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/fef6f54f-8e04-45bf-814f-90d7e04a52a2/call-vcf/inputs/-674580006/upload.txt.gz --id ieu-b-8 --json /data/cromwell-executions/qc/fef6f54f-8e04-45bf-814f-90d7e04a52a2/call-vcf/inputs/-674580006/ieu-b-8_data.json --ref /data/cromwell-executions/qc/fef6f54f-8e04-45bf-814f-90d7e04a52a2/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/fef6f54f-8e04-45bf-814f-90d7e04a52a2/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-8/ieu-b-8.vcf.gz --rm_chr_prefix --cohort_cases 15212 --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/fef6f54f-8e04-45bf-814f-90d7e04a52a2/call-ldsc/inputs/-674580006/ieu-b-8.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-8/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Fri Jun 26 15:27:17 2020
Reading summary statistics from /data/cromwell-executions/qc/fef6f54f-8e04-45bf-814f-90d7e04a52a2/call-ldsc/inputs/-674580006/ieu-b-8.vcf.gz ...
Read summary statistics for 4880479 SNPs.
Dropped 11459 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, 932586 SNPs remain.
After merging with regression SNP LD, 932586 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1042 (0.0166)
Lambda GC: 1.2631
Mean Chi^2: 1.2708
Intercept: 1.168 (0.0106)
Ratio: 0.6205 (0.0392)
Analysis finished at Fri Jun 26 15:28:13 2020
Total time elapsed: 56.19sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9391,
"inflation_factor": 1.2544,
"mean_EFFECT": 0.0002,
"n": "-Inf",
"n_snps": 4880492,
"n_clumped_hits": 3,
"n_p_sig": 118,
"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": 29052,
"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": 932586,
"ldsc_nsnp_merge_regression_ld": 932586,
"ldsc_observed_scale_h2_beta": 0.1042,
"ldsc_observed_scale_h2_se": 0.0166,
"ldsc_intercept_beta": 1.168,
"ldsc_intercept_se": 0.0106,
"ldsc_lambda_gc": 1.2631,
"ldsc_mean_chisq": 1.2708,
"ldsc_ratio": 0.6204
}
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 | TRUE |
| 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 | 4880489 | 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 | 4880492 | 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 | 8.643045e+00 | 5.873503e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.987905e+07 | 5.500345e+07 | 3.30120e+04 | 3.486021e+07 | 7.141238e+07 | 1.144980e+08 | 2.49219e+08 | ▇▇▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.621000e-04 | 1.427390e-02 | -1.20622e-01 | -7.694700e-03 | 1.820000e-05 | 7.861200e-03 | 1.72556e-01 | ▁▅▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.162850e-02 | 5.518900e-03 | 7.19060e-03 | 7.759800e-03 | 9.390500e-03 | 1.336680e-02 | 7.19243e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.633444e-01 | 2.974830e-01 | 0.00000e+00 | 1.971002e-01 | 4.500005e-01 | 7.199992e-01 | 1.00000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.633493e-01 | 2.974842e-01 | 0.00000e+00 | 1.970509e-01 | 4.502473e-01 | 7.203435e-01 | 1.00000e+00 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.044716e-01 | 2.572226e-01 | 2.80000e-03 | 8.810000e-02 | 2.228000e-01 | 4.723000e-01 | 9.90000e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 29052 | 0.9940473 | NA | NA | NA | NA | NA | NA | NA | 3.064329e-01 | 2.468090e-01 | 1.99700e-04 | 1.030350e-01 | 2.344250e-01 | 4.658550e-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 | 0.0046683 | 0.0096853 | 0.6300007 | 0.6298059 | 0.1695 | 0.315695 | NA |
| 1 | 1031973 | rs9651270 | C | T | 0.0081627 | 0.0100156 | 0.4151997 | 0.4150720 | 0.1614 | 0.310703 | NA |
| 1 | 1033596 | rs6604964 | T | C | 0.0081661 | 0.0100198 | 0.4151997 | 0.4150744 | 0.1613 | 0.311701 | NA |
| 1 | 1033670 | rs6604966 | T | C | 0.0075903 | 0.0100268 | 0.4492003 | 0.4490509 | 0.1612 | 0.315895 | NA |
| 1 | 1033680 | rs6604967 | T | A | 0.0074992 | 0.0100256 | 0.4545995 | 0.4544589 | 0.1612 | 0.311701 | NA |
| 1 | 1033994 | rs6698368 | C | T | 0.0075294 | 0.0100258 | 0.4527005 | 0.4526512 | 0.1612 | 0.311502 | NA |
| 1 | 1034200 | rs77977351 | T | C | 0.0078305 | 0.0100262 | 0.4346003 | 0.4348020 | 0.1612 | 0.311502 | NA |
| 1 | 1036860 | rs11579922 | A | C | -0.0049122 | 0.0108918 | 0.6515999 | 0.6519890 | 0.1304 | 0.282748 | NA |
| 1 | 1036959 | rs11579015 | T | C | -0.0142564 | 0.0113236 | 0.2079998 | 0.2080307 | 0.1165 | 0.156949 | NA |
| 1 | 1037303 | rs11260592 | T | C | 0.0008073 | 0.0103497 | 0.9379999 | 0.9378281 | 0.1433 | 0.282548 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 139277416 | rs435268 | G | A | 0.0154301 | 0.0073268 | 0.0352298 | 0.0352048 | 0.4886 | 0.650861 | NA |
| 23 | 139279657 | rs369604 | G | A | 0.0171617 | 0.0072473 | 0.0178698 | 0.0178845 | 0.4477 | 0.442384 | NA |
| 23 | 139279671 | rs382435 | A | G | 0.0188326 | 0.0073023 | 0.0099010 | 0.0099088 | 0.4494 | 0.435762 | NA |
| 23 | 139279881 | rs414554 | C | G | 0.0144002 | 0.0072986 | 0.0484998 | 0.0484955 | 0.4962 | 0.655894 | NA |
| 23 | 139282091 | rs426349 | C | T | 0.0160941 | 0.0073188 | 0.0278702 | 0.0278776 | 0.4862 | 0.471788 | NA |
| 23 | 139282915 | rs419307 | C | T | 0.0139442 | 0.0072475 | 0.0543400 | 0.0543537 | 0.4873 | 0.539868 | NA |
| 23 | 139284404 | rs430026 | G | A | 0.0161309 | 0.0074473 | 0.0303103 | 0.0303111 | 0.4174 | 0.308609 | NA |
| 23 | 139287243 | rs412811 | T | C | 0.0204486 | 0.0075428 | 0.0066999 | 0.0067082 | 0.4504 | 0.460397 | NA |
| 23 | 139288359 | rs367697 | C | T | 0.0137191 | 0.0072511 | 0.0585302 | 0.0584903 | 0.4839 | 0.488477 | NA |
