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/63bb28fa-a561-450c-bcb0-16805f8d742e/call-vcf/inputs/562856196/upload.txt.gz --id ieu-b-39 --json /data/cromwell-executions/qc/63bb28fa-a561-450c-bcb0-16805f8d742e/call-vcf/inputs/562856196/ieu-b-39_data.json --ref /data/cromwell-executions/qc/63bb28fa-a561-450c-bcb0-16805f8d742e/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/63bb28fa-a561-450c-bcb0-16805f8d742e/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-39/ieu-b-39.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/63bb28fa-a561-450c-bcb0-16805f8d742e/call-ldsc/inputs/562856196/ieu-b-39.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-39/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Thu Aug 20 18:37:16 2020
Reading summary statistics from /data/cromwell-executions/qc/63bb28fa-a561-450c-bcb0-16805f8d742e/call-ldsc/inputs/562856196/ieu-b-39.vcf.gz ...
Read summary statistics for 7160603 SNPs.
Dropped 19197 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, 1205340 SNPs remain.
After merging with regression SNP LD, 1205340 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1284 (0.0049)
Lambda GC: 2.0306
Mean Chi^2: 3.118
Intercept: 1.1571 (0.0207)
Ratio: 0.0742 (0.0098)
Analysis finished at Thu Aug 20 18:40:22 2020
Total time elapsed: 3.0m:6.08sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9405,
"inflation_factor": 1.8727,
"mean_EFFECT": -0.0004,
"n": 757569,
"n_snps": 7160619,
"n_clumped_hits": 460,
"n_p_sig": 83836,
"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": 45357,
"n_est": 756172.8539,
"ratio_se_n": 0.9991,
"mean_diff": 0.0004,
"ratio_diff": 320791.8942,
"sd_y_est1": 10.7664,
"sd_y_est2": 10.7565,
"r2_sum1": 5.5471,
"r2_sum2": 0.0479,
"r2_sum3": 0.0479,
"r2_sum4": 0.0477,
"ldsc_nsnp_merge_refpanel_ld": 1205340,
"ldsc_nsnp_merge_regression_ld": 1205340,
"ldsc_observed_scale_h2_beta": 0.1284,
"ldsc_observed_scale_h2_se": 0.0049,
"ldsc_intercept_beta": 1.1571,
"ldsc_intercept_se": 0.0207,
"ldsc_lambda_gc": 2.0306,
"ldsc_mean_chisq": 3.118,
"ldsc_ratio": 0.0742
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| n | FALSE |
| is_snpid_non_unique | TRUE |
| 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 | TRUE |
| 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 | 58 | 0 | 7160610 | 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 | 8.600707e+00 | 5.729117e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.901202e+07 | 5.621918e+07 | 6.68900e+03 | 3.266366e+07 | 6.973271e+07 | 1.147094e+08 | 2.492183e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -4.247000e-04 | 5.261330e-02 | -8.38500e-01 | -2.650000e-02 | -2.000000e-04 | 2.600000e-02 | 7.360000e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.302250e-02 | 1.832200e-02 | 1.66000e-02 | 1.910000e-02 | 2.500000e-02 | 