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-30680_raw/ukb-d-30680_raw.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-30680_raw/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 14:53:32 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30680_raw/ukb-d-30680_raw.vcf.gz ...
Read summary statistics for 13585308 SNPs.
Dropped 12711 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1095 (0.0117)
Lambda GC: 1.3798
Mean Chi^2: 1.7865
Intercept: 1.0962 (0.0144)
Ratio: 0.1223 (0.0183)
Analysis finished at Mon Nov 25 14:55:57 2019
Total time elapsed: 2.0m:24.78sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9521,
"inflation_factor": 1.2361,
"mean_EFFECT": 3.7028e-07,
"n": 315153,
"n_snps": 13585308,
"n_clumped_hits": 198,
"n_p_sig": 26536,
"n_mono": 0,
"n_ns": 1251737,
"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": 569018,
"n_est": 316376.5437,
"ratio_se_n": 1.0019,
"mean_diff": 1.4484e-06,
"ratio_diff": 0.6682,
"sd_y_est1": 0.0927,
"sd_y_est2": 0.0929,
"r2_sum1": 0.0005,
"r2_sum2": 0.053,
"r2_sum3": 0.0527,
"r2_sum4": 0.0527,
"ldsc_nsnp_merge_refpanel_ld": 1283502,
"ldsc_nsnp_merge_regression_ld": 1283502,
"ldsc_observed_scale_h2_beta": 0.1095,
"ldsc_observed_scale_h2_se": 0.0117,
"ldsc_intercept_beta": 1.0962,
"ldsc_intercept_se": 0.0144,
"ldsc_lambda_gc": 1.3798,
"ldsc_mean_chisq": 1.7865,
"ldsc_ratio": 0.1223
}
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 | 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 | 94 | 0 | 13573261 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57081 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33334 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051279e+00 | 6.184962e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.902532e+07 | 5.591522e+07 | 3.02000e+02 | 3.293038e+07 | 7.013892e+07 | 1.148601e+08 | 2.492309e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.000000e-07 | 1.418400e-03 | -5.08120e-02 | -4.186000e-04 | -2.300000e-06 | 4.128000e-04 | 2.825600e-02 | ▁▁▁▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.810000e-04 | 9.463000e-04 | 1.91700e-04 | 2.794000e-04 | 5.147000e-04 | 1.409700e-03 | 4.771300e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.639553e-01 | 2.999500e-01 | 0.00000e+00 | 1.947798e-01 | 4.533201e-01 | 7.239807e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.639547e-01 | 2.999503e-01 | 0.00000e+00 | 1.947760e-01 | 4.533182e-01 | 7.239792e-01 | 9.999998e-01 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.908195e-01 | 2.544076e-01 | 1.00000e-03 | 7.433500e-03 | 6.004300e-02 | 2.953300e-01 | 9.989990e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 569018 | 0.9581152 | NA | NA | NA | NA | NA | 1.963465e-01 | 2.471049e-01 | 0.00000e+00 | 5.591000e-03 | 8.426520e-02 | 3.081070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.151530e+05 | 0.000000e+00 | 3.15153e+05 | 3.151530e+05 | 3.151530e+05 | 3.151530e+05 | 3.151530e+05 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 692794 | rs530212009 | CA | C | 0.0000511 | 0.0004090 | 0.9005701 | 0.9005739 | 0.1105000 | 0.1894970 | 315153 |
