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-90/ieu-a-90.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-90/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 10:58:51 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-90/ieu-a-90.vcf.gz ...
Read summary statistics for 2377582 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, 1133956 SNPs remain.
After merging with regression SNP LD, 1133956 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1718 (0.0078)
Lambda GC: 1.0303
Mean Chi^2: 1.1058
Intercept: 0.7942 (0.007)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 10:59:20 2020
Total time elapsed: 28.97s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9128,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 0.0005,
    "n": 98697,
    "n_snps": 2377582,
    "n_clumped_hits": 17,
    "n_p_sig": 569,
    "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": 3593,
    "n_miss_AF_reference": 19684,
    "n_est": 103452.2481,
    "ratio_se_n": 1.0238,
    "mean_diff": -0.0003,
    "ratio_diff": 134.8593,
    "sd_y_est1": 2.7516,
    "sd_y_est2": 2.8171,
    "r2_sum1": 0.0807,
    "r2_sum2": 0.0107,
    "r2_sum3": 0.0102,
    "r2_sum4": 0.0112,
    "ldsc_nsnp_merge_refpanel_ld": 1133956,
    "ldsc_nsnp_merge_regression_ld": 1133956,
    "ldsc_observed_scale_h2_beta": 0.1718,
    "ldsc_observed_scale_h2_se": 0.0078,
    "ldsc_intercept_beta": 0.7942,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.0303,
    "ldsc_mean_chisq": 1.1058,
    "ldsc_ratio": -1.9452
}

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 2377582 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 8.580741e+00 5.655387e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.884569e+07 5.564803e+07 1.15230e+04 3.268772e+07 7.027656e+07 1.143652e+08 2.492107e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 4.777000e-04 2.226800e-02 -3.10000e-01 -1.100000e-02 3.000000e-04 1.200000e-02 3.000000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.981360e-02 1.136600e-02 1.20000e-02 1.300000e-02 1.500000e-02 2.100000e-02 1.600000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.925582e-01 2.920187e-01 0.00000e+00 2.399999e-01 4.899999e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.925489e-01 2.921009e-01 0.00000e+00 2.420769e-01 4.917677e-01 7.462943e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 3593 0.9984888 NA NA NA NA NA 3.639383e-01 2.710376e-01 8.00000e-03 1.270000e-01 3.000000e-01 5.670000e-01 9.920000e-01 ▇▅▃▃▂
numeric AF_reference 19684 0.9917210 NA NA NA NA NA 3.667091e-01 2.524240e-01 1.99700e-04 1.545530e-01 3.077080e-01 5.499200e-01 1.000000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 9.056408e+04 1.247555e+04 4.43076e+04 9.061910e+04 9.644060e+04 9.760210e+04 9.869700e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 775659 rs2905035 A G -0.0100 0.026 0.6999999 0.7005224 0.875 0.745008 48417.0
1 777122 rs2980319 A T -0.0110 0.026 0.6899999 0.6722391 0.875 0.747204 48417.0
1 779322 rs4040617 A G 0.0039 0.027 0.8800001 0.8851495 0.125 0.226438 48367.0
1 780785 rs2977612 T A -0.0049 0.027 0.8499999 0.8559897 0.866 0.669329 48417.0
1 785050 rs2905062 G A -0.0074 0.027 0.7800007 0.7840277 0.856 0.626997 48417.0
1 785989 rs2980300 T C -0.0094 0.026 0.7199992 0.7176970 0.873 0.626997 48343.0
1 990380 rs3121561 C T 0.0016 0.022 0.9400001 0.9420231 0.267 0.343450 73457.7
1 998501 rs3813193 G C 0.0200 0.022 0.3700002 0.3633021 0.150 0.206669 68941.3
1 1003629 rs4075116 C T 0.0140 0.016 0.4000000 0.3815739 0.737 0.720647 93793.8
1 1005806 rs3934834 C T 0.0260 0.022 0.2300001 0.2372779 0.119 0.223442 68924.0
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216564 rs9616970 T C 0.0088 0.030 0.7700005 0.7692674 0.150 0.1563500 64010.0
22 51217134 rs117417021 A G 0.0140 0.023 0.5400003 0.5427262 0.442 0.2671730 52319.0
22 51222100 rs114553188 G T -0.0170 0.038 0.6499995 0.6546091 0.067 0.0880591 72911.3
22 51223637 rs375798137 G A -0.0140 0.038 0.7099994 0.7125593 0.067 0.0788738 72911.2
22 51229805 rs9616985 T C 0.0088 0.044 0.8400000 0.8414806 0.092 0.0730831 49183.0
23 35921591 rs2204667 C G 0.0110 0.017 0.5400003 0.5175939 0.167 NA 95559.8
23 51666786 rs14115 A G 0.0091 0.032 0.7700005 0.7761230 0.025 NA 74299.0
23 70163799 rs1626496 A C -0.0520 0.026 0.0449997 0.0455003 0.075 NA 78957.7
23 91415872 rs6562597 G A 0.0600 0.062 0.3400001 0.3331733 0.008 0.0021192 47524.9
23 118495837 rs12882977 G A 0.0084 0.012 0.5000000 0.4839273 0.509 0.2307280 98668.7

