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/503b4139-888c-4c9f-b141-800e373129ee/call-vcf/inputs/562856192/upload.txt.gz --id ieu-b-35 --json /data/cromwell-executions/qc/503b4139-888c-4c9f-b141-800e373129ee/call-vcf/inputs/562856192/ieu-b-35_data.json --ref /data/cromwell-executions/qc/503b4139-888c-4c9f-b141-800e373129ee/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/503b4139-888c-4c9f-b141-800e373129ee/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-35/ieu-b-35.vcf.gz --rm_chr_prefix; 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/503b4139-888c-4c9f-b141-800e373129ee/call-ldsc/inputs/562856192/ieu-b-35.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-35/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Thu Aug 20 12:23:38 2020
Reading summary statistics from /data/cromwell-executions/qc/503b4139-888c-4c9f-b141-800e373129ee/call-ldsc/inputs/562856192/ieu-b-35.vcf.gz ...
Read summary statistics for 2414061 SNPs.
Dropped 720 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, 1091968 SNPs remain.
After merging with regression SNP LD, 1091968 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1186 (0.019)
Lambda GC: 1.2536
Mean Chi^2: 1.5037
Intercept: 1.0191 (0.0119)
Ratio: 0.0379 (0.0237)
Analysis finished at Thu Aug 20 12:25:19 2020
Total time elapsed: 1.0m:41.19sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9277,
"inflation_factor": 1.2536,
"mean_EFFECT": 0,
"n": 204402,
"n_snps": 2414067,
"n_clumped_hits": 57,
"n_p_sig": 3951,
"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": 16170,
"n_est": 197888.9141,
"ratio_se_n": 0.9839,
"mean_diff": -8.0174e-06,
"ratio_diff": 3.7083,
"sd_y_est1": 1.1883,
"sd_y_est2": 1.1692,
"r2_sum1": 0.0715,
"r2_sum2": 0.0506,
"r2_sum3": 0.0523,
"r2_sum4": 0.0489,
"ldsc_nsnp_merge_refpanel_ld": 1091968,
"ldsc_nsnp_merge_regression_ld": 1091968,
"ldsc_observed_scale_h2_beta": 0.1186,
"ldsc_observed_scale_h2_se": 0.019,
"ldsc_intercept_beta": 1.0191,
"ldsc_intercept_se": 0.0119,
"ldsc_lambda_gc": 1.2536,
"ldsc_mean_chisq": 1.5037,
"ldsc_ratio": 0.0379
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| n | FALSE |
| is_snpid_non_unique | FALSE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | TRUE |
| n_p_sig | TRUE |
| 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 | 1 | 0.9999996 | 3 | 34 | 0 | 2414065 | 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 | 8.590225e+00 | 5.659567e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.20000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.884755e+07 | 5.567668e+07 | 1.15430e+04 | 3.267132e+07 | 7.029276e+07 | 1.143525e+08 | 2.49219e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.050000e-05 | 7.267800e-03 | -2.83378e-01 | -3.753000e-03 | 2.700000e-05 | 3.817000e-03 | 2.58380e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.682000e-03 | 3.028700e-03 | 3.48800e-03 | 3.852000e-03 | 4.499000e-03 | 6.163000e-03 | 3.33850e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.626415e-01 | 2.993023e-01 | 0.00000e+00 | 1.939389e-01 | 4.501342e-01 | 7.219664e-01 | 9.99999e-01 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.626412e-01 | 2.993035e-01 | 0.00000e+00 | 1.939562e-01 | 4.501233e-01 | 7.219589e-01 | 1.00000e+00 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.600342e-01 | 2.695850e-01 | 9.98200e-03 | 1.267370e-01 | 2.958900e-01 | 5.560950e-01 | 9.89947e-01 | ▇▅▃▂▂ |