4.140000e-02 | 1.220000e-01 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.986060e-01 | 3.121293e-01 | 0.00000e+00 | 1.024000e-01 | 3.560000e-01 | 6.665995e-01 | 1.000000e+00 | ▇▅▃▃▃ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.986069e-01 | 3.121305e-01 | 0.00000e+00 | 1.023989e-01 | 3.559671e-01 | 6.665767e-01 | 1.000000e+00 | ▇▅▃▃▃ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.670224e-01 | 2.606937e-01 | 1.00000e-02 | 5.170000e-02 | 1.678000e-01 | 4.208000e-01 | 9.900000e-01 | ▇▃▂▁▁ |
| numeric | AF_reference | 45357 | 0.9936658 | NA | NA | NA | NA | NA | 2.662075e-01 | 2.523196e-01 | 1.99700e-04 | 5.970450e-02 | 1.801120e-01 | 4.141370e-01 | 1.000000e+00 | ▇▃▂▁▁ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.285855e+05 | 3.321851e+04 | 2.65357e+05 | 7.210080e+05 | 7.422390e+05 | 7.501990e+05 | 7.575690e+05 | ▁▁▁▁▇ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 752566 | rs3094315 | G | A | 0.0605 | 0.0254 | 0.0171400 | 0.0172241 | 0.8365 | 0.718251 | 656466 |
| 1 | 752721 | rs3131972 | A | G | 0.0567 | 0.0254 | 0.0258202 | 0.0255962 | 0.8322 | 0.653355 | 645396 |
| 1 | 753405 | rs3115860 | C | A | 0.0410 | 0.0274 | 0.1339001 | 0.1345624 | 0.8641 | 0.751797 | 642593 |
| 1 | 753541 | rs2073813 | G | A | -0.0450 | 0.0276 | 0.1028000 | 0.1030096 | 0.1355 | 0.301917 | 634735 |
| 1 | 754182 | rs3131969 | A | G | 0.0435 | 0.0274 | 0.1123999 | 0.1123788 | 0.8625 | 0.678514 | 635438 |
| 1 | 754192 | rs3131968 | A | G | 0.0423 | 0.0274 | 0.1227001 | 0.1226379 | 0.8626 | 0.678514 | 635121 |
| 1 | 755890 | rs3115858 | A | T | 0.0430 | 0.0274 | 0.1163001 | 0.1165680 | 0.8642 | 0.751398 | 641017 |
| 1 | 757734 | rs4951929 | C | T | 0.0424 | 0.0274 | 0.1217001 | 0.1217559 | 0.8653 | 0.748203 | 644609 |
| 1 | 757936 | rs4951862 | C | A | 0.0429 | 0.0274 | 0.1175000 | 0.1174204 | 0.8652 | 0.748802 | 643917 |
| 1 | 758144 | rs3131956 | A | G | 0.0404 | 0.0271 | 0.1354001 | 0.1360206 | 0.8587 | 0.740216 | 642929 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51172460 | rs5770824 | T | C | 0.0237 | 0.0637 | 0.7093997 | 0.7098508 | 0.0225 | 0.0684904 | 640487 |
| 22 | 51173542 | rs4824147 | T | C | 0.0566 | 0.0407 | 0.1649001 | 0.1643275 | 0.9412 | 0.9812300 | 639581 |
| 22 | 51174331 | rs5770825 | C | G | 0.0162 | 0.0230 | 0.4831000 | 0.4812162 | 0.7632 | 0.7917330 | 592064 |
| 22 | 51174662 | rs1858748 | T | C | 0.0205 | 0.0219 | 0.3509999 | 0.3492356 | 0.7322 | 0.7328270 | 602743 |
| 22 | 51175626 | rs3810648 | A | G | 0.0369 | 0.0366 | 0.3140003 | 0.3133600 | 0.0613 | 0.1084270 | 743317 |
| 22 | 51177257 | rs73174437 | C | T | 0.0223 | 0.0517 | 0.6659996 | 0.6662251 | 0.0350 | 0.0091853 | 652005 |
| 22 | 51178090 | rs2285395 | G | A | 0.0328 | 0.0392 | 0.4028998 | 0.4027417 | 0.0548 | 0.0666933 | 722761 |