| 23 | 139289049 | rs387193 | A | G | 0.0198387 | 0.0075490 | 0.0086000 | 0.0085888 | 0.4483 | 0.450331 | NA |
bcf preview
1 1029805 rs891281851 A G . PASS AF=0.1695 ES:SE:LP:AF:ID 0.00466833:0.00968533:0.200659:0.1695:rs891281851
1 1031973 rs9651270 C T . PASS AF=0.1614 ES:SE:LP:AF:ID 0.00816272:0.0100156:0.381743:0.1614:rs9651270
1 1033596 rs6604964 T C . PASS AF=0.1613 ES:SE:LP:AF:ID 0.0081661:0.0100198:0.381743:0.1613:rs6604964
1 1033670 rs1370950991 T C . PASS AF=0.1612 ES:SE:LP:AF:ID 0.00759027:0.0100268:0.34756:0.1612:rs1370950991
1 1033680 rs1370950991 T A . PASS AF=0.1612 ES:SE:LP:AF:ID 0.00749917:0.0100256:0.342371:0.1612:rs1370950991
1 1033994 rs6698368 C T . PASS AF=0.1612 ES:SE:LP:AF:ID 0.0075294:0.0100258:0.344189:0.1612:rs6698368
1 1034200 rs77977351 T C . PASS AF=0.1612 ES:SE:LP:AF:ID 0.00783047:0.0100262:0.36191:0.1612:rs77977351
1 1036860 rs11579922 A C . PASS AF=0.1304 ES:SE:LP:AF:ID -0.00491221:0.0108918:0.186019:0.1304:rs11579922
1 1036959 rs1162868282 T C . PASS AF=0.1165 ES:SE:LP:AF:ID -0.0142564:0.0113236:0.681937:0.1165:rs1162868282
1 1037303 rs11260592 T C . PASS AF=0.1433 ES:SE:LP:AF:ID 0.000807276:0.0103497:0.0277972:0.1433:rs11260592
1 1037313 rs11260593 A G . PASS AF=0.1484 ES:SE:LP:AF:ID 0.00318051:0.010129:0.122801:0.1484:rs11260593
1 1037367 rs11260594 G A . PASS AF=0.1433 ES:SE:LP:AF:ID 0.000672813:0.010351:0.0232833:0.1433:rs11260594
1 1038088 rs66622470 G C . PASS AF=0.1433 ES:SE:LP:AF:ID 0.000641652:0.0103492:0.0219565:0.1433:rs66622470
1 1039268 rs9329410 T C . PASS AF=0.1435 ES:SE:LP:AF:ID 0.000258532:0.0103413:0.00872961:0.1435:rs9329410
1 1039817 rs1205065516 A G . PASS AF=0.1433 ES:SE:LP:AF:ID -0.00012418:0.0103483:0.00423322:0.1433:rs1205065516
1 1040026 rs6671356 T C . PASS AF=0.1437 ES:SE:LP:AF:ID -9.29753e-05:0.0103306:0.00300702:0.1437:rs6671356
1 1040472 rs6664124 C T . PASS AF=0.1436 ES:SE:LP:AF:ID -0.000609749:0.0103347:0.0207704:0.1436:rs6664124
1 1040794 rs6687681 G A . PASS AF=0.1436 ES:SE:LP:AF:ID -0.000733819:0.0103355:0.0253502:0.1436:rs6687681
1 1040824 rs6656379 T C . PASS AF=0.1488 ES:SE:LP:AF:ID 0.00213344:0.0101111:0.0792507:0.1488:rs6656379
1 1040985 rs6697379 C G . PASS AF=0.1436 ES:SE:LP:AF:ID -0.000516762:0.0103352:0.0175478:0.1436:rs6697379
1 1041700 rs6604968 A G . PASS AF=0.1437 ES:SE:LP:AF:ID -0.000919998:0.0103371:0.032031:0.1437:rs6604968
1 1041786 rs6604969 T C . PASS AF=0.1437 ES:SE:LP:AF:ID -0.00144741:0.0103386:0.0512448:0.1437:rs6604969
1 1042483 rs12733365 C T . PASS AF=0.1436 ES:SE:LP:AF:ID -0.00119906:0.0103367:0.0422491:0.1436:rs12733365
1 1042527 rs1486993720 G C . PASS AF=0.1155 ES:SE:LP:AF:ID -0.0108693:0.0114293:0.466482:0.1155:rs1486993720
