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-962/ieu-a-962.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-962/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 10:39:04 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-962/ieu-a-962.vcf.gz ...
Read summary statistics for 2454753 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, 1158723 SNPs remain.
After merging with regression SNP LD, 1158723 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0754 (0.0068)
Lambda GC: 1.0879
Mean Chi^2: 1.103
Intercept: 0.9956 (0.006)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 10:39:34 2020
Total time elapsed: 29.65s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9164,
    "inflation_factor": 1.0931,
    "mean_EFFECT": -0.0003,
    "n": 74035,
    "n_snps": 2454753,
    "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": 20318,
    "n_est": 70432.585,
    "ratio_se_n": 0.9754,
    "mean_diff": 0.0001,
    "ratio_diff": 2.9308,
    "sd_y_est1": 2.4658,
    "sd_y_est2": 2.4051,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1158723,
    "ldsc_nsnp_merge_regression_ld": 1158723,
    "ldsc_observed_scale_h2_beta": 0.0754,
    "ldsc_observed_scale_h2_se": 0.0068,
    "ldsc_intercept_beta": 0.9956,
    "ldsc_intercept_se": 0.006,
    "ldsc_lambda_gc": 1.0879,
    "ldsc_mean_chisq": 1.103,
    "ldsc_ratio": -0.0427
}

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 1.000000 3 42 0 2454753 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 8.593623e+00 5.661174e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.881507e+07 5.567091e+07 1.1523e+04 3.265416e+07 7.022509e+07 1.142859e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA -3.011000e-04 4.236270e-02 -2.3868e+00 -1.240000e-02 -4.000000e-04 1.150000e-02 2.38940e+00 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 2.323360e-02 3.511630e-02 1.1300e-02 1.260000e-02 1.500000e-02 2.140000e-02 1.07150e+00 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.854945e-01 2.931211e-01 2.0000e-07 2.274998e-01 4.806999e-01 7.397006e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.854954e-01 2.931252e-01 2.0000e-07 2.275280e-01 4.806843e-01 7.391187e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA 3.720298e-01 2.483973e-01 1.0000e-02 1.582000e-01 3.120000e-01 5.529000e-01 9.90000e-01 ▇▆▅▃▂
numeric AF_reference 20318 0.991723 NA NA NA NA NA 3.614416e-01 2.554425e-01 0.0000e+00 1.463660e-01 2.991210e-01 5.455270e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.000000 NA NA NA NA NA 7.403500e+04 0.000000e+00 7.4035e+04 7.403500e+04 7.403500e+04 7.403500e+04 7.40350e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 721290 rs12565286 G C -0.0885 0.0736 0.2293000 0.2291909 0.2410 0.0371406 74035
1 723819 rs11804171 T A -0.0890 0.0739 0.2290003 0.2284620 0.2394 0.1345850 74035
1 752566 rs3094315 G A -0.0031 0.0237 0.8949000 0.8959322 0.7737 0.7182510 74035
1 754192 rs3131968 A G 0.0210 0.0435 0.6293004 0.6292671 0.8651 0.6785140 74035
1 768448 rs12562034 G A -0.0610 0.0483 0.2065998 0.2066108 0.1099 0.1918930 74035
1 775659 rs2905035 A G 0.0079 0.0285 0.7811007 0.7816319 0.7793 0.7450080 74035
1 776546 rs12124819 A G -0.0559 0.0594 0.3468998 0.3466652 0.2478 0.0756789 74035
1 777122 rs2980319 A T 0.0077 0.0282 0.7842996 0.7848151 0.7777 0.7472040 74035
1 779322 rs4040617 A G -0.0064 0.0296 0.8300000 0.8288192 0.2260 0.2264380 74035
1 780785 rs2977612 T A 0.0089 0.0282 0.7513997 0.7523040 0.7786 0.6693290 74035
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51171693 rs756638 G A -0.0075 0.0166 0.6533005 0.6514079 0.2745 0.3049120 74035
22 51175626 rs3810648 A G 0.0019 0.0255 0.9409001 0.9406047 0.0947 0.1084270 74035
22 51178090 rs2285395 G A -0.0034 0.0262 0.8979999 0.8967476 0.0932 0.0666933 74035
22 51196164 rs8136603 A T 0.0403 0.0484 0.4053004 0.4050452 0.0565 0.1427720 74035
22 51212875 rs2238837 A C -0.0012 0.0259 0.9631000 0.9630456 0.3987 0.3724040 74035
23 35921591 rs2204667 C G 0.0125 0.0160 0.4327001 0.4346555 0.1850 NA 74035
23 51666786 rs14115 A G 0.0147 0.0259 0.5692998 0.5703286 0.0906 NA 74035
23 70163799 rs1626496 A C -0.0051 0.0229 0.8240000 0.8237632 0.1076 NA 74035
23 91415872 rs6562597 G A 0.0465 0.0454 0.3054000 0.3057271 0.0659 0.0021192 74035
23 118495837 rs12882977 G A 0.0012 0.0117 0.9166001 0.9183089 0.4922 0.2307280 74035