| 22 | 51178756 | rs141844965 | A | T | -0.0688 | 0.0924 | 0.4564004 | 0.4565204 | 0.0116 | 0.0059904 | 597850 |
| 22 | 51180501 | rs5770999 | T | C | 0.0203 | 0.0214 | 0.3445998 | 0.3428250 | 0.7072 | 0.6369810 | 598471 |
| 22 | 51182399 | rs56238942 | A | G | 0.0017 | 0.0359 | 0.9612999 | 0.9622313 | 0.0773 | 0.0992412 | 623205 |
bcf preview
1 752566 rs3094315 G A . PASS AF=0.8365 ES:SE:LP:AF:SS:ID 0.0605:0.0254:1.76599:0.8365:656466:rs3094315
1 752721 rs3131972 A G . PASS AF=0.8322 ES:SE:LP:AF:SS:ID 0.0567:0.0254:1.58804:0.8322:645396:rs3131972
1 753405 rs3115860 C A . PASS AF=0.8641 ES:SE:LP:AF:SS:ID 0.041:0.0274:0.873219:0.8641:642593:rs3115860
1 753541 rs1388595942 G A . PASS AF=0.1355 ES:SE:LP:AF:SS:ID -0.045:0.0276:0.988007:0.1355:634735:rs1388595942
1 754182 rs3131969 A G . PASS AF=0.8625 ES:SE:LP:AF:SS:ID 0.0435:0.0274:0.949234:0.8625:635438:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8626 ES:SE:LP:AF:SS:ID 0.0423:0.0274:0.911155:0.8626:635121:rs3131968
1 755890 rs1280367067 A T . PASS AF=0.8642 ES:SE:LP:AF:SS:ID 0.043:0.0274:0.93442:0.8642:641017:rs1280367067
1 757734 rs1557551770 C T . PASS AF=0.8653 ES:SE:LP:AF:SS:ID 0.0424:0.0274:0.914709:0.8653:644609:rs1557551770
1 757936 rs1360886751 C A . PASS AF=0.8652 ES:SE:LP:AF:SS:ID 0.0429:0.0274:0.929962:0.8652:643917:rs1360886751
1 758144 rs3131956 A G . PASS AF=0.8587 ES:SE:LP:AF:SS:ID 0.0404:0.0271:0.868381:0.8587:642929:rs3131956
1 758626 rs3131954 C T . PASS AF=0.8655 ES:SE:LP:AF:SS:ID 0.0421:0.0275:0.901702:0.8655:640038:rs3131954
1 798959 rs11240777 G A . PASS AF=0.2105 ES:SE:LP:AF:SS:ID -0.0037:0.0232:0.0590853:0.2105:628069:rs11240777
1 879687 rs2839 T C . PASS AF=0.9459 ES:SE:LP:AF:SS:ID 0.134:0.0415:2.90553:0.9459:641223:rs2839
1 880238 rs3748592 A G . PASS AF=0.946 ES:SE:LP:AF:SS:ID 0.1347:0.0415:2.93517:0.946:642237:rs3748592
1 882803 rs2340582 A G . PASS AF=0.9459 ES:SE:LP:AF:SS:ID 0.1339:0.0413:2.92118:0.9459:645161:rs2340582
1 884815 rs1235102225 A G . PASS AF=0.9457 ES:SE:LP:AF:SS:ID 0.1348:0.0412:2.96819:0.9457:646681:rs1235102225
1 885676 rs4970377 C A . PASS AF=0.9404 ES:SE:LP:AF:SS:ID 0.1261:0.0397:2.82218:0.9404:636930:rs4970377
1 885689 rs533420572 G A . PASS AF=0.9464 ES:SE:LP:AF:SS:ID 0.1369:0.0414:3.03297:0.9464:649141:rs533420572
1 885699 rs1387393173 A G . PASS AF=0.9459 ES:SE:LP:AF:SS:ID 0.1341:0.0412:2.94885:0.9459:649759:rs1387393173
1 886006 rs1430555697 T C . PASS AF=0.9459 ES:SE:LP:AF:SS:ID 0.1346:0.0411:2.97184:0.9459:651397:rs1430555697
1 887801 rs3828047 A G . PASS AF=0.9459 ES:SE:LP:AF:SS:ID 0.1306:0.041:2.84164:0.9459:655264:rs3828047
1 888639 rs3748596 T C . PASS AF=0.9461 ES:SE:LP:AF:SS:ID 0.133:0.0413:2.89654:0.9461:656524:rs3748596
1 888659 rs3748597 T C . PASS AF=0.9456 ES:SE:LP:AF:SS:ID 0.1277:0.0408:2.7607:0.9456:657542:rs3748597
