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/ieu-a-import/processed/ieu-a-1136/ieu-a-1136.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/ieu-a-import/processed/ieu-a-1136/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Wed Feb 5 09:02:00 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1136/ieu-a-1136.vcf.gz ...
Read summary statistics for 10165059 SNPs.
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, 1220160 SNPs remain.
After merging with regression SNP LD, 1220160 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0526 (0.0111)
Lambda GC: 1.0578
Mean Chi^2: 1.0685
Intercept: 1.0162 (0.0069)
Ratio: 0.2363 (0.101)
Analysis finished at Wed Feb 5 09:03:37 2020
Total time elapsed: 1.0m:37.83sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9535,
"inflation_factor": 1.0465,
"mean_EFFECT": -0.0011,
"n": 50225,
"n_snps": 10165059,
"n_clumped_hits": 6,
"n_p_sig": 278,
"n_mono": 0,
"n_ns": 619862,
"n_mac": 5,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 131461,
"n_est": 49031.6514,
"ratio_se_n": 0.988,
"mean_diff": 0.0012,
"ratio_diff": 2.6232,
"sd_y_est1": 3.3912,
"sd_y_est2": 3.3507,
"r2_sum1": 0.0571,
"r2_sum2": 0.005,
"r2_sum3": 0.0051,
"r2_sum4": 0.0059,
"ldsc_nsnp_merge_refpanel_ld": 1220160,
"ldsc_nsnp_merge_regression_ld": 1220160,
"ldsc_observed_scale_h2_beta": 0.0526,
"ldsc_observed_scale_h2_se": 0.0111,
"ldsc_intercept_beta": 1.0162,
"ldsc_intercept_se": 0.0069,
"ldsc_lambda_gc": 1.0578,
"ldsc_mean_chisq": 1.0685,
"ldsc_ratio": 0.2365
}
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 | FALSE |
| 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 | 47 | 0 | 10165057 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 99 | 0 | 30497 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 103 | 0 | 16152 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.954062e+00 | 6.300724e+00 | 1.00000e+00 | 4.000000e+00 | 7.000000e+00 | 1.400000e+01 | 2.400000e+01 | ▇▆▂▃▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.912629e+07 | 5.684511e+07 | 8.28000e+02 | 3.226763e+07 | 6.948129e+07 | 1.156567e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.062500e-03 | 7.712470e-02 | -6.30109e+00 | -2.757000e-02 | 7.000000e-05 | 2.736000e-02 | 8.448430e+00 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.887240e-02 | 4.852090e-02 | 1.87800e-02 | 2.422000e-02 | 3.654000e-02 | 7.985000e-02 | 1.658060e+01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.924540e-01 | 2.907429e-01 | 0.00000e+00 | 2.386701e-01 | 4.901895e-01 | 7.445502e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.924540e-01 | 2.907428e-01 | 0.00000e+00 | 2.386701e-01 | 4.901870e-01 | 7.445504e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.291102e-01 | 2.639237e-01 | 1.44000e-05 | 2.166750e-02 | 1.098900e-01 | 3.653455e-01 | 9.998590e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 131461 | 0.9870674 | NA | NA | NA | NA | NA | 2.275859e-01 | 2.512164e-01 | 1.99700e-04 | 2.456070e-02 | 1.265970e-01 | 3.582270e-01 | 9.996010e-01 | ▇▂▂▁▁ |
| numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.022500e+04 | 0.000000e+00 | 5.02250e+04 | 5.022500e+04 | 5.022500e+04 | 5.022500e+04 | 5.022500e+04 | ▁▁▇▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 10616 | rs376342519 | CCGCCGTTGCAAAGGCGCGCCG | C | 0.02675 | 0.25431 | 0.9162399 | 0.9162278 | 0.9947430 | 0.9930110 | 50225 |
| 1 | 14933 | rs199856693 | G | A | 0.03864 | 0.08851 | 0.6624498 | 0.6624299 | 0.0389022 | 0.0283546 | 50225 |
| 1 | 15774 | rs374029747 | G | A | 0.00199 | 0.24016 | 0.9933700 | 0.9933887 | 0.0069126 | 0.0119808 | 50225 |
| 1 | 16949 | rs199745162 | A | C | -0.36267 | 0.16148 | 0.0247110 | 0.0247096 | 0.0155093 | 0.0139776 | 50225 |
| 1 | 51479 | rs116400033 | T | A | -0.04136 | 0.03962 | 0.2965801 | 0.2965237 | 0.2232820 | 0.1281950 | 50225 |
| 1 | 52185 | rs201374420 | TTAA | T | -0.02681 | 0.18827 | 0.8867500 | 0.8867626 | 0.0065541 | 0.0053914 | 50225 |
| 1 | 54490 | rs141149254 | G | A | -0.06600 | 0.04573 | 0.1489701 | 0.1489490 | 0.1599310 | 0.0960463 | 50225 |
| 1 | 55164 | rs3091274 | C | A | -0.02653 | 0.11017 | 0.8096900 | 0.8097026 | 0.9788310 | 0.9233230 | 50225 |
| 1 | 55326 | rs3107975 | T | C | -0.04196 | 0.10096 | 0.6777398 | 0.6776953 | 0.0286523 | 0.0459265 | 50225 |
| 1 | 55545 | rs28396308 | C | T | 0.11634 | 0.04036 | 0.0039478 | 0.0039446 | 0.2396340 | 0.2392170 | 50225 |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 154925045 | rs509981 | C | T | -0.00445 | 0.02246 | 0.8428199 | 0.8429433 | 0.2382400 | 0.3634440 | 50225 |
| 23 | 154925895 | rs538470 | C | T | -0.00787 | 0.02254 | 0.7269508 | 0.7269714 | 0.2461850 | 0.3634440 | 50225 |
| 23 | 154927185 | rs185685661 | T | C | 0.02567 | 0.04289 | 0.5494498 | 0.5495011 | 0.1101870 | 0.1796030 | 50225 |
| 23 | 154927199 | rs645904 | C | T | -0.00576 | 0.02250 | 0.7977999 | 0.7979508 | 0.2396980 | 0.3674170 | 50225 |
| 23 | 154927581 | rs644138 | G | A | -0.00969 | 0.02183 | 0.6570403 | 0.6571260 | 0.2887790 | 0.4635760 | 50225 |
| 23 | 154928151 | rs144607509 | C | T | -0.10186 | 0.14224 | 0.4739396 | 0.4739212 | 0.0225378 | 0.0084768 | 50225 |
| 23 | 154929412 | rs557132 | C | T | -0.00453 | 0.02247 | 0.8401799 | 0.8402278 | 0.2378480 | 0.3568210 | 50225 |
| 23 | 154929952 | rs4012982 | CAA | C | -0.02203 | 0.03288 | 0.5028599 | 0.5028500 | 0.2082930 | 0.3165560 | 50225 |
| 23 | 154930230 | rs781880 | A | G | -0.00467 | 0.02248 | 0.8355201 | 0.8354318 | 0.2377160 | 0.3618540 | 50225 |
| 24 | 13537468 | rs7203107 | A | G | -0.16470 | 0.11901 | 0.1663700 | 0.1663838 | 0.9832420 | NA | 50225 |
bcf preview
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C . PASS AF=0.994743 ES:SE:LP:AF:SS:ID 0.02675:0.25431:0.0379908:0.994743:50225:rs376342519
