Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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-2/ieu-a-2.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-2/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 10:58:37 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-2/ieu-a-2.vcf.gz ...
Read summary statistics for 2554285 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, 1177013 SNPs remain.
After merging with regression SNP LD, 1177013 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1344 (0.0054)
Lambda GC: 1.1148
Mean Chi^2: 1.3108
Intercept: 0.7046 (0.007)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 10:59:07 2020
Total time elapsed: 29.92s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9183,
    "inflation_factor": 1.1116,
    "mean_EFFECT": 0.0001,
    "n": 339224,
    "n_snps": 2554285,
    "n_clumped_hits": 79,
    "n_p_sig": 2041,
    "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": 54864,
    "n_miss_AF_reference": 23058,
    "n_est": 328183.7264,
    "ratio_se_n": 0.9836,
    "mean_diff": -0,
    "ratio_diff": 7.5485,
    "sd_y_est1": 1.5387,
    "sd_y_est2": 1.5134,
    "r2_sum1": 0.0236,
    "r2_sum2": 0.01,
    "r2_sum3": 0.0103,
    "r2_sum4": 0.0153,
    "ldsc_nsnp_merge_refpanel_ld": 1177013,
    "ldsc_nsnp_merge_regression_ld": 1177013,
    "ldsc_observed_scale_h2_beta": 0.1344,
    "ldsc_observed_scale_h2_se": 0.0054,
    "ldsc_intercept_beta": 0.7046,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 1.1148,
    "ldsc_mean_chisq": 1.3108,
    "ldsc_ratio": -0.9505
}

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 TRUE
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 2554285 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 8.599732e+00 5.665262e+00 1.0000 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 <U+2587><U+2585><U+2585><U+2582><U+2582>
numeric POS 0 1.0000000 NA NA NA NA NA 7.878794e+07 5.567688e+07 11523.0000 3.262390e+07 7.016154e+07 1.142167e+08 2.49219e+08 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.082000e-04 8.249100e-03 -0.2540 -3.700000e-03 1.000000e-04 3.800000e-03 2.49900e-01 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA 6.470100e-03 5.872400e-03 0.0029 3.900000e-03 4.600000e-03 6.500000e-03 2.39200e-01 <U+2587><U+2581><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.805441e-01 2.966777e-01 0.0000 2.206002e-01 4.769996e-01 7.389006e-01 1.00000e+00 <U+2587><U+2587><U+2587><U+2586><U+2586>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.805442e-01 2.966802e-01 0.0000 2.205752e-01 4.770154e-01 7.388827e-01 1.00000e+00 <U+2587><U+2587><U+2587><U+2586><U+2586>
numeric AF 54864 0.9785208 NA NA NA NA NA 3.543042e-01 2.770664e-01 0.0083 1.167000e-01 2.833000e-01 5.583000e-01 9.91700e-01 <U+2587><U+2585><U+2583><U+2582><U+2582>
numeric AF_reference 23058 0.9909728 NA NA NA NA NA 3.592546e-01 2.580299e-01 0.0000 1.421730e-01 2.957270e-01 5.449280e-01 1.00000e+00 <U+2587><U+2586><U+2583><U+2583><U+2582>
numeric N 0 1.0000000 NA NA NA NA NA 2.269688e+05 3.630437e+04 50002.0000 2.244090e+05 2.356780e+05 2.361130e+05 3.39224e+05 <U+2581><U+2581><U+2582><U+2587><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C 0.0067 0.0145 0.6412007 0.6440319 0.06780 0.0371406 109823.0
1 723819 rs11804171 T A 0.0146 0.0175 0.4041001 0.4041200 0.03704 0.1345850 84828.0
1 723891 rs2977670 G C -0.0044 0.0184 0.8110001 0.8110044 0.92857 0.7799520 68458.9
1 750235 rs12138618 G A 0.0045 0.0202 0.8237001 0.8237127 0.05833 NA 59954.0
1 752566 rs3094315 G A -0.0060 0.0065 0.3560000 0.3559671 0.84480 0.7182510 131544.0
1 753541 rs2073813 G A -0.0035 0.0102 0.7314994 0.7314952 NA 0.3019170 64351.3
1 754192 rs3131968 A G -0.0077 0.0089 0.3869002 0.3869463 0.87500 0.6785140 98348.7
1 768448 rs12562034 G A 0.0027 0.0108 0.8026001 0.8025873 0.09167 0.1918930 87508.9
1 775659 rs2905035 A G -0.0029 0.0073 0.6912004 0.6911755 0.87500 0.7450080 140187.0
1 777122 rs2980319 A T -0.0031 0.0072 0.6668006 0.6667916 0.87500 0.7472040 143053.0
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51217134 rs117417021 A G 0.0114 0.0066 0.0841201 0.0841187 0.441700 0.2671730 131080.0
22 51222100 rs114553188 G T -0.0111 0.0105 0.2904003 0.2904464 0.066700 0.0880591 190892.0
22 51223637 rs375798137 G A -0.0124 0.0106 0.2421001 0.2420769 0.066700 0.0788738 189615.0
22 51229805 rs9616985 T C 0.0151 0.0126 0.2308001 0.2307564 0.091700 0.0730831 129801.0
23 35921591 rs2204667 C G -0.0006 0.0049 0.9025000 0.9025435 0.166700 NA 236057.0
23 51666786 rs14115 A G 0.0157 0.0082 0.0555405 0.0555392 0.025000 NA 223708.0
23 70163799 rs1626496 A C -0.0080 0.0071 0.2597999 0.2598437 0.075000 NA 235854.0
23 74963352 rs1053838 T G -0.0295 0.0489 0.5462997 0.5463278 0.991379 NA 97215.8
23 91415872 rs6562597 G A -0.0029 0.0136 0.8311000 0.8311434 0.008300 0.0021192 210254.0
23 118495837 rs12882977 G A 0.0007 0.0036 0.8458000 0.8458279 0.516700 0.2307280 236143.0

