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-1064/ieu-a-1064.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-1064/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-1064/ieu-a-1064.vcf.gz ...
Read summary statistics for 2412589 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, 1144084 SNPs remain.
After merging with regression SNP LD, 1144084 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0727 (0.165)
Lambda GC: 0.9957
Mean Chi^2: 0.9968
Intercept: 1.0006 (0.007)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Wed Feb  5 11:11:17 2020
Total time elapsed: 29.59s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9212,
    "inflation_factor": 0.9916,
    "mean_EFFECT": 0.0002,
    "n": 2602,
    "n_snps": 2412589,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 0,
    "n_miss_AF_reference": 20500,
    "n_est": 2560.4203,
    "ratio_se_n": 0.992,
    "mean_diff": 0,
    "ratio_diff": 1.0604,
    "sd_y_est1": 1.0044,
    "sd_y_est2": 0.9964,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1144084,
    "ldsc_nsnp_merge_regression_ld": 1144084,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0006,
    "ldsc_intercept_se": 0.007,
    "ldsc_lambda_gc": 0.9957,
    "ldsc_mean_chisq": 0.9968,
    "ldsc_ratio": -0.1875
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 2412589 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 8.596485e+00 5.662805e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.879057e+07 5.566495e+07 1.1523e+04 3.265532e+07 7.017933e+07 1.142893e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.888000e-04 4.697760e-02 -6.1500e-01 -2.480000e-02 1.000000e-04 2.500000e-02 7.87400e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 4.191550e-02 2.136420e-02 2.6300e-02 2.900000e-02 3.370000e-02 4.560000e-02 2.94800e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.012799e-01 2.887005e-01 3.0000e-07 2.513998e-01 5.018004e-01 7.513997e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.012794e-01 2.887009e-01 3.0000e-07 2.514333e-01 5.019147e-01 7.514180e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.621720e-01 2.718538e-01 1.0060e-02 1.269000e-01 2.984000e-01 5.616000e-01 9.89940e-01 ▇▅▃▃▂
numeric AF_reference 20500 0.9915029 NA NA NA NA NA 3.641291e-01 2.536731e-01 1.9970e-04 1.509580e-01 3.037140e-01 5.475240e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.602000e+03 0.000000e+00 2.6020e+03 2.602000e+03 2.602000e+03 2.602000e+03 2.60200e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.1644 0.1264 0.1933001 0.1933841 0.03048 0.0371406 2602
1 723819 rs11804171 T A -0.1644 0.1264 0.1933001 0.1933841 0.03048 0.1345850 2602
1 723891 rs2977670 G C 0.1539 0.1254 0.2197000 0.2197201 0.96924 0.7799520 2602
1 750235 rs12138618 G A 0.0628 0.0775 0.4178996 0.4177548 0.08166 NA 2602
1 752566 rs3094315 G A -0.0306 0.0528 0.5622999 0.5622212 0.79180 0.7182510 2602
1 754192 rs3131968 A G -0.0500 0.0547 0.3600999 0.3606765 0.81280 0.6785140 2602
1 768448 rs12562034 G A 0.0279 0.0658 0.6712001 0.6715569 0.11050 0.1918930 2602
1 775659 rs2905035 A G -0.0500 0.0547 0.3600999 0.3606765 0.81280 0.7450080 2602
1 777122 rs2980319 A T -0.0500 0.0547 0.3600999 0.3606765 0.81280 0.7472040 2602
1 779322 rs4040617 A G 0.0500 0.0547 0.3600999 0.3606765 0.18720 0.2264380 2602
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51212875 rs2238837 A C -0.0182 0.0417 0.6633000 0.6625097 0.40970 0.3724040 2602
22 51216564 rs9616970 T C 0.0532 0.0443 0.2307002 0.2297889 0.13400 0.1563500 2602
22 51217134 rs117417021 A G 0.0282 0.0425 0.5073995 0.5069915 0.48450 0.2671730 2602
22 51222100 rs114553188 G T 0.0566 0.0560 0.3115997 0.3121532 0.07936 0.0880591 2602
22 51223637 rs375798137 G A 0.0566 0.0560 0.3115997 0.3121532 0.07936 0.0788738 2602
22 51229805 rs9616985 T C 0.0368 0.0631 0.5593002 0.5597578 0.05405 0.0730831 2602
23 35921591 rs2204667 C G 0.0541 0.0365 0.1385001 0.1382893 0.15410 NA 2602
23 51666786 rs14115 A G 0.0514 0.0636 0.4184996 0.4189892 0.06200 NA 2602
23 70163799 rs1626496 A C -0.0149 0.0596 0.8021000 0.8025873 0.03939 NA 2602
23 118495837 rs12882977 G A 0.0319 0.0283 0.2581000 0.2596543 0.42180 0.2307280 2602

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.03048  ES:SE:LP:AF:SS:ID   -0.1644:0.1264:0.713768:0.03048:2602:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03048  ES:SE:LP:AF:SS:ID   -0.1644:0.1264:0.713768:0.03048:2602:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.96924  ES:SE:LP:AF:SS:ID   0.1539:0.1254:0.65817:0.96924:2602:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.08166  ES:SE:LP:AF:SS:ID   0.0628:0.0775:0.378928:0.08166:2602:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.7918   ES:SE:LP:AF:SS:ID   -0.0306:0.0528:0.250032:0.7918:2602:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.05:0.0547:0.443577:0.8128:2602:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.1105   ES:SE:LP:AF:SS:ID   0.0279:0.0658:0.173148:0.1105:2602:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.05:0.0547:0.443577:0.8128:2602:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.05:0.0547:0.443577:0.8128:2602:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1872   ES:SE:LP:AF:SS:ID   0.05:0.0547:0.443577:0.1872:2602:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8128   ES:SE:LP:AF:SS:ID   -0.05:0.0547:0.443577:0.8128:2602:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.8131   ES:SE:LP:AF:SS:ID   -0.0521:0.0547:0.467755:0.8131:2602:rs2905062