1 14933 rs199856693 G A . PASS AF=0.0389022 ES:SE:LP:AF:SS:ID 0.03864:0.08851:0.178847:0.0389022:50225:rs199856693
1 15774 rs374029747 G A . PASS AF=0.00691262 ES:SE:LP:AF:SS:ID 0.00199:0.24016:0.00288896:0.00691262:50225:rs374029747
1 16949 rs199745162 A C . PASS AF=0.0155093 ES:SE:LP:AF:SS:ID -0.36267:0.16148:1.60711:0.0155093:50225:rs199745162
1 51479 rs116400033 T A . PASS AF=0.223282 ES:SE:LP:AF:SS:ID -0.04136:0.03962:0.527858:0.223282:50225:rs116400033
1 52185 rs201374420 TTAA T . PASS AF=0.00655406 ES:SE:LP:AF:SS:ID -0.02681:0.18827:0.0521988:0.00655406:50225:rs201374420
1 54490 rs141149254 G A . PASS AF=0.159931 ES:SE:LP:AF:SS:ID -0.066:0.04573:0.826901:0.159931:50225:rs141149254
1 55164 rs3091274 C A . PASS AF=0.978831 ES:SE:LP:AF:SS:ID -0.02653:0.11017:0.0916812:0.978831:50225:rs3091274
1 55326 rs3107975 T C . PASS AF=0.0286523 ES:SE:LP:AF:SS:ID -0.04196:0.10096:0.168937:0.0286523:50225:rs3107975
1 55545 rs28396308 C T . PASS AF=0.239634 ES:SE:LP:AF:SS:ID 0.11634:0.04036:2.40364:0.239634:50225:rs28396308
1 57292 rs201418760 C T . PASS AF=0.027706 ES:SE:LP:AF:SS:ID -0.02629:0.10064:0.100223:0.027706:50225:rs201418760
1 58814 rs114420996 G A . PASS AF=0.098398 ES:SE:LP:AF:SS:ID 0.10573:0.05963:1.11811:0.098398:50225:rs114420996
1 61743 rs184286948 G C . PASS AF=0.0080842 ES:SE:LP:AF:SS:ID -0.10186:0.19725:0.217836:0.0080842:50225:rs184286948
1 61920 rs62637820 G A . PASS AF=0.0208792 ES:SE:LP:AF:SS:ID 0.08435:0.13436:0.275609:0.0208792:50225:rs62637820
1 63093 rs200092917 G A . PASS AF=0.0249372 ES:SE:LP:AF:SS:ID 0.19867:0.10566:1.22141:0.0249372:50225:rs200092917
1 64649 rs181431124 A C . PASS AF=0.0180492 ES:SE:LP:AF:SS:ID 0.06558:0.14406:0.187789:0.0180492:50225:rs181431124
1 66219 rs181028663 A T . PASS AF=0.0127175 ES:SE:LP:AF:SS:ID 0.02359:0.15554:0.0557888:0.0127175:50225:rs181028663
1 68082 rs367789441 T C . PASS AF=0.0692865 ES:SE:LP:AF:SS:ID 0.0332:0.06571:0.212313:0.0692865:50225:rs367789441
1 69428 rs140739101 T G . PASS AF=0.0377036 ES:SE:LP:AF:SS:ID -0.12124:0.09261:0.720128:0.0377036:50225:rs140739101
1 69761 rs200505207 A T . PASS AF=0.0730549 ES:SE:LP:AF:SS:ID 0.03211:0.06475:0.207643:0.0730549:50225:rs200505207
1 69897 rs200676709 T C . PASS AF=0.755089 ES:SE:LP:AF:SS:ID -0.04035:0.03985:0.506723:0.755089:50225:rs200676709
1 72297 rs200651397 G GTAT . PASS AF=0.00266121 ES:SE:LP:AF:SS:ID -0.02603:0.44693:0.020652:0.00266121:50225:rs200651397
1 74790 rs13328700 C G . PASS AF=0.0243933 ES:SE:LP:AF:SS:ID -0.01846:0.11688:0.0582352:0.0243933:50225:rs13328700
1 74792 rs13328684 G A . PASS AF=0.0243933 ES:SE:LP:AF:SS:ID -0.01846:0.11688:0.0582352:0.0243933:50225:rs13328684
1 76854 rs367666799 A G . PASS AF=0.0552342 ES:SE:LP:AF:SS:ID 0.07546:0.07446:0.507407:0.0552342:50225:rs367666799
