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/dafa59e0-ae23-4783-b3c5-54d4cc0ae51a/call-vcf/inputs/268670741/upload.txt.gz --id ieu-b-102 --json /data/cromwell-executions/qc/dafa59e0-ae23-4783-b3c5-54d4cc0ae51a/call-vcf/inputs/268670741/ieu-b-102_data.json --ref /data/cromwell-executions/qc/dafa59e0-ae23-4783-b3c5-54d4cc0ae51a/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/dafa59e0-ae23-4783-b3c5-54d4cc0ae51a/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-102/ieu-b-102.vcf.gz --alias alias.txt; 1.3.0",
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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/dafa59e0-ae23-4783-b3c5-54d4cc0ae51a/call-ldsc/inputs/268670741/ieu-b-102.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-102/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Wed Feb 24 02:06:20 2021
Reading summary statistics from /data/cromwell-executions/qc/dafa59e0-ae23-4783-b3c5-54d4cc0ae51a/call-ldsc/inputs/268670741/ieu-b-102.vcf.gz ...
Read summary statistics for 0 SNPs.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
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] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
Traceback (most recent call last):
File "./ldsc/ldsc.py", line 647, in <module>
sumstats.estimate_h2(args, log)
File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
args, log, args.h2)
File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.
Analysis finished at Wed Feb 24 02:07:06 2021
Total time elapsed: 46.4sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9466,
"inflation_factor": 1.3513,
"mean_EFFECT": 0.0004,
"n": "-Inf",
"n_snps": 8481297,
"n_clumped_hits": 50,
"n_p_sig": 4625,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 60160,
"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": 0,
"ldsc_nsnp_merge_regression_ld": "NA",
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": "NA",
"ldsc_intercept_se": "NA",
"ldsc_lambda_gc": "NA",
"ldsc_mean_chisq": "NA",
"ldsc_ratio": "NA"
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| n | TRUE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | NA |
| n_p_sig | TRUE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | NA |
| ldsc_intercept_beta | NA |
| 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 | 6 | 0.9999993 | 3 | 58 | 0 | 8481225 | 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 | 8481297 | 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 | 8.602345e+00 | 5.736386e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.922904e+07 | 5.628012e+07 | 828.0000 | 3.296317e+07 | 7.003405e+07 | 1.148662e+08 | 2.492297e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.211000e-04 | 1.352880e-02 | -0.1635 | -5.900000e-03 | 2.000000e-04 | 6.400000e-03 | 1.466000e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.024150e-02 | 7.196600e-03 | 0.0043 | 4.900000e-03 | 7.000000e-03 | 1.340000e-02 | 8.630000e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.508194e-01 | 3.017967e-01 | 0.0000 | 1.771002e-01 | 4.330001e-01 | 7.119000e-01 | 1.000000e+00 | ▇▆▅▅▅ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.507946e-01 | 3.018251e-01 | 0.0000 | 1.773893e-01 | 4.328560e-01 | 7.117065e-01 | 1.000000e+00 | ▇▆▅▅▅ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.368834e-01 | 2.610631e-01 | 0.0050 | 2.900000e-02 | 1.240000e-01 | 3.767000e-01 | 9.950000e-01 | ▇▂▂▁▁ |
