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-62/ieu-a-62.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-62/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 20:51:46 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-62/ieu-a-62.vcf.gz ...
Read summary statistics for 2444518 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, 1142425 SNPs remain.
After merging with regression SNP LD, 1142425 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1534 (0.0076)
Lambda GC: 1.032
Mean Chi^2: 1.0824
Intercept: 0.819 (0.0069)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 20:52:16 2020
Total time elapsed: 30.03s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.917,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 0.0001,
    "n": 134594,
    "n_snps": 2444518,
    "n_clumped_hits": 19,
    "n_p_sig": 495,
    "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": 10391,
    "n_miss_AF_reference": 20929,
    "n_est": 133982.1411,
    "ratio_se_n": 0.9977,
    "mean_diff": -0,
    "ratio_diff": 17.8219,
    "sd_y_est1": 1.3906,
    "sd_y_est2": 1.3874,
    "r2_sum1": 0.0106,
    "r2_sum2": 0.0055,
    "r2_sum3": 0.0055,
    "r2_sum4": 0.0086,
    "ldsc_nsnp_merge_refpanel_ld": 1142425,
    "ldsc_nsnp_merge_regression_ld": 1142425,
    "ldsc_observed_scale_h2_beta": 0.1534,
    "ldsc_observed_scale_h2_se": 0.0076,
    "ldsc_intercept_beta": 0.819,
    "ldsc_intercept_se": 0.0069,
    "ldsc_lambda_gc": 1.032,
    "ldsc_mean_chisq": 1.0824,
    "ldsc_ratio": -2.1966
}

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 2444518 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 8.587686e+00 5.657760e+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 7.884066e+07 5.565276e+07 11523.0000 3.269805e+07 7.026171e+07 1.143083e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 6.290000e-05 1.034090e-02 -0.1900 -5.000000e-03 0.000000e+00 5.100000e-03 1.90000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.786200e-03 6.064100e-03 0.0042 5.600000e-03 6.600000e-03 9.200000e-03 9.60000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.946754e-01 2.914129e-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 4.946804e-01 2.912100e-01 0.0000 2.420769e-01 4.933871e-01 7.475746e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 10391 0.9957493 NA NA NA NA NA 3.570004e-01 2.753646e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.91700e-01 ▇▅▃▂▂
numeric AF_reference 20929 0.9914384 NA NA NA NA NA 3.604140e-01 2.563685e-01 0.0000 1.447680e-01 2.979230e-01 5.449280e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 9.076049e+04 1.010572e+04 50004.0000 8.846200e+04 9.254800e+04 9.263500e+04 1.34594e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 775659 rs2905035 A G 0.0120 0.0110 0.2900000 0.2753129 0.87500 0.745008 50562
1 777122 rs2980319 A T 0.0120 0.0110 0.2800000 0.2753129 0.87500 0.747204 50563
1 785050 rs2905062 G A 0.0048 0.0089 0.5900000 0.5896620 NA 0.626997 68064
1 990380 rs3121561 C T -0.0052 0.0094 0.5800000 0.5801323 0.26670 0.343450 69016
1 998501 rs3813193 G C 0.0030 0.0096 0.7499995 0.7546606 0.15000 0.206669 65358
1 1003629 rs4075116 C T 0.0073 0.0070 0.2999998 0.2970145 0.73730 0.720647 89719
1 1005806 rs3934834 C T 0.0067 0.0087 0.4400003 0.4412317 0.11670 0.223442 71855
1 1017170 rs3766193 C G 0.0063 0.0064 0.3200000 0.3249312 0.56670 0.575479 90609
1 1017197 rs3766192 C T 0.0063 0.0061 0.2999998 0.3017036 0.57630 0.511182 90986
1 1017587 rs3766191 C T 0.0052 0.0091 0.5700002 0.5677092 0.09649 0.171126 71771
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C 0.0082 0.0120 0.5099998 0.4943962 0.1500 0.1563500 67948
22 51217134 rs117417021 A G 0.0190 0.0095 0.0439997 0.0455003 0.4417 0.2671730 57461
22 51222100 rs114553188 G T -0.0120 0.0150 0.4400003 0.4237108 0.0667 0.0880591 72516
22 51223637 rs375798137 G A -0.0120 0.0150 0.4299995 0.4237108 0.0667 0.0788738 72515
22 51229805 rs9616985 T C 0.0280 0.0190 0.1400000 0.1405666 0.0917 0.0730831 54476
23 35921591 rs2204667 C G 0.0048 0.0073 0.5099998 0.5108375 0.1667 NA 92611
23 51666786 rs14115 A G 0.0180 0.0120 0.1199999 0.1336144 0.0250 NA 86003
23 70163799 rs1626496 A C -0.0110 0.0100 0.3100002 0.2713321 0.0750 NA 92490
23 91415872 rs6562597 G A -0.0130 0.0200 0.5199996 0.5156922 0.0083 0.0021192 82123
23 118495837 rs12882977 G A -0.0028 0.0053 0.5999997 0.5972898 0.5167 0.2307280 92638

