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-1106/ieu-a-1106.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-1106/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 11:29:52 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1106/ieu-a-1106.vcf.gz ...
Read summary statistics for 2195189 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, 1071297 SNPs remain.
After merging with regression SNP LD, 1071297 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1886 (0.0508)
Lambda GC: 1.0291
Mean Chi^2: 1.0829
Intercept: 0.9588 (0.0068)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 11:30:20 2020
Total time elapsed: 28.17sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9015,
"inflation_factor": 1.0475,
"mean_EFFECT": 0,
"n": 33152,
"n_snps": 2195189,
"n_clumped_hits": 5,
"n_p_sig": 255,
"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": 626,
"n_miss_AF_reference": 18533,
"n_est": 32909.9666,
"ratio_se_n": 0.9963,
"mean_diff": 0,
"ratio_diff": 7.5303,
"sd_y_est1": 0.2419,
"sd_y_est2": 0.2411,
"r2_sum1": 0.0022,
"r2_sum2": 0.0379,
"r2_sum3": 0.0381,
"r2_sum4": 0.033,
"ldsc_nsnp_merge_refpanel_ld": 1071297,
"ldsc_nsnp_merge_regression_ld": 1071297,
"ldsc_observed_scale_h2_beta": 0.1886,
"ldsc_observed_scale_h2_se": 0.0508,
"ldsc_intercept_beta": 0.9588,
"ldsc_intercept_se": 0.0068,
"ldsc_lambda_gc": 1.0291,
"ldsc_mean_chisq": 1.0829,
"ldsc_ratio": -0.497
}
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 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 | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 0 | 1.0000000 | 3 | 42 | 0 | 2195189 | 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 | 8.602495e+00 | 5.665355e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.873911e+07 | 5.574298e+07 | 1.1523e+04 | 3.244615e+07 | 7.008364e+07 | 1.143869e+08 | 2.491808e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.170000e-05 | 2.738900e-03 | -7.2000e-02 | -1.600000e-03 | 0.000000e+00 | 1.700000e-03 | 9.000000e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.535100e-03 | 8.487000e-04 | 1.8000e-03 | 1.900000e-03 | 2.200000e-03 | 2.900000e-03 | 5.200000e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.955961e-01 | 2.897844e-01 | 0.0000e+00 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.930424e-01 | 2.906769e-01 | 0.0000e+00 | 2.410310e-01 | 4.938422e-01 | 7.470129e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 626 | 0.9997148 | NA | NA | NA | NA | NA | 3.803936e-01 | 2.568628e-01 | 4.0000e-03 | 1.590000e-01 | 3.230000e-01 | 5.730000e-01 | 9.960000e-01 | ▇▆▅▃▂ |
| numeric | AF_reference | 18533 | 0.9915574 | NA | NA | NA | NA | NA | 3.802387e-01 | 2.429228e-01 | 1.9970e-04 | 1.767170e-01 | 3.286740e-01 | 5.591050e-01 | 1.000000e+00 | ▇▇▅▃▂ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.272360e+04 | 1.122257e+03 | 8.8710e+03 | 3.313400e+04 | 3.314400e+04 | 3.314500e+04 | 3.315200e+04 | ▁▁▁▁▇ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 721290 | rs12565286 | G | C | -0.0047 | 0.0058 | 0.4199997 | 0.4177420 | 0.032 | 0.0371406 | 25341 |
| 1 | 723819 | rs11804171 | T | A | -0.0048 | 0.0058 | 0.4100001 | 0.4079049 | 0.034 | 0.1345850 | 25341 |
| 1 | 723891 | rs2977670 | G | C | 0.0032 | 0.0055 | 0.5700002 | 0.5606892 | 0.934 | 0.7799520 | 25584 |
| 1 | 752566 | rs3094315 | G | A | -0.0036 | 0.0028 | 0.1800002 | 0.1985428 | 0.835 | 0.7182510 | 31289 |
| 1 | 754192 | rs3131968 | A | G | -0.0066 | 0.0031 | 0.0299999 | 0.0332516 | 0.885 | 0.6785140 | 29647 |
