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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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/8df62438-7698-4906-a791-eb7c23c12153/call-vcf/inputs/-674580005/upload.txt.gz --id ieu-b-9 --json /data/cromwell-executions/qc/8df62438-7698-4906-a791-eb7c23c12153/call-vcf/inputs/-674580005/ieu-b-9_data.json --ref /data/cromwell-executions/qc/8df62438-7698-4906-a791-eb7c23c12153/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/8df62438-7698-4906-a791-eb7c23c12153/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-9/ieu-b-9.vcf.gz --rm_chr_prefix --cohort_cases 3769 --cohort_controls 29677; 1.2.1",
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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 /data/cromwell-executions/qc/8df62438-7698-4906-a791-eb7c23c12153/call-ldsc/inputs/-674580005/ieu-b-9.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-9/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Fri Jun 26 15:26:18 2020
Reading summary statistics from /data/cromwell-executions/qc/8df62438-7698-4906-a791-eb7c23c12153/call-ldsc/inputs/-674580005/ieu-b-9.vcf.gz ...
Read summary statistics for 4867055 SNPs.
Dropped 11484 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 928180 SNPs remain.
After merging with regression SNP LD, 928180 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.262 (0.0248)
Lambda GC: 1.2597
Mean Chi^2: 1.2926
Intercept: 1.0983 (0.011)
Ratio: 0.336 (0.0378)
Analysis finished at Fri Jun 26 15:27:51 2020
Total time elapsed: 1.0m:33.53sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9333,
"inflation_factor": 1.2455,
"mean_EFFECT": -0.0012,
"n": "-Inf",
"n_snps": 4867068,
"n_clumped_hits": 11,
"n_p_sig": 279,
"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": 29192,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NA",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 928180,
"ldsc_nsnp_merge_regression_ld": 928180,
"ldsc_observed_scale_h2_beta": 0.262,
"ldsc_observed_scale_h2_se": 0.0248,
"ldsc_intercept_beta": 1.0983,
"ldsc_intercept_se": 0.011,
"ldsc_lambda_gc": 1.2597,
"ldsc_mean_chisq": 1.2926,
"ldsc_ratio": 0.336
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| 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 betweenAFandAF_reference.inflation_factor(lambda): Genomic inflation factor.mean_EFFECT: Mean ofEFFECTsize.n: Maximum value of reported sample size across all SNPs, \(n\).n_clumped_hits: Number of clumped hits.n_snps: Number of SNPsn_p_sig: Number of SNPs with pvalue below5e-8.n_mono: Number of monomorphic (MAF == 1orMAF == 0) SNPs.n_ns: Number of SNPs with nonsense values:- alleles other than
A, C, G or T. - P-values
< 0or> 1. - negative or infinite standard errors (
<= 0or= Infinity). - infinite beta estimates or allele frequencies
< 0or> 1.
- alleles other than