1 82163 rs139113303 G A . PASS AF=0.0546127 ES:SE:LP:AF:SS:ID 0.09232:0.07408:0.672253:0.0546127:50225:rs139113303
1 82609 rs149189449 C G . PASS AF=0.0560999 ES:SE:LP:AF:SS:ID 0.07828:0.0728:0.549381:0.0560999:50225:rs149189449
1 83514 rs201754587 C T . PASS AF=0.350461 ES:SE:LP:AF:SS:ID -0.04152:0.03603:0.603382:0.350461:50225:rs201754587
1 84139 rs183605470 A T . PASS AF=0.0243284 ES:SE:LP:AF:SS:ID 0.11201:0.10912:0.51617:0.0243284:50225:rs183605470
1 86028 rs114608975 T C . PASS AF=0.0405474 ES:SE:LP:AF:SS:ID -0.03918:0.08455:0.191742:0.0405474:50225:rs114608975
1 86065 rs116504101 G C . PASS AF=0.0590685 ES:SE:LP:AF:SS:ID 0.06118:0.07088:0.411135:0.0590685:50225:rs116504101
1 86331 rs115209712 A G . PASS AF=0.0992422 ES:SE:LP:AF:SS:ID 0.06007:0.05898:0.510731:0.0992422:50225:rs115209712
1 87021 rs188486692 T C . PASS AF=0.00832071 ES:SE:LP:AF:SS:ID 0.18814:0.17525:0.548198:0.00832071:50225:rs188486692
1 87360 rs180907504 C T . PASS AF=0.0282358 ES:SE:LP:AF:SS:ID 0.06417:0.09522:0.3007:0.0282358:50225:rs180907504
1 87409 rs139490478 C T . PASS AF=0.0599702 ES:SE:LP:AF:SS:ID 0.06806:0.07034:0.477243:0.0599702:50225:rs139490478
1 88169 rs940550 C T . PASS AF=0.218814 ES:SE:LP:AF:SS:ID -0.02105:0.04194:0.21061:0.218814:50225:rs940550
1 88172 rs940551 G A . PASS AF=0.0694575 ES:SE:LP:AF:SS:ID 0.0311:0.06575:0.196386:0.0694575:50225:rs940551
1 88177 rs143215837 G C . PASS AF=0.0685722 ES:SE:LP:AF:SS:ID 0.0373:0.06584:0.243303:0.0685722:50225:rs143215837
1 88188 rs148331237 C A . PASS AF=0.00639527 ES:SE:LP:AF:SS:ID 0.1321:0.18731:0.318144:0.00639527:50225:rs148331237
1 88236 rs186918018 C T . PASS AF=0.0141311 ES:SE:LP:AF:SS:ID 0.22368:0.11986:1.20746:0.0141311:50225:rs186918018
1 88316 rs113759966 G A . PASS AF=0.0688447 ES:SE:LP:AF:SS:ID 0.03026:0.06545:0.191215:0.0688447:50225:rs113759966
1 88338 rs55700207 G A . PASS AF=0.0846248 ES:SE:LP:AF:SS:ID 0.0493:0.06486:0.349488:0.0846248:50225:rs55700207
1 88710 rs186575039 C G . PASS AF=0.0597994 ES:SE:LP:AF:SS:ID 0.06718:0.07038:0.468789:0.0597994:50225:rs186575039
1 89599 rs375955515 A T . PASS AF=0.0597994 ES:SE:LP:AF:SS:ID 0.06718:0.07038:0.468789:0.0597994:50225:rs375955515
1 89946 rs138808727 A T . PASS AF=0.221743 ES:SE:LP:AF:SS:ID -0.03545:0.0397:0.429574:0.221743:50225:rs138808727
1 91190 rs143856811 G A . PASS AF=0.0608308 ES:SE:LP:AF:SS:ID 0.07683:0.06947:0.570603:0.0608308:50225:rs143856811
1 91421 rs28619159 T C . PASS AF=0.0120568 ES:SE:LP:AF:SS:ID -0.13438:0.16794:0.373024:0.0120568:50225:rs28619159
1 91515 rs376723915 A C . PASS AF=0.552395 ES:SE:LP:AF:SS:ID -0.02388:0.03424:0.313802:0.552395:50225:rs376723915
1 92633 rs149776517 C T . PASS AF=0.0332067 ES:SE:LP:AF:SS:ID -0.00734:0.09184:0.028585:0.0332067:50225:rs149776517
1 92858 rs147061536 G T . PASS AF=0.227322 ES:SE:LP:AF:SS:ID -0.04424:0.03957:0.579153:0.227322:50225:rs147061536