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-68/ieu-a-68.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-68/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 11:10:47 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-68/ieu-a-68.vcf.gz ...
Read summary statistics for 2473357 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, 1155434 SNPs remain.
After merging with regression SNP LD, 1155434 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1084 (0.0083)
Lambda GC: 1.0291
Mean Chi^2: 1.0824
Intercept: 0.8968 (0.0072)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:11:17 2020
Total time elapsed: 29.83s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.917,
    "inflation_factor": 1,
    "mean_EFFECT": 3.3129e-06,
    "n": 134039,
    "n_snps": 2473357,
    "n_clumped_hits": 28,
    "n_p_sig": 517,
    "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": 10515,
    "n_miss_AF_reference": 21246,
    "n_est": 135329.487,
    "ratio_se_n": 1.0048,
    "mean_diff": -1.582e-06,
    "ratio_diff": 1.8918,
    "sd_y_est1": 1.3457,
    "sd_y_est2": 1.3521,
    "r2_sum1": 0.0131,
    "r2_sum2": 0.0072,
    "r2_sum3": 0.0071,
    "r2_sum4": 0.0103,
    "ldsc_nsnp_merge_refpanel_ld": 1155434,
    "ldsc_nsnp_merge_regression_ld": 1155434,
    "ldsc_observed_scale_h2_beta": 0.1084,
    "ldsc_observed_scale_h2_se": 0.0083,
    "ldsc_intercept_beta": 0.8968,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.0291,
    "ldsc_mean_chisq": 1.0824,
    "ldsc_ratio": -1.2524
}

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 2473357 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 8.587006e+00 5.657446e+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 7.884730e+07 5.564946e+07 11523.0000 3.270341e+07 7.027896e+07 1.143191e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.300000e-06 1.032120e-02 -0.2600 -4.900000e-03 0.000000e+00 4.900000e-03 2.00000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.599800e-03 5.944600e-03 0.0042 5.600000e-03 6.500000e-03 9.000000e-03 1.20000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.961288e-01 2.913722e-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 4.960996e-01 2.912634e-01 0.0000 2.433450e-01 4.953539e-01 7.483963e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 10515 0.9957487 NA NA NA NA NA 3.569130e-01 2.753816e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.91700e-01 ▇▅▃▂▂
numeric AF_reference 21246 0.9914101 NA NA NA NA NA 3.603214e-01 2.563893e-01 0.0000 1.447680e-01 2.977240e-01 5.449280e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 8.997306e+04 9.935872e+03 50001.0000 8.752900e+04 9.129800e+04 9.209300e+04 1.34039e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 775659 rs2905035 A G 0.0011 0.0110 0.9199999 0.9203443 0.8750 0.745008 50463
1 777122 rs2980319 A T -0.0013 0.0110 0.9100000 0.9059236 0.8750 0.747204 50459
1 785050 rs2905062 G A -0.0029 0.0090 0.7499995 0.7472844 NA 0.626997 67913
1 990380 rs3121561 C T -0.0077 0.0092 0.4000000 0.4026170 0.2667 0.343450 68515
1 998501 rs3813193 G C -0.0061 0.0093 0.5099998 0.5118795 0.1500 0.206669 64894
1 1003629 rs4075116 C T 0.0006 0.0068 0.9299999 0.9296897 0.7373 0.720647 89270
1 1005806 rs3934834 C T -0.0100 0.0087 0.2399999 0.2503807 0.1167 0.223442 70086
1 1017170 rs3766193 C G 0.0058 0.0063 0.3599996 0.3572411 0.5667 0.575479 90098
1 1017197 rs3766192 C T 0.0060 0.0060 0.3200000 0.3173105 0.5763 0.511182 89617
1 1017587 rs3766191 C T -0.0120 0.0089 0.1900002 0.1775572 0.0965 0.171126 70468
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C 0.0150 0.0120 0.2099999 0.2112995 0.1500 0.1563500 69678
22 51217134 rs117417021 A G 0.0240 0.0092 0.0094000 0.0090888 0.4417 0.2671730 59455
22 51222100 rs114553188 G T -0.0073 0.0150 0.6300007 0.6264946 0.0667 0.0880591 73399
22 51223637 rs375798137 G A -0.0072 0.0150 0.6400000 0.6312274 0.0667 0.0788738 73398
22 51229805 rs9616985 T C 0.0230 0.0180 0.1800002 0.2013278 0.0917 0.0730831 58562
23 35921591 rs2204667 C G 0.0084 0.0071 0.2399999 0.2367701 0.1667 NA 92056
23 51666786 rs14115 A G 0.0140 0.0120 0.2300001 0.2433450 0.0250 NA 84403
23 70163799 rs1626496 A C -0.0039 0.0100 0.6999999 0.6965365 0.0750 NA 91986
23 91415872 rs6562597 G A -0.0360 0.0200 0.0680002 0.0718606 0.0083 0.0021192 81639
23 118495837 rs12882977 G A -0.0060 0.0051 0.2399999 0.2394069 0.5167 0.2307280 92004