| numeric | AF_reference | 16170 | 0.9933018 | NA | NA | NA | NA | NA | 3.624849e-01 | 2.547557e-01 | 1.99700e-04 | 1.483630e-01 | 3.009190e-01 | 5.461260e-01 | 1.00000e+00 | ▇▆▅▃▂ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.044020e+05 | 0.000000e+00 | 2.04402e+05 | 2.044020e+05 | 2.044020e+05 | 2.044020e+05 | 2.04402e+05 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 752566 | rs3094315 | G | A | 0.005999 | 0.006932 | 0.3867559 | 0.3868155 | 0.825194 | 0.718251 | 204402 |
| 1 | 754192 | rs3131968 | A | G | 0.003449 | 0.007635 | 0.6515144 | 0.6514596 | 0.864553 | 0.678514 | 204402 |
| 1 | 777122 | rs2980319 | A | T | 0.005608 | 0.007389 | 0.4479371 | 0.4478729 | 0.866865 | 0.747204 | 204402 |
| 1 | 779322 | rs4040617 | A | G | -0.002483 | 0.008306 | 0.7649799 | 0.7649854 | 0.131014 | 0.226438 | 204402 |
| 1 | 780785 | rs2977612 | T | A | 0.003737 | 0.008183 | 0.6479373 | 0.6479022 | 0.867943 | 0.669329 | 204402 |
| 1 | 785050 | rs2905062 | G | A | 0.000971 | 0.008032 | 0.9037260 | 0.9037770 | 0.864035 | 0.626997 | 204402 |
| 1 | 785989 | rs2980300 | T | C | 0.000849 | 0.007974 | 0.9151810 | 0.9152086 | 0.861180 | 0.626997 | 204402 |
| 1 | 798959 | rs11240777 | G | A | 0.007985 | 0.007988 | 0.3174739 | 0.3174923 | 0.199799 | 0.409944 | 204402 |
| 1 | 990380 | rs3121561 | C | T | -0.003432 | 0.006539 | 0.5996999 | 0.5996868 | 0.281370 | 0.343450 | 204402 |
| 1 | 998501 | rs3813193 | G | C | -0.003702 | 0.006446 | 0.5658105 | 0.5657583 | 0.169037 | 0.206669 | 204402 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51165664 | rs8137951 | G | A | 0.001153 | 0.004111 | 0.7791822 | 0.7791192 | 0.297352 | 0.4063500 | 204402 |
| 22 | 51171497 | rs2301584 | G | A | 0.013630 | 0.007801 | 0.0806176 | 0.0806006 | 0.169348 | 0.2533950 | 204402 |
| 22 | 51171693 | rs756638 | G | A | 0.004070 | 0.004869 | 0.4031744 | 0.4032108 | 0.262940 | 0.3049120 | 204402 |
| 22 | 51173542 | rs4824147 | T | C | -0.014248 | 0.015460 | 0.3567196 | 0.3567351 | 0.951078 | 0.9812300 | 204402 |
| 22 | 51175626 | rs3810648 | A | G | 0.001749 | 0.008236 | 0.8318710 | 0.8318259 | 0.057197 | 0.1084270 | 204402 |
| 22 | 51178090 | rs2285395 | G | A | 0.002870 | 0.008418 | 0.7332127 | 0.7331517 | 0.054950 | 0.0666933 | 204402 |
| 22 | 51196164 | rs8136603 | A | T | 0.011109 | 0.010710 | 0.2996181 | 0.2996171 | 0.059305 | 0.1427720 | 204402 |
| 22 | 51212875 | rs2238837 | A | C | 0.009104 | 0.006847 | 0.1836230 | 0.1836391 | 0.381566 | 0.3724040 | 204402 |
| 22 | 51216564 | rs9616970 | T | C | 0.009620 | 0.009109 | 0.2909029 | 0.2909233 | 0.145196 | 0.1563500 | 204402 |