| numeric | AF_reference | 60160 | 0.9929067 | NA | NA | NA | NA | NA | NA | NA | 2.369228e-01 | 2.526886e-01 | 0.0000 | 2.975240e-02 | 1.405750e-01 | 3.730030e-01 | 1.000000e+00 | ▇▂▂▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 714277 | rs138660747 | C | A | -0.0050 | 0.0380 | 0.8960000 | 0.8953173 | 0.0074 | 0.0011981 | NA |
| 1 | 734349 | rs141242758 | T | C | 0.0075 | 0.0070 | 0.2900000 | 0.2839768 | 0.1195 | 0.1525560 | NA |
| 1 | 753541 | rs2073813 | G | A | 0.0062 | 0.0064 | 0.3352000 | 0.3326699 | 0.1328 | 0.3019170 | NA |
| 1 | 754182 | rs3131969 | A | G | -0.0068 | 0.0064 | 0.2890999 | 0.2880088 | 0.8661 | 0.6785140 | NA |
| 1 | 754192 | rs3131968 | A | G | -0.0069 | 0.0064 | 0.2789003 | 0.2809780 | 0.8662 | 0.6785140 | NA |
| 1 | 754334 | rs3131967 | T | C | -0.0077 | 0.0064 | 0.2326998 | 0.2289280 | 0.8610 | 0.6843050 | NA |
| 1 | 755890 | rs3115858 | A | T | -0.0063 | 0.0065 | 0.3317997 | 0.3324301 | 0.8676 | 0.7513980 | NA |
| 1 | 756604 | rs3131962 | A | G | -0.0067 | 0.0064 | 0.2963002 | 0.2951572 | 0.8628 | 0.7480030 | NA |
| 1 | 757640 | rs3115853 | G | A | -0.0058 | 0.0064 | 0.3703002 | 0.3648035 | 0.8639 | 0.6401760 | NA |
| 1 | 757734 | rs4951929 | C | T | -0.0074 | 0.0065 | 0.2547998 | 0.2549278 | 0.8691 | 0.7482030 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51217556 | rs187294336 | C | T | -0.0398 | 0.0268 | 0.1382000 | 0.1375241 | 0.0089 | 0.0023962 | NA |
| 22 | 51217954 | rs9616974 | G | A | -0.0081 | 0.0087 | 0.3493003 | 0.3518357 | 0.0722 | 0.0621006 | NA |
| 22 | 51218224 | rs9616975 | C | A | -0.0081 | 0.0087 | 0.3495997 | 0.3518357 | 0.0722 | 0.0619010 | NA |
| 22 | 51219006 | rs28729663 | G | A | -0.0054 | 0.0066 | 0.4153001 | 0.4132534 | 0.1440 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | -0.0087 | 0.0087 | 0.3192001 | 0.3173105 | 0.0726 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | -0.0102 | 0.0114 | 0.3735003 | 0.3709278 | 0.0430 | 0.0473243 | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0078 | 0.0087 | 0.3674997 | 0.3699582 | 0.0724 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0015 | 0.0101 | 0.8799000 | 0.8819365 | 0.0537 | 0.0880591 | NA |
| 22 | 51222766 | rs139240849 | G | A | -0.0043 | 0.0108 | 0.6866003 | 0.6905210 | 0.0509 | 0.0321486 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0075 | 0.0087 | 0.3887998 | 0.3886496 | 0.0730 | 0.0730831 | NA |
bcf preview
1 714277 rs138660747 C A . PASS AF=0.0074 ES:SE:LP:AF:ID -0.005:0.038:0.047692:0.0074:rs138660747
1 734349 rs141242758 T C . PASS AF=0.1195 ES:SE:LP:AF:ID 0.0075:0.007:0.537602:0.1195:rs141242758
1 753541 rs1388595942 G A . PASS AF=0.1328 ES:SE:LP:AF:ID 0.0062:0.0064:0.474696:0.1328:rs1388595942
1 754182 rs3131969 A G . PASS AF=0.8661 ES:SE:LP:AF:ID -0.0068:0.0064:0.538952:0.8661:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8662 ES:SE:LP:AF:ID -0.0069:0.0064:0.554551:0.8662:rs3131968
1 754334 rs3131967 T C . PASS AF=0.861 ES:SE:LP:AF:ID -0.0077:0.0064:0.633204:0.861:rs3131967
1 755890 rs1280367067 A T . PASS AF=0.8676 ES:SE:LP:AF:ID -0.0063:0.0065:0.479124:0.8676:rs1280367067
1 756604 rs3131962 A G . PASS AF=0.8628 ES:SE:LP:AF:ID -0.0067:0.0064:0.528268:0.8628:rs3131962
1 757640 rs3115853 G A . PASS AF=0.8639 ES:SE:LP:AF:ID -0.0058:0.0064:0.431446:0.8639:rs3115853
1 757734 rs1557551770 C T . PASS AF=0.8691 ES:SE:LP:AF:ID -0.0074:0.0065:0.593801:0.8691:rs1557551770
1 757936 rs1360886751 C A . PASS AF=0.8689 ES:SE:LP:AF:ID -0.0075:0.0065:0.610302:0.8689:rs1360886751
1 758144 rs3131956 A G . PASS AF=0.8652 ES:SE:LP:AF:ID -0.006:0.0065:0.450751:0.8652:rs3131956
1 758626 rs3131954 C T . PASS AF=0.8695 ES:SE:LP:AF:ID -0.0066:0.0065:0.500313:0.8695:rs3131954