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   0.0067:0.0145:0.193006:0.0678:109823:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03704  ES:SE:LP:AF:SS:ID   0.0146:0.0175:0.393511:0.03704:84828:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.92857  ES:SE:LP:AF:SS:ID   -0.0044:0.0184:0.0909791:0.92857:68458.9:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.0045:0.0202:0.0842309:0.05833:59954:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   -0.006:0.0065:0.44855:0.8448:131544:rs3094315
1   753541  rs2073813   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0035:0.0102:0.135786:64351.3:rs2073813
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0077:0.0089:0.412401:0.875:98348.7:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.0027:0.0108:0.0955008:0.09167:87508.9:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0029:0.0073:0.160396:0.875:140187:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.0031:0.0072:0.176004:0.875:143053:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.0062:0.0077:0.376027:0.125:131198:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   -0.0058:0.0078:0.339989:0.8661:128446:rs2977612
1   785050  rs2905062   G   A   .   PASS    .   ES:SE:LP:SS:ID  -0.0046:0.006:0.353989:187047:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   -0.0055:0.0076:0.328549:0.8729:131206:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   -0.0044:0.0126:0.138525:0.9:83845.5:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1083   ES:SE:LP:AF:SS:ID   0.0047:0.0129:0.14533:0.1083:79908.8:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   0.0003:0.008:0.0131835:0.1667:107014:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   0.0028:0.0081:0.136915:0.425:92745:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.0034:0.0064:0.225337:0.2667:168169:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.15 ES:SE:LP:AF:SS:ID   0.0101:0.0064:0.941195:0.15:166940:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7373   ES:SE:LP:AF:SS:ID   0.0059:0.0047:0.679023:0.7373:224000:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1167   ES:SE:LP:AF:SS:ID   0.011:0.006:1.17555:0.1167:178981:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   0:0.0045:-0:0.5667:220327:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5763   ES:SE:LP:AF:SS:ID   0.0003:0.0042:0.0254423:0.5763:222155:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.0122:0.0061:1.34199:0.09649:182119:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5917   ES:SE:LP:AF:SS:ID   -0.0006:0.0041:0.0536951:0.5917:226488:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.6017   ES:SE:LP:AF:SS:ID   -0.0006:0.0041:0.0536951:0.6017:226440:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.0115:0.0063:1.16787:0.1271:181924:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7167   ES:SE:LP:AF:SS:ID   0.004:0.0043:0.453087:0.7167:229068:rs3737728
1   1021583 rs10907178  A   C   .   PASS    .   ES:SE:LP:SS:ID  0.0119:0.0063:1.22981:178910:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.725    ES:SE:LP:AF:SS:ID   0.0041:0.0046:0.428524:0.725:228012:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5667   ES:SE:LP:AF:SS:ID   -0.002:0.0045:0.182633:0.5667:206365:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.94737  ES:SE:LP:AF:SS:ID   -0.0017:0.0179:0.034187:0.94737:83573.5:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6  ES:SE:LP:AF:SS:ID   -0.0078:0.0047:1.01323:0.6:178166:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.08333  ES:SE:LP:AF:SS:ID   0.0094:0.0057:1.00384:0.08333:186003:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.08621  ES:SE:LP:AF:SS:ID   0.0096:0.0063:0.894149:0.08621:165051:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.6583   ES:SE:LP:AF:SS:ID   -0.0029:0.0048:0.263046:0.6583:177137:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0153:0.0067:1.64975:0.05:205974:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.075    ES:SE:LP:AF:SS:ID   0.0096:0.0061:0.937418:0.075:194944:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0093:0.0063:0.854182:0.06667:201254:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05172  ES:SE:LP:AF:SS:ID   0.0137:0.0067:1.38849:0.05172:206868:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.06667  ES:SE:LP:AF:SS:ID   0.0087:0.0061:0.813044:0.06667:201301:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.05 ES:SE:LP:AF:SS:ID   0.0139:0.007:1.32726:0.05:200958:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3981   ES:SE:LP:AF:SS:ID   -0.0017:0.0058:0.113848:0.3981:140678:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0126:0.0133:0.464073:0.01667:166242:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.0142:0.007:1.37161:0.05833:205753:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.05455  ES:SE:LP:AF:SS:ID   0.0145:0.007:1.41657:0.05455:205789:rs17160826
1   1061152 rs12748370  T   C   .   PASS    .   ES:SE:LP:SS:ID  0.0151:0.0071:1.47573:200804:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4123   ES:SE:LP:AF:SS:ID   0.0044:0.0048:0.444543:0.4123:170135:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.01667  ES:SE:LP:AF:SS:ID   -0.0116:0.0143:0.379552:0.01667:153801:rs9659914