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-48/ieu-a-48.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-48/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 11:14:53 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-48/ieu-a-48.vcf.gz ...
Read summary statistics for 2528889 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, 1172864 SNPs remain.
After merging with regression SNP LD, 1172864 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1388 (0.0067)
Lambda GC: 1.039
Mean Chi^2: 1.1573
Intercept: 0.7743 (0.0068)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 11:15:26 2020
Total time elapsed: 33.02s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9177,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -0,
    "n": 227429,
    "n_snps": 2528889,
    "n_clumped_hits": 50,
    "n_p_sig": 1061,
    "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": 44003,
    "n_miss_AF_reference": 22244,
    "n_est": 227306.5098,
    "ratio_se_n": 0.9997,
    "mean_diff": -1.5693e-06,
    "ratio_diff": 0.2129,
    "sd_y_est1": 1.5063,
    "sd_y_est2": 1.5059,
    "r2_sum1": 0.0174,
    "r2_sum2": 0.0077,
    "r2_sum3": 0.0077,
    "r2_sum4": 0.0124,
    "ldsc_nsnp_merge_refpanel_ld": 1172864,
    "ldsc_nsnp_merge_regression_ld": 1172864,
    "ldsc_observed_scale_h2_beta": 0.1388,
    "ldsc_observed_scale_h2_se": 0.0067,
    "ldsc_intercept_beta": 0.7743,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.039,
    "ldsc_mean_chisq": 1.1573,
    "ldsc_ratio": -1.4348
}

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 TRUE
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 2528889 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 8.594238e+00 5.662972e+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 7.881450e+07 5.566835e+07 11523.0000 3.266493e+07 7.021032e+07 1.142580e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.790000e-05 9.431500e-03 -0.2400 -4.300000e-03 0.000000e+00 4.300000e-03 2.50000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 7.637200e-03 6.271100e-03 0.0034 4.700000e-03 5.500000e-03 7.800000e-03 1.30000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.920833e-01 2.929913e-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 4.920796e-01 2.929369e-01 0.0000 2.372779e-01 4.917677e-01 7.451811e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 44003 0.9825999 NA NA NA NA NA 3.553895e-01 2.763575e-01 0.0083 1.167000e-01 2.917000e-01 5.583000e-01 9.91700e-01 ▇▅▃▂▂
numeric AF_reference 22244 0.9912040 NA NA NA NA NA 3.600586e-01 2.571873e-01 0.0000 1.435700e-01 2.973240e-01 5.453270e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 1.404939e+05 2.231957e+04 50001.0000 1.352240e+05 1.452680e+05 1.454280e+05 2.27429e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0089 0.0170 0.6100002 0.6006059 0.06780 0.0371406 68912
1 723819 rs11804171 T A 0.0063 0.0210 0.7600007 0.7641772 0.03704 0.1345850 52583
1 752566 rs3094315 G A 0.0035 0.0079 0.6600001 0.6577383 0.84480 0.7182510 78741
1 754192 rs3131968 A G -0.0028 0.0110 0.8000000 0.7990742 0.87500 0.6785140 57928
1 768448 rs12562034 G A 0.0005 0.0130 0.9699999 0.9693197 0.09167 0.1918930 55895
1 775659 rs2905035 A G 0.0050 0.0086 0.5600000 0.5609740 0.87500 0.7450080 90221
1 777122 rs2980319 A T 0.0048 0.0086 0.5800000 0.5767491 0.87500 0.7472040 90223
1 779322 rs4040617 A G -0.0028 0.0095 0.7700005 0.7681949 0.12500 0.2264380 76695
1 780785 rs2977612 T A 0.0032 0.0094 0.7300002 0.7335361 0.86610 0.6693290 78483
1 785050 rs2905062 G A -0.0039 0.0069 0.5700002 0.5719259 NA 0.6269970 124497
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51217134 rs117417021 A G 0.0025 0.0079 0.7499995 0.7516566 0.441700 0.2671730 87440
22 51222100 rs114553188 G T -0.0083 0.0130 0.5099998 0.5231733 0.066700 0.0880591 113616
22 51223637 rs375798137 G A -0.0083 0.0130 0.5099998 0.5231733 0.066700 0.0788738 113615
22 51229805 rs9616985 T C -0.0054 0.0160 0.7300002 0.7357400 0.091700 0.0730831 84852
23 35921591 rs2204667 C G -0.0025 0.0061 0.6800001 0.6819262 0.166700 NA 145385
23 51666786 rs14115 A G 0.0140 0.0100 0.1700000 0.1615133 0.025000 NA 133485
23 70163799 rs1626496 A C -0.0062 0.0088 0.4799997 0.4810932 0.075000 NA 145269
23 74963352 rs1053838 T G 0.0360 0.0650 0.5800000 0.5796841 0.991379 NA 52190
23 91415872 rs6562597 G A 0.0110 0.0170 0.5099998 0.5175939 0.008300 0.0021192 126806
23 118495837 rs12882977 G A -0.0029 0.0044 0.5099998 0.5098374 0.516700 0.2307280 145434

