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/67b72ce5-eed5-4fed-8e9f-6a621a87603e/call-vcf/inputs/-261021474/upload.txt.gz --id ieu-b-5115 --json /data/cromwell-executions/qc/67b72ce5-eed5-4fed-8e9f-6a621a87603e/call-vcf/inputs/-261021474/ieu-b-5115_data.json --ref /data/cromwell-executions/qc/67b72ce5-eed5-4fed-8e9f-6a621a87603e/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/67b72ce5-eed5-4fed-8e9f-6a621a87603e/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-5115/ieu-b-5115.vcf.gz --alias alias.txt; 1.3.0",
"file_date": "2024-01-24T18:20:39.725750",
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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/67b72ce5-eed5-4fed-8e9f-6a621a87603e/call-ldsc/inputs/-261021474/ieu-b-5115.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5115/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Wed Jan 24 18:46:47 2024
Reading summary statistics from /data/cromwell-executions/qc/67b72ce5-eed5-4fed-8e9f-6a621a87603e/call-ldsc/inputs/-261021474/ieu-b-5115.vcf.gz ...
Traceback (most recent call last):
File "./ldsc/ldsc.py", line 647, in <module>
sumstats.estimate_h2(args, log)
File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
args, log, args.h2)
File "/ldsc/ldscore/sumstats.py", line 246, in _read_ld_sumstats
sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
File "/ldsc/ldscore/sumstats.py", line 167, in _read_sumstats
sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna)
File "/ldsc/ldscore/parse.py", line 97, in sumstats
x = read_vcf(fh, alleles, slh)
File "/ldsc/ldscore/parse.py", line 152, in read_vcf
o = [[rec.id, rec.samples[sample]['ES'][0]/rec.samples[sample]['SE'][0]] for rec in vcf_in.fetch()]
ZeroDivisionError: float division by zero
Analysis finished at Wed Jan 24 18:46:47 2024
Total time elapsed: 0.06sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9593,
"inflation_factor": 1.1371,
"mean_EFFECT": -0.0016,
"n": "-Inf",
"n_snps": 21607554,
"n_clumped_hits": 65,
"n_p_sig": 7817,
"n_mono": 4844855,
"n_ns": 1495029,
"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": 2304631,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NaN",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": "NA",
"ldsc_nsnp_merge_regression_ld": "NA",
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": "NA",
"ldsc_intercept_se": "NA",
"ldsc_lambda_gc": "NA",
"ldsc_mean_chisq": "NA",
"ldsc_ratio": "NA"
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | NA |
| n_p_sig | TRUE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | NA |
| ldsc_intercept_beta | NA |
| 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 | 31 | 0.9999986 | 3 | 58 | 0 | 21598229 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 64 | 0 | 75452 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 76 | 0 | 41864 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 21607554 | 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 | 8.671832e+00 | 5.781868e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.886094e+07 | 5.619273e+07 | 52.0000 | 3.276092e+07 | 6.944368e+07 | 1.144561e+08 | 2.492395e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.616600e-03 | 3.043524e-01 | -5.1271 | -1.560000e-02 | 0.000000e+00 | 1.590000e-02 | 5.024300e+00 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.403824e-01 | 2.687927e-01 | 0.0000 | 6.300200e-03 | 2.796610e-02 | 1.068890e-01 | 3.103770e+01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.798080e-01 | 2.934372e-01 | 0.0000 | 2.209999e-01 | 4.720000e-01 | 7.339999e-01 | 9.990000e-01 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 65578 | 0.9969650 | NA | NA | NA | NA | NA | NA | NA | 4.782337e-01 | 2.924908e-01 | 0.0000 | 2.209995e-01 | 4.700019e-01 | 7.319998e-01 | 9.990000e-01 | ▇▇▇▇▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.115543e-01 | 2.177790e-01 | 0.0000 | 1.000000e-04 | 4.300000e-03 | 1.004000e-01 | 1.000000e+00 | ▇▁▁▁▁ |