1 761732 rs2286139 C T . PASS AF=0.8512 ES:SE:LP:AF:ID -0.0073:0.0064:0.595851:0.8512:rs2286139
1 761752 rs1057213 C T . PASS AF=0.8669 ES:SE:LP:AF:ID -0.0059:0.0066:0.430626:0.8669:rs1057213
1 762273 rs3115849 G A . PASS AF=0.8603 ES:SE:LP:AF:ID -0.0076:0.0065:0.608712:0.8603:rs3115849
1 764191 rs7515915 T G . PASS AF=0.1266 ES:SE:LP:AF:ID 0.0041:0.0067:0.264641:0.1266:rs7515915
1 766007 rs61768174 A C . PASS AF=0.1057 ES:SE:LP:AF:ID 0.0085:0.0073:0.618704:0.1057:rs61768174
1 768253 rs2977608 A C . PASS AF=0.7566 ES:SE:LP:AF:ID -0.0053:0.0052:0.511449:0.7566:rs2977608
1 768448 rs12562034 G A . PASS AF=0.106 ES:SE:LP:AF:ID 0.0012:0.0072:0.059932:0.106:rs12562034
1 769223 rs60320384 C G . PASS AF=0.1285 ES:SE:LP:AF:ID 0.0068:0.0066:0.526367:0.1285:rs60320384
1 769963 rs7518545 G A . PASS AF=0.1048 ES:SE:LP:AF:ID 0.0015:0.0073:0.075204:0.1048:rs7518545
1 771823 rs2977605 T C . PASS AF=0.8693 ES:SE:LP:AF:ID -0.0081:0.0065:0.66736:0.8693:rs2977605
1 771967 rs59066358 G A . PASS AF=0.1289 ES:SE:LP:AF:ID 0.0069:0.0066:0.530325:0.1289:rs59066358
1 772755 rs2905039 A C . PASS AF=0.8693 ES:SE:LP:AF:ID -0.0081:0.0065:0.663941:0.8693:rs2905039
1 773503 rs183122171 C T . PASS AF=0.0129 ES:SE:LP:AF:ID -0.0102:0.0374:0.105407:0.0129:rs183122171
1 775181 rs61768182 A G . PASS AF=0.1298 ES:SE:LP:AF:ID 0.0059:0.0066:0.43735:0.1298:rs61768182
1 776556 rs151160018 C T . PASS AF=0.0088 ES:SE:LP:AF:ID -0.0341:0.026:0.720789:0.0088:rs151160018
1 777122 rs2980319 A T . PASS AF=0.8708 ES:SE:LP:AF:ID -0.0071:0.0065:0.554085:0.8708:rs2980319
1 777232 rs112618790 C T . PASS AF=0.0916 ES:SE:LP:AF:ID 0.0054:0.0079:0.302683:0.0916:rs112618790
1 778745 rs1055606 A G . PASS AF=0.1275 ES:SE:LP:AF:ID 0.0059:0.0066:0.431681:0.1275:rs1055606
1 779322 rs4040617 A G . PASS AF=0.1279 ES:SE:LP:AF:ID 0.0058:0.0066:0.423774:0.1279:rs4040617
1 780785 rs2977612 T A . PASS AF=0.8653 ES:SE:LP:AF:ID -0.0068:0.0065:0.53432:0.8653:rs2977612
1 781845 rs1391043716 A G . PASS AF=0.1006 ES:SE:LP:AF:ID 0.0072:0.0075:0.477165:0.1006:rs1391043716
1 782981 rs6594026 C T . PASS AF=0.135 ES:SE:LP:AF:ID 0.0046:0.0065:0.322849:0.135:rs6594026
1 783318 rs6686696 A G . PASS AF=0.1258 ES:SE:LP:AF:ID 0.0049:0.0067:0.328272:0.1258:rs6686696
1 785050 rs2905062 G A . PASS AF=0.8647 ES:SE:LP:AF:ID -0.0065:0.0065:0.504594:0.8647:rs2905062
1 785989 rs2980300 T C . PASS AF=0.8622 ES:SE:LP:AF:ID -0.0059:0.0065:0.439854:0.8622:rs2980300
1 786995 rs61768202 G A . PASS AF=0.1278 ES:SE:LP:AF:ID 0.0051:0.0067:0.349595:0.1278:rs61768202
1 787399 rs2905055 G T . PASS AF=0.8544 ES:SE:LP:AF:ID -0.0086:0.0065:0.732594:0.8544:rs2905055
1 787606 rs3863622 G T . PASS AF=0.1274 ES:SE:LP:AF:ID 0.0055:0.0067:0.389021:0.1274:rs3863622
1 787685 rs2905054 G T . PASS AF=0.8532 ES:SE:LP:AF:ID -0.0053:0.0065:0.379864:0.8532:rs2905054
1 787844 rs2905053 C T . PASS AF=0.8663 ES:SE:LP:AF:ID -0.0063:0.0065:0.475215:0.8663:rs2905053
1 790465 rs61768207 G A . PASS AF=0.0977 ES:SE:LP:AF:ID 0.0096:0.0077:0.676129:0.0977:rs61768207
1 791191 rs111818025 G A . PASS AF=0.1263 ES:SE:LP:AF:ID 0.0064:0.0067:0.465086:0.1263:rs111818025
1 791853 rs6684487 G A . PASS AF=0.0912 ES:SE:LP:AF:ID 0.0085:0.0079:0.548214:0.0912:rs6684487
1 795222 rs12131377 C G . PASS AF=0.0792 ES:SE:LP:AF:ID 0.0041:0.0084:0.199971:0.0792:rs12131377
1 796375 rs1338880683 T C . PASS AF=0.123 ES:SE:LP:AF:ID 0.0091:0.0069:0.730721:0.123:rs1338880683
1 797281 rs1347695410 G C . PASS AF=0.0786 ES:SE:LP:AF:ID 0.0047:0.0085:0.237171:0.0786:rs1347695410
1 797325 rs1338750774 T C . PASS AF=0.0791 ES:SE:LP:AF:ID 0.0048:0.0084:0.245575:0.0791:rs1338750774