bcf preview

1   721290  rs12565286  G   C   .   PASS    AF=0.241    ES:SE:LP:AF:SS:ID   -0.0885:0.0736:0.639596:0.241:74035:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.2394   ES:SE:LP:AF:SS:ID   -0.089:0.0739:0.640164:0.2394:74035:rs11804171
1   752566  rs3094315   G   A   .   PASS    AF=0.7737   ES:SE:LP:AF:SS:ID   -0.0031:0.0237:0.0482255:0.7737:74035:rs3094315
1   754192  rs3131968   A   G   .   PASS    AF=0.8651   ES:SE:LP:AF:SS:ID   0.021:0.0435:0.201142:0.8651:74035:rs3131968
1   768448  rs12562034  G   A   .   PASS    AF=0.1099   ES:SE:LP:AF:SS:ID   -0.061:0.0483:0.68487:0.1099:74035:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.7793   ES:SE:LP:AF:SS:ID   0.0079:0.0285:0.107293:0.7793:74035:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.2478   ES:SE:LP:AF:SS:ID   -0.0559:0.0594:0.459796:0.2478:74035:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.7777   ES:SE:LP:AF:SS:ID   0.0077:0.0282:0.105518:0.7777:74035:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.226    ES:SE:LP:AF:SS:ID   -0.0064:0.0296:0.0809219:0.226:74035:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.7786   ES:SE:LP:AF:SS:ID   0.0089:0.0282:0.124129:0.7786:74035:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.7777   ES:SE:LP:AF:SS:ID   0.0107:0.0282:0.151441:0.7777:74035:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.7764   ES:SE:LP:AF:SS:ID   0.0111:0.0282:0.158515:0.7764:74035:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.9143   ES:SE:LP:AF:SS:ID   0.072:0.1021:0.317855:0.9143:74035:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1104   ES:SE:LP:AF:SS:ID   -0.0536:0.0936:0.24657:0.1104:74035:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.298    ES:SE:LP:AF:SS:ID   -0.0112:0.0275:0.165071:0.298:74035:rs11240777
1   998501  rs3813193   G   C   .   PASS    AF=0.1739   ES:SE:LP:AF:SS:ID   -0.013:0.0268:0.202663:0.1739:74035:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.6733   ES:SE:LP:AF:SS:ID   -0.0183:0.024:0.350081:0.6733:74035:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1474   ES:SE:LP:AF:SS:ID   -0.0146:0.0233:0.274824:0.1474:74035:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5309   ES:SE:LP:AF:SS:ID   0.0031:0.0211:0.0543837:0.5309:74035:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5552   ES:SE:LP:AF:SS:ID   0.0144:0.015:0.472886:0.5552:74035:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1434   ES:SE:LP:AF:SS:ID   -0.0265:0.0236:0.581367:0.1434:74035:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5627   ES:SE:LP:AF:SS:ID   0.0139:0.0147:0.463947:0.5627:74035:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5627   ES:SE:LP:AF:SS:ID   0.0145:0.0146:0.496618:0.5627:74035:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1465   ES:SE:LP:AF:SS:ID   -0.0297:0.0251:0.628009:0.1465:74035:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7235   ES:SE:LP:AF:SS:ID   0.0023:0.0163:0.0526153:0.7235:74035:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1444   ES:SE:LP:AF:SS:ID   -0.03:0.0259:0.607303:0.1444:74035:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.736    ES:SE:LP:AF:SS:ID   0.0002:0.0179:0.00361969:0.736:74035:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5583   ES:SE:LP:AF:SS:ID   0.023:0.0178:0.704433:0.5583:74035:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.6072   ES:SE:LP:AF:SS:ID   0.0236:0.0164:0.818156:0.6072:74035:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1586   ES:SE:LP:AF:SS:ID   -0.0142:0.0198:0.32661:0.1586:74035:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.161    ES:SE:LP:AF:SS:ID   -0.0398:0.0349:0.595508:0.161:74035:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.729    ES:SE:LP:AF:SS:ID   0.0206:0.0167:0.660549:0.729:74035:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1087   ES:SE:LP:AF:SS:ID   -0.0275:0.0239:0.601539:0.1087:74035:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1422   ES:SE:LP:AF:SS:ID   -0.0219:0.0215:0.50962:0.1422:74035:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1362   ES:SE:LP:AF:SS:ID   -0.0213:0.0212:0.501965:0.1362:74035:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1084   ES:SE:LP:AF:SS:ID   -0.0165:0.0234:0.318397:0.1084:74035:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1386   ES:SE:LP:AF:SS:ID   -0.008:0.0207:0.156456:0.1386:74035:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1101   ES:SE:LP:AF:SS:ID   -0.0284:0.0236:0.643401:0.1101:74035:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.323    ES:SE:LP:AF:SS:ID   -0.0324:0.0464:0.31399:0.323:74035:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0295   ES:SE:LP:AF:SS:ID   0.0101:0.051:0.0744816:0.0295:74035:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1185   ES:SE:LP:AF:SS:ID   -0.0227:0.0243:0.457299:0.1185:74035:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1088   ES:SE:LP:AF:SS:ID   -0.0296:0.0241:0.661344:0.1088:74035:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1086   ES:SE:LP:AF:SS:ID   -0.03:0.0242:0.667764:0.1086:74035:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4112   ES:SE:LP:AF:SS:ID   -0.0005:0.0302:0.00612309:0.4112:74035:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0275   ES:SE:LP:AF:SS:ID   0.009:0.0556:0.0596828:0.0275:74035:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5497   ES:SE:LP:AF:SS:ID   0.007:0.03:0.0888957:0.5497:74035:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.1491   ES:SE:LP:AF:SS:ID   -0.0175:0.0213:0.384681:0.1491:74035:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.084    ES:SE:LP:AF:SS:ID   -0.0277:0.0549:0.211619:0.084:74035:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.6294   ES:SE:LP:AF:SS:ID   -0.0243:0.0582:0.169989:0.6294:74035:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6363   ES:SE:LP:AF:SS:ID   -0.0646:0.1099:0.254223:0.6363:74035:rs10907183