 0.0043 0.0072 0.5500004 0.5503590 0.1667 NA 87529
23 51666786 rs14115 A G 0.0170 0.0120 0.1499999 0.1565804 0.0250 NA 81067
23 70163799 rs1626496 A C -0.0002 0.0100 0.9800000 0.9840434 0.0750 NA 87409
23 91415872 rs6562597 G A -0.0380 0.0200 0.0619998 0.0574331 0.0083 0.0021192 76441
23 118495837 rs12882977 G A -0.0045 0.0052 0.3900004 0.3868277 0.5167 0.2307280 87556

bcf preview

1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0062:0.0091:0.309804:62914:rs2905062
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0027:0.0092:0.113509:0.2667:66409:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0072:0.0093:0.356547:0.15:62751:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0065:0.0068:0.468521:0.7373:84643:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   0.0085:0.0085:0.49485:0.1167:69246:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0022:0.0063:0.136677:0.5667:85528:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0022:0.006:0.148742:0.5763:85904:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.0064:0.0089:0.327902:0.09649:69163:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0017:0.0059:0.113509:0.5917:85956:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0015:0.0059:0.09691:0.6017:85944:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.0087:0.0089:0.481486:0.1271:69138:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.0051:0.0063:0.376751:0.7167:86275:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0072:0.0091:0.366532:66936:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0058:0.0065:0.431798:0.725:86136:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0002:0.0063:0.0132283:0.5667:80395:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0011:0.0067:0.0604807:0.6:70462:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0089:0.008:0.568636:0.08333:70276:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0055:0.009:0.267606:0.08621:61689:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   0.001:0.0068:0.0555173:0.6583:68447:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0037:0.0095:0.154902:0.05:77643:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0084:0.0086:0.481486:0.075:72434:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.011:0.0089:0.657577:0.06667:75872:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.0033:0.0095:0.136677:0.05172:77587:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.012:0.0088:0.769551:0.06667:75865:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0066:0.01:0.29243:0.05:75409:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0004:0.0088:0.0177288:0.3981:52286:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   0.019:0.019:0.522879:0.01667:63295:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.005:0.0099:0.21467:0.05833:77557:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.0074:0.01:0.337242:0.05455:77566:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0078:0.01:0.346787:75364:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0022:0.007:0.124939:0.4123:67693:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   0.027:0.021:0.69897:0.01667:56899:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0037:0.0069:0.229148:0.5517:67231:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.011:0.01:0.552842:0.7542:54409:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.011:0.009:0.69897:0.08333:63881:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.0069:0.0074:0.455932:0.675:65431:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.0076:0.008:0.468521:0.6833:62912:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92373  ES:SE:LP:AF:SS:ID   -0.014:0.012:0.585027:0.92373:76306:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.91228  ES:SE:LP:AF:SS:ID   -0.0082:0.011:0.337242:0.91228:79309:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   -0.015:0.014:0.522879:0.9661:79496:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.94167  ES:SE:LP:AF:SS:ID   -0.0085:0.011:0.366532:0.94167:84634:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.94068  ES:SE:LP:AF:SS:ID   -0.0055:0.01:0.221849:0.94068:85842:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.95833  ES:SE:LP:AF:SS:ID   0.0023:0.015:0.0555173:0.95833:84428:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.1441   ES:SE:LP:AF:SS:ID   0.0017:0.011:0.0555173:0.1441:51079:rs4970420
1   1113121 rs12092254  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.016:0.015:0.552842:0.1:57472:rs12092254
1   1119858 rs1320565   C   T   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.0056:0.012:0.187087:0.09167:53950:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.04167  ES:SE:LP:AF:SS:ID   0.027:0.018:0.920819:0.04167:71210:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.004:0.01:0.154902:0.1121:63101:rs3813204
1   1121794 rs11260549  G   A   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0039:0.0085:0.187087:0.125:75950:rs11260549
1   1124663 rs6684820   G   A   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0037:0.0064:0.251812:0.2667:85195:rs6684820