| 1 | 765948 | rs2519016 | C | T | -0.0180 | 0.0260 | 0.4799997 | 0.4887441 | 0.950 | NA | 12440 |
| 1 | 768448 | rs12562034 | G | A | -0.0042 | 0.0062 | 0.5099998 | 0.4981399 | 0.102 | 0.1918930 | 23352 |
| 1 | 775659 | rs2905035 | A | G | -0.0067 | 0.0030 | 0.0259998 | 0.0255270 | 0.885 | 0.7450080 | 30445 |
| 1 | 776546 | rs12124819 | A | G | -0.0095 | 0.0043 | 0.0250000 | 0.0271536 | 0.288 | 0.0756789 | 28057 |
| 1 | 777122 | rs2980319 | A | T | -0.0066 | 0.0030 | 0.0259998 | 0.0278069 | 0.866 | 0.7472040 | 31289 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51212875 | rs2238837 | A | C | -0.0041 | 0.0026 | 0.1100001 | 0.1148132 | 0.385 | 0.3724040 | 28560 |
| 22 | 51216564 | rs9616970 | T | C | -0.0015 | 0.0040 | 0.6999999 | 0.7076605 | 0.146 | 0.1563500 | 28560 |
| 22 | 51217134 | rs117417021 | A | G | -0.0045 | 0.0027 | 0.0879995 | 0.0955807 | 0.415 | 0.2671730 | 28560 |
| 22 | 51222100 | rs114553188 | G | T | -0.0013 | 0.0056 | 0.8200001 | 0.8164271 | 0.062 | 0.0880591 | 24343 |
| 22 | 51223637 | rs375798137 | G | A | -0.0021 | 0.0054 | 0.6999999 | 0.6973583 | 0.062 | 0.0788738 | 25329 |
| 22 | 51229805 | rs9616985 | T | C | -0.0012 | 0.0060 | 0.8400000 | 0.8414806 | 0.092 | 0.0730831 | 24086 |
| 23 | 35921591 | rs2204667 | C | G | -0.0014 | 0.0026 | 0.5700002 | 0.5902585 | 0.162 | NA | 33136 |
| 23 | 51666786 | rs14115 | A | G | 0.0008 | 0.0040 | 0.8400000 | 0.8414806 | 0.027 | NA | 31254 |
| 23 | 70163799 | rs1626496 | A | C | -0.0056 | 0.0037 | 0.1299999 | 0.1301493 | 0.069 | NA | 33145 |
| 23 | 118495837 | rs12882977 | G | A | 0.0023 | 0.0018 | 0.2300001 | 0.2013278 | 0.508 | 0.2307280 | 33145 |
bcf preview
1 721290 rs12565286 G C . PASS AF=0.032 ES:SE:LP:AF:SS:ID -0.0047:0.0058:0.376751:0.032:25341:rs12565286
1 723819 rs11804171 T A . PASS AF=0.034 ES:SE:LP:AF:SS:ID -0.0048:0.0058:0.387216:0.034:25341:rs11804171
1 723891 rs2977670 G C . PASS AF=0.934 ES:SE:LP:AF:SS:ID 0.0032:0.0055:0.244125:0.934:25584:rs2977670
1 752566 rs3094315 G A . PASS AF=0.835 ES:SE:LP:AF:SS:ID -0.0036:0.0028:0.744727:0.835:31289:rs3094315
1 754192 rs3131968 A G . PASS AF=0.885 ES:SE:LP:AF:SS:ID -0.0066:0.0031:1.52288:0.885:29647:rs3131968
1 765948 rs2519016 C T . PASS AF=0.95 ES:SE:LP:AF:SS:ID -0.018:0.026:0.318759:0.95:12440:rs2519016
1 768448 rs12562034 G A . PASS AF=0.102 ES:SE:LP:AF:SS:ID -0.0042:0.0062:0.29243:0.102:23352:rs12562034
1 775659 rs2905035 A G . PASS AF=0.885 ES:SE:LP:AF:SS:ID -0.0067:0.003:1.58503:0.885:30445:rs2905035
1 776546 rs12124819 A G . PASS AF=0.288 ES:SE:LP:AF:SS:ID -0.0095:0.0043:1.60206:0.288:28057:rs12124819
1 777122 rs2980319 A T . PASS AF=0.866 ES:SE:LP:AF:SS:ID -0.0066:0.003:1.58503:0.866:31289:rs2980319
1 779322 rs4040617 A G . PASS AF=0.133 ES:SE:LP:AF:SS:ID 0.0047:0.0032:0.886057:0.133:29060:rs4040617
1 780785 rs2977612 T A . PASS AF=0.877 ES:SE:LP:AF:SS:ID -0.0063:0.0031:1.40894:0.877:30445:rs2977612
1 785050 rs2905062 G A . PASS AF=0.868 ES:SE:LP:AF:SS:ID -0.0061:0.0031:1.35655:0.868:31289:rs2905062
1 785989 rs2980300 T C . PASS AF=0.868 ES:SE:LP:AF:SS:ID -0.0068:0.003:1.63827:0.868:31289:rs2980300
1 798026 rs4951864 C T . PASS AF=0.9 ES:SE:LP:AF:SS:ID -0.0025:0.0055:0.180456:0.9:26584:rs4951864
1 798801 rs12132517 G A . PASS AF=0.108 ES:SE:LP:AF:SS:ID 0.0024:0.0056:0.173925:0.108:25740:rs12132517
1 798959 rs11240777 G A . PASS AF=0.219 ES:SE:LP:AF:SS:ID 0.0046:0.0029:0.958607:0.219:31289:rs11240777
1 846864 rs950122 G C . PASS AF=0.138 ES:SE:LP:AF:SS:ID 0.011:0.0064:1.10791:0.138:20908:rs950122