| 1 | 693731 | rs12238997 | A | G | 0.0000713 | 0.0003864 | 0.8536599 | 0.8536566 | 0.1158300 | 0.1417730 | 315153 |
| 1 | 707522 | rs371890604 | G | C | -0.0001402 | 0.0004347 | 0.7470093 | 0.7470106 | 0.0971880 | 0.1293930 | 315153 |
| 1 | 717587 | rs144155419 | G | A | 0.0024023 | 0.0010350 | 0.0202862 | 0.0202835 | 0.0157130 | 0.0045926 | 315153 |
| 1 | 723329 | rs189787166 | A | T | 0.0034144 | 0.0030578 | 0.2641502 | 0.2641569 | 0.0017331 | 0.0003994 | 315153 |
| 1 | 730087 | rs148120343 | T | C | 0.0000468 | 0.0005382 | 0.9307700 | 0.9307686 | 0.0564600 | 0.0127796 | 315153 |
| 1 | 731718 | rs142557973 | T | C | 0.0000665 | 0.0003665 | 0.8560401 | 0.8560363 | 0.1217000 | 0.1543530 | 315153 |
| 1 | 732032 | rs61770163 | A | C | -0.0000009 | 0.0003911 | 0.9980600 | 0.9980627 | 0.1210600 | 0.1555510 | 315153 |
| 1 | 734349 | rs141242758 | T | C | 0.0000699 | 0.0003667 | 0.8489300 | 0.8489328 | 0.1209200 | 0.1525560 | 315153 |
| 1 | 740284 | rs61770167 | C | T | -0.0003520 | 0.0016825 | 0.8342699 | 0.8342731 | 0.0057460 | 0.0023962 | 315153 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154923311 | rs141127553 | C | T | 0.0004640 | 0.0004232 | 0.2728500 | 0.2728538 | 0.056101 | 0.0309934 | 315153 |
| 23 | 154923374 | rs111332691 | T | A | 0.0007003 | 0.0004632 | 0.1306201 | 0.1306156 | 0.044972 | 0.0116556 | 315153 |
| 23 | 154925045 | rs509981 | C | T | 0.0003363 | 0.0002236 | 0.1325501 | 0.1325517 | 0.245750 | 0.3634440 | 315153 |
| 23 | 154925895 | rs538470 | C | T | 0.0003055 | 0.0002287 | 0.1815399 | 0.1815348 | 0.242040 | 0.3634440 | 315153 |
| 23 | 154927581 | rs644138 | G | A | 0.0003988 | 0.0002103 | 0.0578602 | 0.0578607 | 0.302230 | 0.4635760 | 315153 |
| 23 | 154929412 | rs557132 | C | T | 0.0003315 | 0.0002236 | 0.1382700 | 0.1382628 | 0.245600 | 0.3568210 | 315153 |
| 23 | 154929637 | rs35185538 | CT | C | 0.0004084 | 0.0002334 | 0.0801198 | 0.0801257 | 0.229980 | 0.3011920 | 315153 |
| 23 | 154929952 | rs4012982 | CAA | C | 0.0003315 | 0.0002352 | 0.1587000 | 0.1587077 | 0.239540 | 0.3165560 | 315153 |
| 23 | 154930230 | rs781880 | A | G | 0.0003139 | 0.0002236 | 0.1603799 | 0.1603913 | 0.245980 | 0.3618540 | 315153 |
| 23 | 154930487 | rs781879 | T | A | -0.0000778 | 0.0007682 | 0.9193801 | 0.9193812 | 0.019476 | 0.1263580 | 315153 |
bcf preview
1 692794 rs530212009 CA C . PASS AF=0.1105 ES:SE:LP:AF:SS:ID 5.1104e-05:0.00040904:0.0454825:0.1105:315153:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID 7.1266e-05:0.00038636:0.0687151:0.11583:315153:rs12238997