bcf preview

1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.01:0.026:0.154902:0.875:48417:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.011:0.026:0.161151:0.875:48417:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0039:0.027:0.0555173:0.125:48367:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.866    ES:SE:LP:AF:SS:ID   -0.0049:0.027:0.0705811:0.866:48417:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.856    ES:SE:LP:AF:SS:ID   -0.0074:0.027:0.107905:0.856:48417:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.873    ES:SE:LP:AF:SS:ID   -0.0094:0.026:0.142668:0.873:48343:rs2980300
1   990380  rs3121561   C   T   .   PASS    AF=0.267    ES:SE:LP:AF:SS:ID   0.0016:0.022:0.0268721:0.267:73457.7:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.02:0.022:0.431798:0.15:68941.3:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.737    ES:SE:LP:AF:SS:ID   0.014:0.016:0.39794:0.737:93793.8:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.119    ES:SE:LP:AF:SS:ID   0.026:0.022:0.638272:0.119:68924:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.569    ES:SE:LP:AF:SS:ID   0.0021:0.016:0.05061:0.569:94953.8:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.576    ES:SE:LP:AF:SS:ID   0.0026:0.015:0.0655015:0.576:95551.8:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.096    ES:SE:LP:AF:SS:ID   0.021:0.023:0.443698:0.096:68645.4:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.592    ES:SE:LP:AF:SS:ID   0.0035:0.015:0.091515:0.592:95671.7:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.602    ES:SE:LP:AF:SS:ID   0.0033:0.015:0.0861861:0.602:95671.2:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.017:0.023:0.327902:0.127:68519.4:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   0.0064:0.015:0.167491:0.717:95634:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.113    ES:SE:LP:AF:SS:ID   0.016:0.023:0.30103:0.113:68577:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0085:0.016:0.229148:0.725:95032.9:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.567    ES:SE:LP:AF:SS:ID   0.0065:0.016:0.167491:0.567:86873.5:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0079:0.017:0.19382:0.6:71500.9:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.021:0.021:0.508638:0.083:70498:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.086    ES:SE:LP:AF:SS:ID   0.018:0.022:0.387216:0.086:59409.7:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.658    ES:SE:LP:AF:SS:ID   0.01:0.017:0.251812:0.658:69542:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.056:0.025:1.5376:0.05:74962.6:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.035:0.022:0.920819:0.075:75032.7:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.037:0.022:1.03152:0.067:80898.1:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.052    ES:SE:LP:AF:SS:ID   0.053:0.025:1.4437:0.052:74942:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.067    ES:SE:LP:AF:SS:ID   0.034:0.021:0.958607:0.067:80574:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.054:0.025:1.49485:0.05:76952.5:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.398    ES:SE:LP:AF:SS:ID   -0.018:0.022:0.376751:0.398:54281.9:rs7548798
1   1060608 rs17160824  G   A   .   PASS    AF=0.058    ES:SE:LP:AF:SS:ID   0.055:0.025:1.5376:0.058:77745.2:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.055    ES:SE:LP:AF:SS:ID   0.055:0.025:1.5376:0.055:76924.3:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.056:0.025:1.56864:0.05:76924.2:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.412    ES:SE:LP:AF:SS:ID   0.0023:0.018:0.0457575:0.412:67843.1:rs11807848
1   1062638 rs9442373   C   A   .   PASS    AF=0.552    ES:SE:LP:AF:SS:ID   0.0018:0.018:0.0362122:0.552:67234:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.754    ES:SE:LP:AF:SS:ID   -0.031:0.024:0.721246:0.754:64592.3:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.026:0.022:0.619789:0.083:69945:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   0.0068:0.019:0.136677:0.675:64387:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.683    ES:SE:LP:AF:SS:ID   0.016:0.021:0.346787:0.683:62053.9:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.924    ES:SE:LP:AF:SS:ID   0.011:0.03:0.136677:0.924:78952.9:rs4970357
1   1087683 rs9442380   T   C   .   PASS    AF=0.912    ES:SE:LP:AF:SS:ID   -0.0098:0.027:0.142668:0.912:88325.8:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.966    ES:SE:LP:AF:SS:ID   -0.028:0.04:0.318759:0.966:69596.8:rs4970358
1   1097335 rs9442385   T   G   .   PASS    AF=0.942    ES:SE:LP:AF:SS:ID   -0.022:0.026:0.387216:0.942:84363.9:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.941    ES:SE:LP:AF:SS:ID   -0.024:0.026:0.443698:0.941:84194:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.958    ES:SE:LP:AF:SS:ID   -0.013:0.043:0.119186:0.958:66831.9:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.144    ES:SE:LP:AF:SS:ID   -0.02:0.023:0.408935:0.144:62467:rs4970420
1   1119858 rs1320565   C   T   .   PASS    AF=0.092    ES:SE:LP:AF:SS:ID   -0.039:0.028:0.769551:0.092:63655:rs1320565
1   1120431 rs1320571   G   A   .   PASS    AF=0.042    ES:SE:LP:AF:SS:ID   -0.033:0.045:0.327902:0.042:59017.6:rs1320571
1   1121014 rs3813204   G   A   .   PASS    AF=0.112    ES:SE:LP:AF:SS:ID   0.0086:0.027:0.124939:0.112:59206.7:rs3813204