| 22 | 51229805 | rs9616985 | T | C | 0.009401 | 0.012880 | 0.4654585 | 0.4654566 | 0.092741 | 0.0730831 | 204402 |
bcf preview
1 752566 rs3094315 G A . PASS AF=0.825194 ES:SE:LP:AF:SS:ID 0.005999:0.006932:0.412563:0.825194:204402:rs3094315
1 754192 rs3131968 A G . PASS AF=0.864553 ES:SE:LP:AF:SS:ID 0.003449:0.007635:0.186076:0.864553:204402:rs3131968
1 777122 rs2980319 A T . PASS AF=0.866865 ES:SE:LP:AF:SS:ID 0.005608:0.007389:0.348783:0.866865:204402:rs2980319
1 779322 rs4040617 A G . PASS AF=0.131014 ES:SE:LP:AF:SS:ID -0.002483:0.008306:0.11635:0.131014:204402:rs4040617
1 780785 rs2977612 T A . PASS AF=0.867943 ES:SE:LP:AF:SS:ID 0.003737:0.008183:0.188467:0.867943:204402:rs2977612
1 785050 rs2905062 G A . PASS AF=0.864035 ES:SE:LP:AF:SS:ID 0.000971:0.008032:0.0439632:0.864035:204402:rs2905062
1 785989 rs2980300 T C . PASS AF=0.86118 ES:SE:LP:AF:SS:ID 0.000849:0.007974:0.038493:0.86118:204402:rs2980300
1 798959 rs11240777 G A . PASS AF=0.199799 ES:SE:LP:AF:SS:ID 0.007985:0.007988:0.498292:0.199799:204402:rs11240777
1 990380 rs3121561 C T . PASS AF=0.28137 ES:SE:LP:AF:SS:ID -0.003432:0.006539:0.222066:0.28137:204402:rs3121561
1 998501 rs3813193 G C . PASS AF=0.169037 ES:SE:LP:AF:SS:ID -0.003702:0.006446:0.247329:0.169037:204402:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.74046 ES:SE:LP:AF:SS:ID -0.008233:0.004802:1.06317:0.74046:204402:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.152467 ES:SE:LP:AF:SS:ID -0.003496:0.00579:0.262875:0.152467:204402:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.553402 ES:SE:LP:AF:SS:ID -0.004275:0.004427:0.475879:0.553402:204402:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.561538 ES:SE:LP:AF:SS:ID -0.00431:0.004181:0.519257:0.561538:204402:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.144626 ES:SE:LP:AF:SS:ID -0.002316:0.00603:0.154324:0.144626:204402:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.571215 ES:SE:LP:AF:SS:ID -0.003745:0.003972:0.461275:0.571215:204402:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.574205 ES:SE:LP:AF:SS:ID -0.00326:0.003993:0.382833:0.574205:204402:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.151064 ES:SE:LP:AF:SS:ID -0.002139:0.006045:0.140588:0.151064:204402:rs10907177
1 1021415 rs386627436 A G . PASS AF=0.725732 ES:SE:LP:AF:SS:ID -0.005044:0.004292:0.619836:0.725732:204402:rs386627436
1 1021583 rs10907178 A C . PASS AF=0.148674 ES:SE:LP:AF:SS:ID 0.001723:0.006172:0.107844:0.148674:204402:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.732681 ES:SE:LP:AF:SS:ID -0.005627:0.004682:0.639293:0.732681:204402:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.554822 ES:SE:LP:AF:SS:ID -0.004917:0.004444:0.570868:0.554822:204402:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.608737 ES:SE:LP:AF:SS:ID 0.000138:0.00482:0.0100739:0.608737:204402:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.165239 ES:SE:LP:AF:SS:ID 0.007486:0.005375:0.785946:0.165239:204402:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.154091 ES:SE:LP:AF:SS:ID 0.007538:0.006043:0.67313:0.154091:204402:rs6678318
