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/ukb-d-import/processed/ukb-d-STILL_ADULT/ukb-d-STILL_ADULT.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/ukb-d-import/processed/ukb-d-STILL_ADULT/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 14:47:53 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-STILL_ADULT/ukb-d-STILL_ADULT.vcf.gz ...
Read summary statistics for 9950918 SNPs.
Dropped 7673 SNPs with duplicated rs numbers.
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, 1277677 SNPs remain.
After merging with regression SNP LD, 1277677 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0023 (0.0012)
Lambda GC: 1.0113
Mean Chi^2: 1.0162
Intercept: 1.0001 (0.006)
Ratio: 0.0065 (0.3718)
Analysis finished at Mon Nov 25 14:49:42 2019
Total time elapsed: 1.0m:48.19sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9413,
"inflation_factor": 1.0046,
"mean_EFFECT": 1.2062e-06,
"n": 361194,
"n_snps": 9950918,
"n_clumped_hits": 5,
"n_p_sig": 7497,
"n_mono": 0,
"n_ns": 1079796,
"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": 196899,
"n_est": 361103.345,
"ratio_se_n": 0.9999,
"mean_diff": 0,
"ratio_diff": 31.6298,
"sd_y_est1": 0.0642,
"sd_y_est2": 0.0642,
"r2_sum1": 0,
"r2_sum2": 0.0027,
"r2_sum3": 0.0027,
"r2_sum4": 0.0026,
"ldsc_nsnp_merge_refpanel_ld": 1277677,
"ldsc_nsnp_merge_regression_ld": 1277677,
"ldsc_observed_scale_h2_beta": 0.0023,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0001,
"ldsc_intercept_se": 0.006,
"ldsc_lambda_gc": 1.0113,
"ldsc_mean_chisq": 1.0162,
"ldsc_ratio": 0.0062
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | FALSE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | FALSE |
| 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 | 0 | 1.000000 | 3 | 94 | 0 | 9943795 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.000000 | 1 | 98 | 0 | 48012 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.000000 | 1 | 342 | 0 | 30058 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | 9.080984e+00 | 6.177271e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.875344e+07 | 5.609223e+07 | 3.02000e+02 | 3.246889e+07 | 6.965466e+07 | 1.147334e+08 | 2.492297e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | 1.200000e-06 | 3.652000e-04 | -4.05630e-03 | -1.692000e-04 | -1.000000e-06 | 1.657000e-04 | 5.760100e-03 | ▁▃▇▁▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.089000e-04 | 1.858000e-04 | 1.24300e-04 | 1.662000e-04 | 2.255000e-04 | 3.990000e-04 | 1.030000e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.985074e-01 | 2.897836e-01 | 0.00000e+00 | 2.469602e-01 | 4.990086e-01 | 7.497401e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.985070e-01 | 2.897838e-01 | 0.00000e+00 | 2.469590e-01 | 4.990081e-01 | 7.497394e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | 2.556788e-01 | 2.629399e-01 | 8.41180e-03 | 3.932460e-02 | 1.510120e-01 | 4.076978e-01 | 9.915880e-01 | ▇▂▂▁▁ |
| numeric | AF_reference | 196899 | 0.980213 | NA | NA | NA | NA | NA | 2.553015e-01 | 2.537777e-01 | 0.00000e+00 | 4.392970e-02 | 1.667330e-01 | 4.037540e-01 | 1.000000e+00 | ▇▃▂▁▁ |
| numeric | N | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.611940e+05 | 0.000000e+00 | 3.61194e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 692794 | rs530212009 | CA | C | -0.0000817 | 0.0002647 | 0.7574745 | 0.7574756 | 0.1106400 | 0.1894970 | 361194 |
| 1 | 693731 | rs12238997 | A | G | -0.0001544 | 0.0002501 | 0.5369737 | 0.5369723 | 0.1158300 | 0.1417730 | 361194 |
| 1 | 707522 | rs371890604 | G | C | -0.0003033 | 0.0002811 | 0.2806900 | 0.2806889 | 0.0973034 | 0.1293930 | 361194 |
| 1 | 717587 | rs144155419 | G | A | -0.0001149 | 0.0006709 | 0.8639599 | 0.8639602 | 0.0156880 | 0.0045926 | 361194 |
| 1 | 730087 | rs148120343 | T | C | -0.0003970 | 0.0003484 | 0.2544702 | 0.2544700 | 0.0564602 | 0.0127796 | 361194 |
| 1 | 731718 | rs142557973 | T | C | -0.0001540 | 0.0002372 | 0.5161655 | 0.5161647 | 0.1217380 | 0.1543530 | 361194 |
| 1 | 732032 | rs61770163 | A | C | -0.0002778 | 0.0002530 | 0.2722288 | 0.2722289 | 0.1211710 | 0.1555510 | 361194 |
| 1 | 734349 | rs141242758 | T | C | -0.0001642 | 0.0002373 | 0.4890801 | 0.4890810 | 0.1209650 | 0.1525560 | 361194 |
| 1 | 749963 | rs529266287 | T | TAA | 0.0002817 | 0.0002339 | 0.2285373 | 0.2285367 | 0.8697420 | 0.7641770 | 361194 |
| 1 | 751343 | rs28544273 | T | A | -0.0003152 | 0.0002317 | 0.1736749 | 0.1736733 | 0.1229160 | 0.2426120 | 361194 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154923311 | rs141127553 | C | T | 0.0000705 | 0.0002740 | 0.7968211 | 0.7968211 | 0.0561667 | 0.0309934 | 361194 |
| 23 | 154923374 | rs111332691 | T | A | 0.0000413 | 0.0003011 | 0.8910320 | 0.8910321 | 0.0447862 | 0.0116556 | 361194 |
| 23 | 154925045 | rs509981 | C | T | 0.0001230 | 0.0001449 | 0.3958066 | 0.3958068 | 0.2456060 | 0.3634440 | 361194 |
| 23 | 154925895 | rs538470 | C | T | 0.0001178 | 0.0001482 | 0.4266345 | 0.4266336 | 0.2419150 | 0.3634440 | 361194 |
| 23 | 154927581 | rs644138 | G | A | 0.0001233 | 0.0001363 | 0.3654803 | 0.3654790 | 0.3021620 | 0.4635760 | 361194 |
| 23 | 154929412 | rs557132 | C | T | 0.0001252 | 0.0001449 | 0.3877198 | 0.3877210 | 0.2454590 | 0.3568210 | 361194 |
| 23 | 154929637 | rs35185538 | CT | C | 0.0002763 | 0.0001513 | 0.0677127 | 0.0677127 | 0.2296970 | 0.3011920 | 361194 |