1 1042673 rs897825316 C T . PASS AF=0.1447 ES:SE:LP:AF:ID -0.0018032:0.0103632:0.0644927:0.1447:rs897825316
1 1042927 rs4970354 G T . PASS AF=0.1435 ES:SE:LP:AF:ID -0.00116821:0.0103381:0.0408632:0.1435:rs4970354
1 1043053 rs4970355 A G . PASS AF=0.1435 ES:SE:LP:AF:ID -0.00103389:0.0103389:0.0360706:0.1435:rs4970355
1 1045473 rs11586034 G A . PASS AF=0.1149 ES:SE:LP:AF:ID -0.0120084:0.0114584:0.530915:0.1149:rs11586034
1 1046073 rs11590188 C A . PASS AF=0.1417 ES:SE:LP:AF:ID -0.00311087:0.0104043:0.116509:0.1417:rs11590188
1 1046164 rs386627439 C T . PASS AF=0.1435 ES:SE:LP:AF:ID -0.000899481:0.0103389:0.0310503:0.1435:rs386627439
1 1046717 rs34820586 G C . PASS AF=0.1159 ES:SE:LP:AF:ID -0.0116034:0.0114094:0.50976:0.1159:rs34820586
1 1046861 rs12723165 G A . PASS AF=0.1159 ES:SE:LP:AF:ID -0.0118994:0.0114088:0.527244:0.1159:rs12723165
1 1047374 rs12743678 T A . PASS AF=0.1481 ES:SE:LP:AF:ID 0.00188568:0.0101381:0.0695094:0.1481:rs12743678
1 1048501 rs7518814 G A . PASS AF=0.1418 ES:SE:LP:AF:ID -0.00278747:0.010401:0.103088:0.1418:rs7518814
1 1048955 rs4970405 A G . PASS AF=0.1058 ES:SE:LP:AF:ID -0.0161195:0.0118701:0.758205:0.1058:rs4970405
1 1048989 rs4970406 A G . PASS AF=0.1177 ES:SE:LP:AF:ID -0.00989045:0.011434:0.412177:0.1177:rs4970406
1 1049083 rs4970407 C A . PASS AF=0.1168 ES:SE:LP:AF:ID -0.0113452:0.0114598:0.49174:0.1168:rs4970407
1 1049950 rs12726255 A G . PASS AF=0.1473 ES:SE:LP:AF:ID 0.00127223:0.0101779:0.0453716:0.1473:rs12726255
1 1052946 rs12755848 G T . PASS AF=0.115 ES:SE:LP:AF:ID -0.0103966:0.0114753:0.437945:0.115:rs12755848
1 1053452 rs4970409 G A . PASS AF=0.1149 ES:SE:LP:AF:ID -0.0107421:0.0114766:0.456926:0.1149:rs4970409
1 1053670 rs4970410 G A . PASS AF=0.1409 ES:SE:LP:AF:ID -0.000794728:0.0104569:0.0272882:0.1409:rs4970410
1 1053724 rs4970411 A G . PASS AF=0.1405 ES:SE:LP:AF:ID -0.000932199:0.0104741:0.032031:0.1405:rs4970411
1 1054552 rs12567697 G A . PASS AF=0.114 ES:SE:LP:AF:ID -0.0103564:0.0115199:0.433327:0.114:rs12567697
1 1054893 rs4970412 T C . PASS AF=0.1458 ES:SE:LP:AF:ID 0.00162808:0.0102395:0.0587371:0.1458:rs4970412
1 1055653 rs34808604 C G . PASS AF=0.1142 ES:SE:LP:AF:ID -0.0111456:0.0115141:0.477295:0.1142:rs34808604
1 1055797 rs76744376 A G . PASS AF=0.1155 ES:SE:LP:AF:ID -0.00945663:0.0115466:0.384155:0.1155:rs76744376
1 1055901 rs74865318 C A . PASS AF=0.1142 ES:SE:LP:AF:ID -0.0111473:0.0115159:0.477686:0.1142:rs74865318
1 1056269 rs71628940 C T . PASS AF=0.1155 ES:SE:LP:AF:ID -0.0104284:0.0115486:0.436045:0.1155:rs71628940
1 1056348 rs66868065 G A . PASS AF=0.14 ES:SE:LP:AF:ID -0.000923867:0.0104985:0.0316572:0.14:rs66868065
1 1056715 rs7538862 C T . PASS AF=0.1457 ES:SE:LP:AF:ID 0.00261453:0.0102531:0.0976163:0.1457:rs7538862