bcf preview

1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.012:0.011:0.537602:0.875:50562:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.012:0.011:0.552842:0.875:50563:rs2980319
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.0048:0.0089:0.229148:68064:rs2905062
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0052:0.0094:0.236572:0.2667:69016:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.003:0.0096:0.124939:0.15:65358:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0073:0.007:0.522879:0.7373:89719:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   0.0067:0.0087:0.356547:0.1167:71855:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0063:0.0064:0.49485:0.5667:90609:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0063:0.0061:0.522879:0.5763:90986:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.0052:0.0091:0.244125:0.09649:71771:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.005:0.006:0.39794:0.5917:91038:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.005:0.006:0.39794:0.6017:91025:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.0073:0.0092:0.366532:0.1271:71746:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.0087:0.0064:0.769551:0.7167:91357:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0063:0.0093:0.30103:69544:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.009:0.0066:0.769551:0.725:91218:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0045:0.0064:0.318759:0.5667:85023:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.005:0.0069:0.327902:0.6:73071:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.008:0.0082:0.481486:0.08333:72887:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0017:0.0091:0.0705811:0.08621:64294:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   -0.0002:0.007:0.00877392:0.6583:71059:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.013:0.0097:0.69897:0.05:82271:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.01:0.0088:0.585027:0.075:77062:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.012:0.0091:0.69897:0.06667:80499:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.013:0.0097:0.721246:0.05172:82215:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.01:0.009:0.619789:0.06667:80493:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.013:0.01:0.69897:0.05:80037:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0013:0.0088:0.0555173:0.3981:54888:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0059:0.019:0.119186:0.01667:65908:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.011:0.01:0.552842:0.05833:82185:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.013:0.01:0.69897:0.05455:82194:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.014:0.01:0.744727:79992:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.005:0.0072:0.309804:0.4123:70304:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   0.0007:0.021:0.0132283:0.01667:59511:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0023:0.0071:0.124939:0.5517:69840:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.01:0.01:0.522879:0.7542:57005:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.008:0.0092:0.420216:0.08333:66491:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.0041:0.0075:0.236572:0.675:68044:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.0053:0.0081:0.29243:0.6833:65525:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92373  ES:SE:LP:AF:SS:ID   -0.012:0.013:0.455932:0.92373:79360:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.91228  ES:SE:LP:AF:SS:ID   -0.0089:0.011:0.366532:0.91228:84389:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   -0.012:0.015:0.366532:0.9661:85671:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.94167  ES:SE:LP:AF:SS:ID   -0.0074:0.011:0.30103:0.94167:89710:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.94068  ES:SE:LP:AF:SS:ID   -0.0044:0.01:0.167491:0.94068:90923:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.95833  ES:SE:LP:AF:SS:ID   -0.0001:0.015:0.00436481:0.95833:89512:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.1441   ES:SE:LP:AF:SS:ID   -0.0066:0.011:0.259637:0.1441:53680:rs4970420
1   1113121 rs12092254  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.0078:0.015:0.221849:0.1:60178:rs12092254
1   1119858 rs1320565   C   T   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.002:0.013:0.0604807:0.09167:56551:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.04167  ES:SE:LP:AF:SS:ID   0.019:0.018:0.522879:0.04167:73778:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.0075:0.01:0.327902:0.1121:65706:rs3813204