1 889238 rs3828049 G A . PASS AF=0.053 ES:SE:LP:AF:SS:ID -0.1275:0.0413:2.69443:0.053:658624:rs3828049
1 889638 rs13303206 G C . PASS AF=0.9342 ES:SE:LP:AF:SS:ID 0.1182:0.0378:2.75399:0.9342:641828:rs13303206
1 889713 rs13303051 C A . PASS AF=0.9341 ES:SE:LP:AF:SS:ID 0.1161:0.0378:2.67448:0.9341:642058:rs13303051
1 892745 rs13303227 G A . PASS AF=0.9457 ES:SE:LP:AF:SS:ID 0.1317:0.0411:2.87128:0.9457:649808:rs13303227
1 893280 rs4970371 G A . PASS AF=0.9466 ES:SE:LP:AF:SS:ID 0.1332:0.0413:2.89654:0.9466:652082:rs4970371
1 893631 rs1282810538 A G . PASS AF=0.9361 ES:SE:LP:AF:SS:ID 0.1328:0.0384:3.25759:0.9361:638247:rs1282810538
1 898467 rs41285808 C T . PASS AF=0.053 ES:SE:LP:AF:SS:ID -0.1361:0.0419:2.93144:0.053:636985:rs41285808
1 913889 rs2340596 G A . PASS AF=0.5964 ES:SE:LP:AF:SS:ID 0.0306:0.0191:0.963371:0.5964:643549:rs2340596
1 914333 rs1242237977 C G . PASS AF=0.601 ES:SE:LP:AF:SS:ID 0.0326:0.0191:1.05665:0.601:641765:rs1242237977
1 914852 rs1303869164 G C . PASS AF=0.5969 ES:SE:LP:AF:SS:ID 0.0314:0.0191:1.00104:0.5969:643944:rs1303869164
1 914940 rs13303033 T C . PASS AF=0.582 ES:SE:LP:AF:SS:ID 0.034:0.0189:1.13882:0.582:646540:rs13303033
1 916834 rs6694632 G A . PASS AF=0.5898 ES:SE:LP:AF:SS:ID 0.0358:0.0189:1.23062:0.5898:647959:rs6694632
1 918384 rs13303118 G T . PASS AF=0.5821 ES:SE:LP:AF:SS:ID 0.0365:0.0188:1.27959:0.5821:652771:rs13303118
1 918573 rs2341354 A G . PASS AF=0.5895 ES:SE:LP:AF:SS:ID 0.0381:0.0189:1.36181:0.5895:653473:rs2341354
1 921570 rs6662128 T C . PASS AF=0.9644 ES:SE:LP:AF:SS:ID 0.1051:0.0509:1.41072:0.9644:639829:rs6662128
1 923076 rs1439274265 A G . PASS AF=0.9646 ES:SE:LP:AF:SS:ID 0.1063:0.0509:1.4338:0.9646:639986:rs1439274265
1 923459 rs9442609 A G . PASS AF=0.9644 ES:SE:LP:AF:SS:ID 0.1062:0.0507:1.43818:0.9644:644628:rs9442609
1 923749 rs9442610 T C . PASS AF=0.9638 ES:SE:LP:AF:SS:ID 0.1:0.0506:1.32003:0.9638:636772:rs9442610
1 924368 rs1207734311 C T . PASS AF=0.965 ES:SE:LP:AF:SS:ID 0.1041:0.0511:1.38059:0.965:642846:rs1207734311
1 924629 rs1557663941 A G . PASS AF=0.9644 ES:SE:LP:AF:SS:ID 0.1051:0.0507:1.41862:0.9644:645638:rs1557663941
1 924898 rs6665000 C A . PASS AF=0.9644 ES:SE:LP:AF:SS:ID 0.1081:0.0507:1.48466:0.9644:646651:rs6665000
1 926351 rs6671243 C T . PASS AF=0.9644 ES:SE:LP:AF:SS:ID 0.1043:0.0506:1.40384:0.9644:646666:rs6671243
1 926431 rs4970403 A T . PASS AF=0.9644 ES:SE:LP:AF:SS:ID 0.1033:0.0506:1.38521:0.9644:647012:rs4970403
1 926621 rs4970351 A C . PASS AF=0.9644 ES:SE:LP:AF:SS:ID 0.1046:0.0506:1.41117:0.9644:646241:rs4970351
1 927309 rs1557664616 T C . PASS AF=0.9643 ES:SE:LP:AF:SS:ID 0.1041:0.0508:1.39126:0.9643:638844:rs1557664616
1 928373 rs1557664806 A G . PASS AF=0.9649 ES:SE:LP:AF:SS:ID 0.108:0.0511:1.46017:0.9649:639382:rs1557664806
1 928520 rs1162017826 A G . PASS AF=0.9655 ES:SE:LP:AF:SS:ID 0.1072:0.0514:1.43274:0.9655:642593:rs1162017826