n_mac: Number of cases whereMAC(\(2 \times N \times MAF\)) is less than6.is_snpid_unique:trueif the combination ofIDREFALTis unique and therefore no duplication in snpid.n_miss_<*>: Number ofNAobservations 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 expectratio_se_nto 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 ofdiffand the mean ofdiff2(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<*>:r2statistics under various assumptions1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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: NOTis_snpid_unique.mean_EFFECT_nonfinite:mean(EFFECT)isNA,NaN, orInf.mean_EFFECT_05:abs(mean(EFFECT))> 0.5.mean_EFFECT_01:abs(mean(EFFECT))> 0.1.mean_chisq:ldsc_mean_chisq> 1.3 orldsc_mean_chisq< 0.7.n_p_sig:n_p_sig> 1000.miss_<*>:n_miss_<*>/n_snps> 0.01.ldsc_ratio:ldsc_ratio> 0.5ldsc_intercept_beta:ldsc_intercept_beta> 1.5n_clumped_hits:n_clumped_hits> 1000r2_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 | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 1 | 0.9999998 | 3 | 35 | 0 | 4867065 | 0 | NA | NA | 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 | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 4867068 | 0.0000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.640583e+00 | 5.868190e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.979938e+07 | 5.501269e+07 | 3.30120e+04 | 3.479013e+07 | 7.127838e+07 | 1.144224e+08 | 2.49219e+08 | ▇▇▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.225600e-03 | 2.386810e-02 | -2.31175e-01 | -1.431490e-02 | -1.124600e-03 | 1.206160e-02 | 2.46288e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.977680e-02 | 9.326500e-03 | 1.23560e-02 | 1.326020e-02 | 1.601340e-02 | 2.265310e-02 | 1.44980e-01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.656309e-01 | 2.976145e-01 | 0.00000e+00 | 2.000000e-01 | 4.516001e-01 | 7.225002e-01 | 1.00000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.656397e-01 | 2.976167e-01 | 0.00000e+00 | 1.998423e-01 | 4.514507e-01 | 7.225894e-01 | 1.00000e+00 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.061288e-01 | 2.580667e-01 | 1.90000e-03 | 8.900000e-02 | 2.245000e-01 | 4.753000e-01 | 9.90000e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 29192 | 0.9940021 | NA | NA | NA | NA | NA | NA | NA | 3.078942e-01 | 2.470854e-01 | 1.99700e-04 | 1.038340e-01 | 2.366210e-01 | 4.682510e-01 | 1.00000e+00 | ▇▅▃▂▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1029805 | rs6689308 | A | G | 0.0161984 | 0.0166137 | 0.3297000 | 0.3295590 | 0.1708 | 0.315695 | NA |
| 1 | 1031973 | rs9651270 | C | T | 0.0190694 | 0.0172887 | 0.2700001 | 0.2700281 | 0.1610 | 0.310703 | NA |
| 1 | 1033596 | rs6604964 | T | C | 0.0190775 | 0.0172960 | 0.2700001 | 0.2700269 | 0.1609 | 0.311701 | NA |
| 1 | 1033670 | rs6604966 | T | C | 0.0198978 | 0.0173024 | 0.2500000 | 0.2501429 | 0.1609 | 0.315895 | NA |
| 1 | 1033680 | rs6604967 | T | A | 0.0194859 | 0.0173054 | 0.2599998 | 0.2601650 | 0.1608 | 0.311701 | NA |
| 1 | 1033994 | rs6698368 | C | T | 0.0198962 | 0.0173011 | 0.2500000 | 0.2501454 | 0.1609 | 0.311502 | NA |
| 1 | 1034200 | rs77977351 | T | C | 0.0198981 | 0.0173027 | 0.2500000 | 0.2501440 | 0.1609 | 0.311502 | NA |
| 1 | 1036860 | rs11579922 | A | C | 0.0169433 | 0.0189099 | 0.3700002 | 0.3702519 | 0.1278 | 0.282748 | NA |
| 1 | 1036959 | rs11579015 | T | C | 0.0027191 | 0.0197038 | 0.8900000 | 0.8902402 | 0.1136 | 0.156949 | NA |