1 707522 rs371890604 G C . PASS AF=0.097188 ES:SE:LP:AF:SS:ID -0.00014024:0.00043474:0.126674:0.097188:315153:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015713 ES:SE:LP:AF:SS:ID 0.0024023:0.001035:1.6928:0.015713:315153:rs144155419
1 723329 rs189787166 A T . PASS AF=0.0017331 ES:SE:LP:AF:SS:ID 0.0034144:0.0030578:0.578149:0.0017331:315153:rs189787166
1 730087 rs148120343 T C . PASS AF=0.05646 ES:SE:LP:AF:SS:ID 4.6762e-05:0.00053825:0.0311576:0.05646:315153:rs148120343
1 731718 rs58276399 T C . PASS AF=0.1217 ES:SE:LP:AF:SS:ID 6.6493e-05:0.00036651:0.0675059:0.1217:315153:rs58276399
1 732032 rs61770163 A C . PASS AF=0.12106 ES:SE:LP:AF:SS:ID -9.497e-07:0.00039113:0.00084335:0.12106:315153:rs61770163
1 734349 rs141242758 T C . PASS AF=0.12092 ES:SE:LP:AF:SS:ID 6.9851e-05:0.00036671:0.0711281:0.12092:315153:rs141242758
1 740284 rs61770167 C T . PASS AF=0.005746 ES:SE:LP:AF:SS:ID -0.00035202:0.0016825:0.0786934:0.005746:315153:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0018557 ES:SE:LP:AF:SS:ID 2.0383e-07:0.0031916:2.17153e-05:0.0018557:315153:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.86977 ES:SE:LP:AF:SS:ID -8.3113e-05:0.00036151:0.0871565:0.86977:315153:rs529266287
1 750230 rs190826124 G C . PASS AF=0.0015173 ES:SE:LP:AF:SS:ID -0.0021031:0.0032867:0.28213:0.0015173:315153:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12288 ES:SE:LP:AF:SS:ID -1.5278e-05:0.00035806:0.0150364:0.12288:315153:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.1427 ES:SE:LP:AF:SS:ID -1.1012e-05:0.00035384:0.0109197:0.1427:315153:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123 ES:SE:LP:AF:SS:ID -9.5014e-06:0.00035756:0.00930604:0.123:315153:rs28527770
1 753405 rs3115860 C A . PASS AF=0.871 ES:SE:LP:AF:SS:ID -2.2493e-05:0.00034852:0.0229443:0.871:315153:rs3115860
1 753425 rs3131970 T C . PASS AF=0.87552 ES:SE:LP:AF:SS:ID -2.9337e-05:0.0003542:0.0296578:0.87552:315153:rs3131970
1 753541 rs2073813 G A . PASS AF=0.12855 ES:SE:LP:AF:SS:ID -5.2203e-06:0.00034936:0.00520789:0.12855:315153:rs2073813
1 754105 rs12184325 C T . PASS AF=0.036308 ES:SE:LP:AF:SS:ID -0.00055991:0.00063403:0.42344:0.036308:315153:rs12184325
1 754182 rs3131969 A G . PASS AF=0.87059 ES:SE:LP:AF:SS:ID -2.6634e-05:0.00034815:0.0273252:0.87059:315153:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8707 ES:SE:LP:AF:SS:ID -1.1551e-05:0.00034832:0.0116462:0.8707:315153:rs3131968
1 754334 rs3131967 T C . PASS AF=0.87059 ES:SE:LP:AF:SS:ID -2.2641e-05:0.00034814:0.023123:0.87059:315153:rs3131967
1 754433 rs150578204 G A . PASS AF=0.0050269 ES:SE:LP:AF:SS:ID 2.5282e-05:0.0017877:0.00492668:0.0050269:315153:rs150578204
1 754458 rs142682604 G T . PASS AF=0.0049935 ES:SE:LP:AF:SS:ID -6.0273e-05:0.0017926:0.0118068:0.0049935:315153:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0055124 ES:SE:LP:AF:SS:ID 0.0020096:0.0017419:0.604464:0.0055124:315153:rs184270342