1   798026  rs4951864   C   T   .   PASS    AF=0.8899   ES:SE:LP:AF:SS:ID   -0.0279:0.0658:0.173148:0.8899:2602:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1104   ES:SE:LP:AF:SS:ID   0.0317:0.0654:0.202594:0.1104:2602:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.2142   ES:SE:LP:AF:SS:ID   0.0269:0.0516:0.220331:0.2142:2602:rs11240777
1   962210  rs3128126   A   G   .   PASS    AF=0.4612   ES:SE:LP:AF:SS:ID   -0.0013:0.0426:0.0109954:0.4612:2602:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2895   ES:SE:LP:AF:SS:ID   -0.0122:0.0461:0.101769:0.2895:2602:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.2294   ES:SE:LP:AF:SS:ID   -0.0332:0.036:0.44794:0.2294:2602:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.7401   ES:SE:LP:AF:SS:ID   0.0186:0.0317:0.253677:0.7401:2602:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.2293   ES:SE:LP:AF:SS:ID   -0.0335:0.036:0.454075:0.2293:2602:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5155   ES:SE:LP:AF:SS:ID   0.0504:0.041:0.659556:0.5155:2602:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5106   ES:SE:LP:AF:SS:ID   0.0403:0.0405:0.494986:0.5106:2602:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.2174   ES:SE:LP:AF:SS:ID   -0.0248:0.0376:0.293368:0.2174:2602:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5106   ES:SE:LP:AF:SS:ID   0.0278:0.0288:0.475474:0.5106:2602:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5104   ES:SE:LP:AF:SS:ID   0.0277:0.0288:0.472886:0.5104:2602:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.2168   ES:SE:LP:AF:SS:ID   -0.0287:0.0379:0.347754:0.2168:2602:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7174   ES:SE:LP:AF:SS:ID   0.0003:0.0312:0.00313823:0.7174:2602:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.2168   ES:SE:LP:AF:SS:ID   -0.0287:0.0379:0.347754:0.2168:2602:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7424   ES:SE:LP:AF:SS:ID   0.0095:0.0316:0.117077:0.7424:2602:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.4994   ES:SE:LP:AF:SS:ID   0.0111:0.0285:0.156705:0.4994:2602:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.98189  ES:SE:LP:AF:SS:ID   0.1082:0.1516:0.322941:0.98189:2602:rs9442400
1   1026707 rs4074137   C   A   .   PASS    AF=0.6052   ES:SE:LP:AF:SS:ID   0.044:0.0285:0.910802:0.6052:2602:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1886   ES:SE:LP:AF:SS:ID   0.0217:0.0364:0.259085:0.1886:2602:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1857   ES:SE:LP:AF:SS:ID   0.0269:0.0366:0.334138:0.1857:2602:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7296   ES:SE:LP:AF:SS:ID   0.0541:0.0311:1.08741:0.7296:2602:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.0529   ES:SE:LP:AF:SS:ID   -0.0086:0.0521:0.0611302:0.0529:2602:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.09919  ES:SE:LP:AF:SS:ID   0.0423:0.0432:0.484259:0.09919:2602:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.09919  ES:SE:LP:AF:SS:ID   0.0338:0.0427:0.367441:0.09919:2602:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.05322  ES:SE:LP:AF:SS:ID   0.0102:0.0513:0.0747911:0.05322:2602:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1112   ES:SE:LP:AF:SS:ID   0.0385:0.0418:0.447089:0.1112:2602:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.06613  ES:SE:LP:AF:SS:ID   0.0224:0.0494:0.187153:0.06613:2602:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3258   ES:SE:LP:AF:SS:ID   -0.0343:0.0294:0.614394:0.3258:2602:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.04543  ES:SE:LP:AF:SS:ID   0.0693:0.0746:0.452102:0.04543:2602:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.06642  ES:SE:LP:AF:SS:ID   0.0321:0.0498:0.283997:0.06642:2602:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.06642  ES:SE:LP:AF:SS:ID   0.0363:0.0503:0.327533:0.06642:2602:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.06642  ES:SE:LP:AF:SS:ID   0.0363:0.0503:0.327533:0.06642:2602:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.3921   ES:SE:LP:AF:SS:ID   -0.018:0.0285:0.277119:0.3921:2602:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.04457  ES:SE:LP:AF:SS:ID   0.0766:0.0761:0.502241:0.04457:2602:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5233   ES:SE:LP:AF:SS:ID   0.0343:0.0281:0.653256:0.5233:2602:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7884   ES:SE:LP:AF:SS:ID   -0.0043:0.0348:0.0451306:0.7884:2602:rs6682475