| 1 | 1037303 | rs11260592 | T | C | 0.0157483 | 0.0179365 | 0.3800004 | 0.3799421 | 0.1410 | 0.282548 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 139277416 | rs435268 | G | A | 0.0201347 | 0.0125999 | 0.1100001 | 0.1100419 | 0.4850 | 0.650861 | NA |
| 23 | 139279657 | rs369604 | G | A | 0.0216341 | 0.0124836 | 0.0830902 | 0.0830954 | 0.4416 | 0.442384 | NA |
| 23 | 139279671 | rs382435 | A | G | 0.0262823 | 0.0125994 | 0.0369999 | 0.0369790 | 0.4437 | 0.435762 | NA |
| 23 | 139279881 | rs414554 | C | G | 0.0200616 | 0.0125542 | 0.1100001 | 0.1100432 | 0.4933 | 0.655894 | NA |
| 23 | 139282091 | rs426349 | C | T | 0.0214735 | 0.0125870 | 0.0879995 | 0.0880069 | 0.4825 | 0.471788 | NA |
| 23 | 139282915 | rs419307 | C | T | 0.0200721 | 0.0124439 | 0.1067999 | 0.1067429 | 0.4844 | 0.539868 | NA |
| 23 | 139284404 | rs430026 | G | A | 0.0176423 | 0.0128588 | 0.1700000 | 0.1700628 | 0.4169 | 0.308609 | NA |
| 23 | 139287243 | rs412811 | T | C | 0.0213195 | 0.0126902 | 0.0929994 | 0.0929579 | 0.4470 | 0.460397 | NA |
| 23 | 139288359 | rs367697 | C | T | 0.0182255 | 0.0124491 | 0.1432000 | 0.1431936 | 0.4801 | 0.488477 | NA |
| 23 | 139289049 | rs387193 | A | G | 0.0228496 | 0.0127013 | 0.0719996 | 0.0720192 | 0.4452 | 0.450331 | NA |
bcf preview
1 1029805 rs891281851 A G . PASS AF=0.1708 ES:SE:LP:AF:ID 0.0161984:0.0166137:0.481881:0.1708:rs891281851
1 1031973 rs9651270 C T . PASS AF=0.161 ES:SE:LP:AF:ID 0.0190694:0.0172887:0.568636:0.161:rs9651270
1 1033596 rs6604964 T C . PASS AF=0.1609 ES:SE:LP:AF:ID 0.0190775:0.017296:0.568636:0.1609:rs6604964
1 1033670 rs1370950991 T C . PASS AF=0.1609 ES:SE:LP:AF:ID 0.0198978:0.0173024:0.60206:0.1609:rs1370950991
1 1033680 rs1370950991 T A . PASS AF=0.1608 ES:SE:LP:AF:ID 0.0194859:0.0173054:0.585027:0.1608:rs1370950991
1 1033994 rs6698368 C T . PASS AF=0.1609 ES:SE:LP:AF:ID 0.0198962:0.0173011:0.60206:0.1609:rs6698368
1 1034200 rs77977351 T C . PASS AF=0.1609 ES:SE:LP:AF:ID 0.0198981:0.0173027:0.60206:0.1609:rs77977351
1 1036860 rs11579922 A C . PASS AF=0.1278 ES:SE:LP:AF:ID 0.0169433:0.0189099:0.431798:0.1278:rs11579922
1 1036959 rs1162868282 T C . PASS AF=0.1136 ES:SE:LP:AF:ID 0.00271913:0.0197038:0.05061:0.1136:rs1162868282
1 1037303 rs11260592 T C . PASS AF=0.141 ES:SE:LP:AF:ID 0.0157483:0.0179365:0.420216:0.141:rs11260592
1 1037313 rs11260593 A G . PASS AF=0.1475 ES:SE:LP:AF:ID 0.0199417:0.0174468:0.596879:0.1475:rs11260593
1 1037367 rs11260594 G A . PASS AF=0.141 ES:SE:LP:AF:ID 0.0157502:0.0179388:0.420216:0.141:rs11260594
1 1038088 rs66622470 G C . PASS AF=0.1411 ES:SE:LP:AF:ID 0.0164062:0.0179302:0.443698:0.1411:rs66622470
1 1039268 rs9329410 T C . PASS AF=0.1413 ES:SE:LP:AF:ID 0.0163933:0.0179161:0.443698:0.1413:rs9329410
1 1039817 rs1205065516 A G . PASS AF=0.1412 ES:SE:LP:AF:ID 0.0163989:0.0179223:0.443698:0.1412:rs1205065516
1 1040026 rs6671356 T C . PASS AF=0.1416 ES:SE:LP:AF:ID 0.0157091:0.0178919:0.420216:0.1416:rs6671356
1 1040472 rs6664124 C T . PASS AF=0.1415 ES:SE:LP:AF:ID 0.0157146:0.0178982:0.420216:0.1415:rs6664124
1 1040794 rs6687681 G A . PASS AF=0.1414 ES:SE:LP:AF:ID 0.0153981:0.0179047:0.408935:0.1414:rs6687681
1 1040824 rs6656379 T C . PASS AF=0.1481 ES:SE:LP:AF:ID 0.0206935:0.0174041:0.630042:0.1481:rs6656379