1 882033 rs2272756 G A . PASS AF=0.23 ES:SE:LP:AF:SS:ID 0.0038:0.0044:0.408935:0.23:28058:rs2272756
1 962210 rs3128126 A G . PASS AF=0.415 ES:SE:LP:AF:SS:ID -0.0002:0.0036:0.0177288:0.415:28057:rs3128126
1 990380 rs3121561 C T . PASS AF=0.254 ES:SE:LP:AF:SS:ID -0.0007:0.0038:0.0655015:0.254:28926:rs3121561
1 998501 rs3813193 G C . PASS AF=0.146 ES:SE:LP:AF:SS:ID 0.0038:0.0039:0.49485:0.146:33143:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.734 ES:SE:LP:AF:SS:ID 0.0022:0.0023:0.455932:0.734:31289:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.124 ES:SE:LP:AF:SS:ID 0.0038:0.0039:0.481486:0.124:31289:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.587 ES:SE:LP:AF:SS:ID 0.0004:0.0021:0.0655015:0.587:33143:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.571 ES:SE:LP:AF:SS:ID -0.0002:0.0021:0.0362122:0.571:33142:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.124 ES:SE:LP:AF:SS:ID 0.0036:0.0037:0.49485:0.124:33142:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.608 ES:SE:LP:AF:SS:ID -0.0002:0.002:0.0409586:0.608:33145:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.588 ES:SE:LP:AF:SS:ID -0.0004:0.002:0.0705811:0.588:33141:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.137 ES:SE:LP:AF:SS:ID 0.0026:0.0039:0.30103:0.137:33144:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.735 ES:SE:LP:AF:SS:ID 0.0008:0.0023:0.136677:0.735:33143:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.112 ES:SE:LP:AF:SS:ID 0.0026:0.0036:0.327902:0.112:33144:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.726 ES:SE:LP:AF:SS:ID 0.0015:0.0026:0.259637:0.726:33143:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.585 ES:SE:LP:AF:SS:ID 0.0001:0.0023:0.00877392:0.585:33141:rs6701114
1 1025301 rs9442400 T C . PASS AF=0.952 ES:SE:LP:AF:SS:ID -0.0008:0.0091:0.0315171:0.952:19023:rs9442400
1 1026707 rs4074137 C A . PASS AF=0.623 ES:SE:LP:AF:SS:ID -0.0008:0.003:0.107905:0.623:29913:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.133 ES:SE:LP:AF:SS:ID 0.0012:0.0035:0.142668:0.133:33144:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.134 ES:SE:LP:AF:SS:ID 0.0017:0.0037:0.187087:0.134:30515:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.717 ES:SE:LP:AF:SS:ID 0.0002:0.0032:0.0177288:0.717:28926:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.046 ES:SE:LP:AF:SS:ID 0.0016:0.0039:0.161151:0.046:33144:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.115 ES:SE:LP:AF:SS:ID -0.0002:0.0036:0.0177288:0.115:33144:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.062 ES:SE:LP:AF:SS:ID 0.0016:0.0037:0.187087:0.062:33144:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.088 ES:SE:LP:AF:SS:ID 0.0015:0.0038:0.154902:0.088:33144:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.115 ES:SE:LP:AF:SS:ID 0.0002:0.0039:0.0222764:0.115:33140:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.093 ES:SE:LP:AF:SS:ID 0.003:0.0041:0.346787:0.093:32300:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.314 ES:SE:LP:AF:SS:ID -0.0005:0.0035:0.0457575:0.314:27028:rs7548798
1 1060608 rs17160824 G A . PASS AF=0.097 ES:SE:LP:AF:SS:ID 0.0031:0.004:0.356547:0.097:33143:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.051 ES:SE:LP:AF:SS:ID 0.0028:0.004:0.318759:0.051:33144:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.055 ES:SE:LP:AF:SS:ID 0.003:0.0041:0.327902:0.055:32300:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.389 ES:SE:LP:AF:SS:ID 0.0006:0.003:0.0705811:0.389:33144:rs11807848