bcf preview

1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.0011:0.011:0.0362122:0.875:50463:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0013:0.011:0.0409586:0.875:50459:rs2980319
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0029:0.009:0.124939:67913:rs2905062
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   -0.0077:0.0092:0.39794:0.2667:68515:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   -0.0061:0.0093:0.29243:0.15:64894:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0006:0.0068:0.0315171:0.7373:89270:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   -0.01:0.0087:0.619789:0.1167:70086:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0058:0.0063:0.443698:0.5667:90098:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.006:0.006:0.49485:0.5763:89617:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.0965   ES:SE:LP:AF:SS:ID   -0.012:0.0089:0.721246:0.0965:70468:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0051:0.0059:0.408935:0.5917:90529:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0054:0.0059:0.443698:0.6017:89678:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   -0.0097:0.009:0.552842:0.1271:70390:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   -0.0004:0.0062:0.0222764:0.7167:89576:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  -0.011:0.0092:0.638272:68242:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   -0.0002:0.0065:0.00877392:0.725:89854:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0005:0.0063:0.0268721:0.5667:84482:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0026:0.0067:0.154902:0.6:71588:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.0833   ES:SE:LP:AF:SS:ID   0.013:0.008:0.920819:0.0833:71119:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.0862   ES:SE:LP:AF:SS:ID   0.013:0.0086:0.886057:0.0862:67770:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   0.0034:0.0068:0.207608:0.6583:71962:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.012:0.0095:0.657577:0.05:80927:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.013:0.0087:0.853872:0.075:75704:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.0667   ES:SE:LP:AF:SS:ID   0.016:0.0089:1.13077:0.0667:79998:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.0517   ES:SE:LP:AF:SS:ID   0.0074:0.0096:0.356547:0.0517:79256:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.0667   ES:SE:LP:AF:SS:ID   0.015:0.0088:1.04576:0.0667:79494:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.016:0.01:0.920819:0.05:79552:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0013:0.0084:0.0555173:0.3981:57450:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0167   ES:SE:LP:AF:SS:ID   0.0071:0.019:0.154902:0.0167:66649:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.0583   ES:SE:LP:AF:SS:ID   0.012:0.0099:0.677781:0.0583:81710:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.0546   ES:SE:LP:AF:SS:ID   0.015:0.0099:0.920819:0.0546:81720:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.017:0.01:0.958607:79518:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0084:0.0069:0.657577:0.4123:71814:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0167   ES:SE:LP:AF:SS:ID   0.017:0.02:0.376751:0.0167:61108:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   -0.0056:0.0068:0.387216:0.5517:70518:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.012:0.0097:0.657577:0.7542:59959:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.0833   ES:SE:LP:AF:SS:ID   0.012:0.0091:0.744727:0.0833:64727:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   -0.012:0.0073:0.958607:0.675:71009:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.01:0.0078:0.744727:0.6833:67302:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.9237   ES:SE:LP:AF:SS:ID   -0.0053:0.012:0.180456:0.9237:81388:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.9123   ES:SE:LP:AF:SS:ID   -0.0006:0.011:0.0177288:0.9123:83063:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9661   ES:SE:LP:AF:SS:ID   -0.0048:0.014:0.130768:0.9661:85396:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.9417   ES:SE:LP:AF:SS:ID   -0.0016:0.011:0.0555173:0.9417:86519:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.9407   ES:SE:LP:AF:SS:ID   -0.0009:0.01:0.0315171:0.9407:89141:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.9583   ES:SE:LP:AF:SS:ID   -0.0036:0.015:0.091515:0.9583:89278:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.1441   ES:SE:LP:AF:SS:ID   -0.0038:0.011:0.136677:0.1441:55024:rs4970420
1   1113121 rs12092254  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.012:0.015:0.376751:0.1:58707:rs12092254
1   1119858 rs1320565   C   T   .   PASS    AF=0.0917   ES:SE:LP:AF:SS:ID   0.0011:0.012:0.0315171:0.0917:59957:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.0417   ES:SE:LP:AF:SS:ID   0.022:0.018:0.69897:0.0417:74526:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.0006:0.0098:0.0222764:0.1121:68318:rs3813204