1 1040985 rs6697379 C G . PASS AF=0.1414 ES:SE:LP:AF:ID 0.0157198:0.0179041:0.420216:0.1414:rs6697379
1 1041700 rs6604968 A G . PASS AF=0.1416 ES:SE:LP:AF:ID 0.0153934:0.0178993:0.408935:0.1416:rs6604968
1 1041786 rs6604969 T C . PASS AF=0.1416 ES:SE:LP:AF:ID 0.015392:0.0178977:0.408935:0.1416:rs6604969
1 1042483 rs12733365 C T . PASS AF=0.1415 ES:SE:LP:AF:ID 0.0160393:0.017901:0.431798:0.1415:rs12733365
1 1042527 rs1486993720 G C . PASS AF=0.1122 ES:SE:LP:AF:ID 0.00787112:0.0197271:0.161403:0.1122:rs1486993720
1 1042673 rs897825316 C T . PASS AF=0.1426 ES:SE:LP:AF:ID 0.0157605:0.0179504:0.420216:0.1426:rs897825316
1 1042927 rs4970354 G T . PASS AF=0.1414 ES:SE:LP:AF:ID 0.0157195:0.0179037:0.420216:0.1414:rs4970354
1 1043053 rs4970355 A G . PASS AF=0.1414 ES:SE:LP:AF:ID 0.0160432:0.0179053:0.431798:0.1414:rs4970355
1 1045473 rs11586034 G A . PASS AF=0.1116 ES:SE:LP:AF:ID 0.00472771:0.0197812:0.0911398:0.1116:rs11586034
1 1046073 rs11590188 C A . PASS AF=0.1397 ES:SE:LP:AF:ID 0.0115836:0.0180149:0.283997:0.1397:rs11590188
1 1046164 rs386627439 C T . PASS AF=0.1414 ES:SE:LP:AF:ID 0.0163828:0.0179047:0.443698:0.1414:rs386627439
1 1046717 rs34820586 G C . PASS AF=0.1126 ES:SE:LP:AF:ID 0.00858634:0.0196934:0.178486:0.1126:rs34820586
1 1046861 rs12723165 G A . PASS AF=0.1126 ES:SE:LP:AF:ID 0.00858587:0.0196924:0.178486:0.1126:rs12723165
1 1047374 rs12743678 T A . PASS AF=0.1472 ES:SE:LP:AF:ID 0.0218634:0.0174628:0.676335:0.1472:rs12743678
1 1048501 rs7518814 G A . PASS AF=0.1397 ES:SE:LP:AF:ID 0.0115838:0.0180152:0.283997:0.1397:rs7518814
1 1048955 rs4970405 A G . PASS AF=0.1041 ES:SE:LP:AF:ID 0.0159036:0.0203632:0.36181:0.1041:rs4970405
1 1048989 rs4970406 A G . PASS AF=0.1142 ES:SE:LP:AF:ID 0.00348271:0.0197881:0.0655015:0.1142:rs4970406
1 1049083 rs4970407 C A . PASS AF=0.1134 ES:SE:LP:AF:ID 0.00325171:0.0198275:0.0604807:0.1134:rs4970407
1 1049950 rs12726255 A G . PASS AF=0.1459 ES:SE:LP:AF:ID 0.00585346:0.017578:0.131121:0.1459:rs12726255
1 1052946 rs12755848 G T . PASS AF=0.1116 ES:SE:LP:AF:ID 0.00761164:0.019822:0.154406:0.1116:rs12755848
1 1053452 rs4970409 G A . PASS AF=0.1115 ES:SE:LP:AF:ID 0.00675988:0.0198237:0.134659:0.1115:rs4970409
1 1053670 rs4970410 G A . PASS AF=0.1381 ES:SE:LP:AF:ID -0.00136299:0.0181731:0.0268721:0.1381:rs4970410
1 1053724 rs4970411 A G . PASS AF=0.1377 ES:SE:LP:AF:ID 0.00136511:0.0182015:0.0268721:0.1377:rs4970411
1 1054552 rs12567697 G A . PASS AF=0.1105 ES:SE:LP:AF:ID 0.00627138:0.0199091:0.12332:0.1105:rs12567697
1 1054893 rs4970412 T C . PASS AF=0.1442 ES:SE:LP:AF:ID 0.00429952:0.0176935:0.0924812:0.1442:rs4970412
1 1055653 rs34808604 C G . PASS AF=0.1107 ES:SE:LP:AF:ID 0.00386035:0.0198987:0.0724757:0.1107:rs34808604
1 1055797 rs76744376 A G . PASS AF=0.112 ES:SE:LP:AF:ID 0.00275796:0.0199852:0.05061:0.112:rs76744376
1 1055901 rs74865318 C A . PASS AF=0.1107 ES:SE:LP:AF:ID 0.00409914:0.0198987:0.0775341:0.1107:rs74865318
1 1056269 rs71628940 C T . PASS AF=0.112 ES:SE:LP:AF:ID 0.00225845:0.0199863:0.0409586:0.112:rs71628940
1 1056348 rs66868065 G A . PASS AF=0.137 ES:SE:LP:AF:ID -0.00321239:0.0182522:0.0655015:0.137:rs66868065
1 1056715 rs7538862 C T . PASS AF=0.1441 ES:SE:LP:AF:ID 0.00529617:0.0177129:0.116509:0.1441:rs7538862