1 1031540 rs776599533 A G . PASS AF=0.725512 ES:SE:LP:AF:SS:ID -0.000637:0.004772:0.048801:0.725512:204402:rs776599533
1 1036959 rs1162868282 T C . PASS AF=0.102723 ES:SE:LP:AF:SS:ID 0.006327:0.006385:0.492502:0.102723:204402:rs1162868282
1 1040026 rs6671356 T C . PASS AF=0.13847 ES:SE:LP:AF:SS:ID 0.007769:0.005866:0.731975:0.13847:204402:rs6671356
1 1046164 rs386627439 C T . PASS AF=0.124347 ES:SE:LP:AF:SS:ID 0.011053:0.006012:1.18058:0.124347:204402:rs386627439
1 1048955 rs4970405 A G . PASS AF=0.102509 ES:SE:LP:AF:SS:ID 0.007173:0.006176:0.609963:0.102509:204402:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.127112 ES:SE:LP:AF:SS:ID 0.010897:0.005887:1.19265:0.127112:204402:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.093117 ES:SE:LP:AF:SS:ID 0.011692:0.006822:1.06277:0.093117:204402:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.331457 ES:SE:LP:AF:SS:ID -0.007024:0.005734:0.65653:0.331457:204402:rs7548798
1 1060235 rs7540009 G A . PASS AF=0.029061 ES:SE:LP:AF:SS:ID 0.009639:0.013266:0.330251:0.029061:204402:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.103215 ES:SE:LP:AF:SS:ID 0.006014:0.006629:0.438569:0.103215:204402:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.095738 ES:SE:LP:AF:SS:ID 0.007786:0.006642:0.617857:0.095738:204402:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.095174 ES:SE:LP:AF:SS:ID 0.008659:0.00681:0.69135:0.095174:204402:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.413171 ES:SE:LP:AF:SS:ID 0.001668:0.004646:0.142922:0.413171:204402:rs11807848
1 1062015 rs1557446446 C T . PASS AF=0.029512 ES:SE:LP:AF:SS:ID 0.013989:0.0147:0.466866:0.029512:204402:rs1557446446
1 1062638 rs9442373 C A . PASS AF=0.539177 ES:SE:LP:AF:SS:ID -0.002247:0.004577:0.205183:0.539177:204402:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.720203 ES:SE:LP:AF:SS:ID -0.007708:0.006819:0.587931:0.720203:204402:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.145488 ES:SE:LP:AF:SS:ID 0.005702:0.005982:0.467921:0.145488:204402:rs2298217
1 1066403 rs10907182 T C . PASS AF=0.61435 ES:SE:LP:AF:SS:ID -0.002899:0.005084:0.245177:0.61435:204402:rs10907182
1 1071118 rs10907183 G C . PASS AF=0.623985 ES:SE:LP:AF:SS:ID -0.002887:0.005533:0.220569:0.623985:204402:rs10907183
1 1077064 rs4970357 C A . PASS AF=0.906876 ES:SE:LP:AF:SS:ID 0.007531:0.008608:0.418307:0.906876:204402:rs4970357
1 1087683 rs9442380 T C . PASS AF=0.909748 ES:SE:LP:AF:SS:ID 0.005658:0.007809:0.329125:0.909748:204402:rs9442380
1 1089262 rs4970358 A G . PASS AF=0.949983 ES:SE:LP:AF:SS:ID 0.010743:0.010019:0.5473:0.949983:204402:rs4970358
1 1094738 rs4970362 A G . PASS AF=0.642018 ES:SE:LP:AF:SS:ID -0.003388:0.005353:0.278381:0.642018:204402:rs4970362
1 1097335 rs9442385 T G . PASS AF=0.925733 ES:SE:LP:AF:SS:ID 0.006231:0.007386:0.399163:0.925733:204402:rs9442385
1 1099342 rs9660710 A C . PASS AF=0.927832 ES:SE:LP:AF:SS:ID 0.008177:0.007101:0.602933:0.927832:204402:rs9660710