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   -0.0089:0.017:0.21467:0.0678:68912:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03704  ES:SE:LP:AF:SS:ID   0.0063:0.021:0.119186:0.03704:52583:rs11804171
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   0.0035:0.0079:0.180456:0.8448:78741:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0028:0.011:0.09691:0.875:57928:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.0005:0.013:0.0132283:0.09167:55895:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.005:0.0086:0.251812:0.875:90221:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.0048:0.0086:0.236572:0.875:90223:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   -0.0028:0.0095:0.113509:0.125:76695:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   0.0032:0.0094:0.136677:0.8661:78483:rs2977612
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0039:0.0069:0.244125:124497:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   0.0025:0.0094:0.102373:0.8729:78338:rs2980300
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   -0.0031:0.0093:0.130768:0.1667:74127:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   -0.001:0.0094:0.0362122:0.425:59247:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0006:0.0078:0.0268721:0.2667:104342:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0049:0.008:0.267606:0.15:96700:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.005:0.0057:0.420216:0.7373:138449:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   0.0054:0.0074:0.327902:0.1167:108625:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0032:0.0053:0.259637:0.5667:139907:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0036:0.0051:0.318759:0.5763:140569:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.0066:0.0075:0.420216:0.09649:108457:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   0.0026:0.0049:0.221849:0.5917:140650:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   0.0026:0.0049:0.221849:0.6017:140633:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.0064:0.0076:0.39794:0.1271:108321:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.006:0.0053:0.585027:0.7167:141242:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0068:0.0077:0.420216:106208:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0057:0.0055:0.522879:0.725:140916:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0.0021:0.0054:0.154902:0.5667:131265:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0048:0.0059:0.376751:0.6:106446:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0051:0.007:0.327902:0.08333:109800:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0031:0.0078:0.161151:0.08621:96976:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   -0.0015:0.006:0.09691:0.6583:106393:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0094:0.0083:0.585027:0.05:124005:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0049:0.0076:0.283997:0.075:114093:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0055:0.0078:0.318759:0.06667:120356:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.009:0.0083:0.552842:0.05172:123915:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0038:0.0077:0.207608:0.06667:120269:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0097:0.0087:0.585027:0.05:121757:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0013:0.0074:0.0655015:0.3981:81343:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.015:0.016:0.455932:0.01667:99969:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.009:0.0087:0.522879:0.05833:123865:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.0093:0.0087:0.537602:0.05455:123878:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.01:0.009:0.60206:121675:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.003:0.006:0.207608:0.4123:104778:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.014:0.018:0.366532:0.01667:88225:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5517   ES:SE:LP:AF:SS:ID   0.0011:0.0059:0.0705811:0.5517:103981:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7542   ES:SE:LP:AF:SS:ID   -0.0073:0.0088:0.387216:0.7542:79999:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   -0.0011:0.0078:0.05061:0.08333:98056:rs2298217
1   1066403 rs10907182  T   C   .   PASS    AF=0.675    ES:SE:LP:AF:SS:ID   0.0005:0.0062:0.0268721:0.675:101346:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6833   ES:SE:LP:AF:SS:ID   -0.0006:0.0067:0.0315171:0.6833:98593:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92373  ES:SE:LP:AF:SS:ID   0.0005:0.01:0.0177288:0.92373:122910:rs4970357