1 755890 rs3115858 A T . PASS AF=0.87068 ES:SE:LP:AF:SS:ID -3.3385e-05:0.00034756:0.0345725:0.87068:315153:rs3115858
1 756434 rs61768170 G C . PASS AF=0.12589 ES:SE:LP:AF:SS:ID 5.724e-05:0.00035458:0.059608:0.12589:315153:rs61768170
1 756604 rs3131962 A G . PASS AF=0.87025 ES:SE:LP:AF:SS:ID -3.2825e-05:0.00034673:0.0340555:0.87025:315153:rs3131962
1 757640 rs3115853 G A . PASS AF=0.86952 ES:SE:LP:AF:SS:ID -1.6691e-05:0.00034641:0.0170191:0.86952:315153:rs3115853
1 757734 rs4951929 C T . PASS AF=0.8704 ES:SE:LP:AF:SS:ID -3.4296e-05:0.00034702:0.0356131:0.8704:315153:rs4951929
1 757936 rs4951862 C A . PASS AF=0.8704 ES:SE:LP:AF:SS:ID -3.4166e-05:0.00034704:0.035467:0.8704:315153:rs4951862
1 758144 rs3131956 A G . PASS AF=0.87041 ES:SE:LP:AF:SS:ID -3.4946e-05:0.00034706:0.0363113:0.87041:315153:rs3131956
1 758626 rs3131954 C T . PASS AF=0.87085 ES:SE:LP:AF:SS:ID -4.1962e-05:0.00034794:0.0438268:0.87085:315153:rs3131954
1 759293 rs10157329 T A . PASS AF=0.098779 ES:SE:LP:AF:SS:ID -0.0002695:0.00040435:0.296631:0.098779:315153:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.0063936 ES:SE:LP:AF:SS:ID 0.0013453:0.0015741:0.405917:0.0063936:315153:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.87469 ES:SE:LP:AF:SS:ID -7.6921e-05:0.00035302:0.0822267:0.87469:315153:rs3115851
1 761732 rs2286139 C T . PASS AF=0.86414 ES:SE:LP:AF:SS:ID 2.4282e-05:0.00034631:0.024982:0.86414:315153:rs2286139
1 761752 rs1057213 C T . PASS AF=0.86952 ES:SE:LP:AF:SS:ID -6.7446e-05:0.00034959:0.0721063:0.86952:315153:rs1057213
1 762273 rs3115849 G A . PASS AF=0.86647 ES:SE:LP:AF:SS:ID 1.9606e-05:0.00034966:0.0198693:0.86647:315153:rs3115849
1 762485 rs12095200 C A . PASS AF=0.098778 ES:SE:LP:AF:SS:ID 0.00018083:0.00041843:0.176774:0.098778:315153:rs12095200
1 762589 rs3115848 G C . PASS AF=0.87163 ES:SE:LP:AF:SS:ID -3.324e-05:0.00035363:0.0338066:0.87163:315153:rs3115848
1 762592 rs3131950 C G . PASS AF=0.87163 ES:SE:LP:AF:SS:ID -3.3215e-05:0.00035363:0.0337785:0.87163:315153:rs3131950
1 762601 rs3131949 T C . PASS AF=0.87163 ES:SE:LP:AF:SS:ID -3.1297e-05:0.00035363:0.03176:0.87163:315153:rs3131949
1 762632 rs3131948 T A . PASS AF=0.87199 ES:SE:LP:AF:SS:ID -2.1615e-05:0.00035382:0.0216871:0.87199:315153:rs3131948
1 764191 rs7515915 T G . PASS AF=0.12551 ES:SE:LP:AF:SS:ID 4.8738e-05:0.00035409:0.0503563:0.12551:315153:rs7515915
1 766007 rs61768174 A C . PASS AF=0.10534 ES:SE:LP:AF:SS:ID -0.00026596:0.00038569:0.309388:0.10534:315153:rs61768174
1 766105 rs2519015 T A . PASS AF=0.85547 ES:SE:LP:AF:SS:ID -8.1347e-05:0.00034615:0.0892689:0.85547:315153:rs2519015
1 767393 rs538667473 A C . PASS AF=0.0016511 ES:SE:LP:AF:SS:ID 0.0032662:0.0030662:0.542451:0.0016511:315153:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.83825 ES:SE:LP:AF:SS:ID -0.00033097:0.00034048:0.480159:0.83825:315153:rs376645387