| 23 | 154929952 | rs4012982 | CAA | C | 0.0001333 | 0.0001524 | 0.3817122 | 0.3817122 | 0.2394250 | 0.3165560 | 361194 |
| 23 | 154930230 | rs781880 | A | G | 0.0001157 | 0.0001449 | 0.4244954 | 0.4244957 | 0.2458690 | 0.3618540 | 361194 |
| 23 | 154930487 | rs781879 | T | A | -0.0009205 | 0.0004971 | 0.0640678 | 0.0640666 | 0.0195623 | 0.1263580 | 361194 |
bcf preview
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID -8.17282e-05:0.000264666:0.120632:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID -0.000154397:0.000250077:0.270047:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID -0.000303283:0.000281137:0.551773:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID -0.000114943:0.000670866:0.0635064:0.015688:361194:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID -0.000397011:0.00034839:0.594363:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID -0.000153989:0.000237173:0.287211:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID -0.00027777:0.000252991:0.565066:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID -0.000164158:0.000237301:0.31062:0.120965:361194:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID 0.000281697:0.000233941:0.641043:0.869742:361194:rs529266287
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID -0.000315209:0.000231687:0.760263:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID -0.000340529:0.00022901:0.863197:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID -0.00031707:0.000231365:0.768141:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID 0.00022862:0.000225458:0.507839:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID 0.000305363:0.000229194:0.738143:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID -0.000219167:0.000226023:0.478583:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID 0.000477564:0.000410058:0.612304:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID 0.000210914:0.000225223:0.457131:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID 0.000221076:0.000225326:0.486082:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID 0.000209834:0.000225215:0.454087:0.870481:361194:rs3131967
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID 0.000209913:0.000224819:0.455362:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID -0.000218841:0.000229397:0.468401:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID 0.000201531:0.000224278:0.433117:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID 0.000209143:0.000224073:0.45515:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID 0.000208023:0.000224471:0.450911:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID 0.000208037:0.000224487:0.450911:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID 0.000207841:0.000224494:0.450336:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID 0.000204888:0.000225065:0.440527:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID -0.000291389:0.000261539:0.576387:0.0988442:361194:rs10157329
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID 0.000248091:0.000228419:0.556851:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID 0.000151282:0.000223999:0.301513:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID 0.000216242:0.000226174:0.469763:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID 0.000182475:0.00022622:0.376872:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -0.000298504:0.000270827:0.568029:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000207098:0.000228797:0.437253:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.0002071:0.000228797:0.437259:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID 0.000206997:0.000228801:0.436964:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID 0.000212171:0.000228932:0.450949:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID -0.00024983:0.000229112:0.559837:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID -0.000228443:0.00024942:0.444033:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID 0.000166835:0.000223915:0.340822:0.855376:361194:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID -3.41304e-05:0.000220597:0.0569791:0.838358:361194:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763351 ES:SE:LP:AF:SS:ID 8.77427e-05:0.000177539:0.206801:0.763351:361194:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105921 ES:SE:LP:AF:SS:ID 5.67712e-05:0.000244606:0.0880619:0.105921:361194:rs12562034
1 769138 rs59306077 CAT C . PASS AF=0.128938 ES:SE:LP:AF:SS:ID -0.00023243:0.000225907:0.517785:0.128938:361194:rs762168062
1 769223 rs60320384 C G . PASS AF=0.128608 ES:SE:LP:AF:SS:ID -0.000204994:0.000225699:0.439208:0.128608:361194:rs60320384
1 769963 rs7518545 G A . PASS AF=0.105213 ES:SE:LP:AF:SS:ID 6.78254e-05:0.000246453:0.106151:0.105213:361194:rs7518545
1 770181 rs146076599 A G . PASS AF=0.009077 ES:SE:LP:AF:SS:ID -0.000591675:0.000868857:0.30462:0.009077:361194:rs146076599
1 770886 rs371458725 G A . PASS AF=0.104268 ES:SE:LP:AF:SS:ID 3.33118e-05:0.000248423:0.0489886:0.104268:361194:rs371458725
1 771410 rs2519006 C T . PASS AF=0.830106 ES:SE:LP:AF:SS:ID 0.000171095:0.000219917:0.359946:0.830106:361194:rs2519006
1 771823 rs2977605 T C . PASS AF=0.87012 ES:SE:LP:AF:SS:ID 0.000208766:0.000224688:0.452448:0.87012:361194:rs2977605