| numeric | AF_reference | 2304631 | 0.8933414 | NA | NA | NA | NA | NA | NA | NA | 1.262335e-01 | 2.177142e-01 | 0.0000 | 1.397800e-03 | 1.657350e-02 | 1.439700e-01 | 1.000000e+00 | ▇▁▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 13284 | rs548333521 | G | A | -1.7002 | 0.9416900 | 0.0710003 | 0.0710000 | 0e+00 | 0.0013978 | NA |
| 1 | 16141 | rs529651976 | C | T | -0.6851 | 1.0252800 | 0.5040005 | 0.5040010 | 0e+00 | 0.0025958 | NA |
| 1 | 55351 | rs531766459 | T | A | 0.0361 | 0.1197170 | 0.7630008 | 0.7629993 | 4e-04 | 0.0007987 | NA |
| 1 | 57463 | rs531398360 | C | T | 0.1015 | 0.1077060 | 0.3459999 | 0.3459980 | 1e-04 | 0.0003994 | NA |
| 1 | 58834 | rs572549367 | C | T | -0.5901 | 0.3629680 | 0.1039999 | 0.1040000 | 0e+00 | 0.0003994 | NA |
| 1 | 64908 | rs540391097 | A | G | 0.0631 | 0.4480410 | 0.8880001 | 0.8880000 | 0e+00 | 0.0001997 | NA |
| 1 | 67224 | rs566526215 | G | A | -0.0029 | 2.3138600 | 0.9990000 | 0.9990000 | 0e+00 | 0.0097844 | NA |
| 1 | 67580 | rs571658168 | T | A | 0.0245 | 0.0414007 | 0.5540003 | 0.5539996 | 2e-04 | 0.0039936 | NA |
| 1 | 68596 | rs372212855 | T | G | 0.0226 | 0.0790650 | 0.7750005 | 0.7750001 | 0e+00 | 0.0029952 | NA |
| 1 | 72297 | rs200651397 | G | GTAT | 2.1587 | 1.1455100 | 0.0595004 | 0.0594990 | 0e+00 | 0.0041933 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51238328 | rs553081191 | A | C | -0.0834 | 0.0367114 | 0.0230999 | 0.0231002 | 0.0019 | 0.0005990 | NA |
| 22 | 51238364 | rs564490465 | C | G | -0.0446 | 0.0528807 | 0.3990001 | 0.3990004 | 0.0007 | 0.0005990 | NA |
| 22 | 51238420 | rs546719315 | C | T | -0.1086 | 0.0365682 | 0.0029800 | 0.0029800 | 0.0028 | 0.0001997 | NA |
| 22 | 51239584 | rs574579322 | G | C | -0.0119 | 0.0257513 | 0.6440002 | 0.6440006 | 0.0095 | 0.0001997 | NA |
| 22 | 51239586 | rs535432390 | T | G | -0.0103 | 0.0455231 | 0.8210001 | 0.8210002 | 0.0004 | 0.0001997 | NA |
| 22 | 51239637 | rs575912251 | A | G | -0.0093 | 0.0384749 | 0.8090000 | 0.8090002 | 0.0038 | 0.0003994 | NA |
| 22 | 51239678 | rs573137567 | G | T | -0.1093 | 0.0798394 | 0.1710000 | 0.1709998 | 0.0000 | 0.0233626 | NA |
| 22 | 51240820 | rs202228854 | C | T | -0.0173 | 0.0150707 | 0.2510002 | 0.2510004 | 0.0095 | 0.1267970 | NA |
| 22 | 51241101 | rs562711702 | A | T | 0.2546 | 0.2955540 | 0.3890004 | 0.3889995 | 0.0001 | 0.0013978 | NA |
| 22 | 51244237 | rs575160859 | C | T | -0.0243 | 0.0217094 | 0.2630002 | 0.2629990 | 0.0072 | 0.0037939 | NA |
bcf preview
1 13284 rs548333521 G A . PASS AF=0 ES:SE:LP:AF:SI:ID -1.7002:0.94169:1.14874:0:0.898:rs548333521
1 16141 rs529651976 C T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.6851:1.02528:0.297569:0:0.874:rs529651976
1 55351 rs531766459 T A . PASS AF=0.0004 ES:SE:LP:AF:SI:ID 0.0361:0.119717:0.117475:0.0004:0.875:rs531766459
1 57463 rs531398360 C T . PASS AF=0.0001 ES:SE:LP:AF:SI:ID 0.1015:0.107706:0.460924:0.0001:0.806:rs531398360
1 58834 rs572549367 C T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.5901:0.362968:0.982967:0:0.996:rs572549367
1 64908 rs540391097 A G . PASS AF=0 ES:SE:LP:AF:SI:ID 0.0631:0.448041:0.051587:0:0.924:rs540391097
1 67224 rs566526215 G A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0029:2.31386:0.000434512:0:0.999:rs566526215
1 67580 rs571658168 T A . PASS AF=0.0002 ES:SE:LP:AF:SI:ID 0.0245:0.0414007:0.25649:0.0002:0.832:rs571658168
1 68596 rs372212855 T G . PASS AF=0 ES:SE:LP:AF:SI:ID 0.0226:0.079065:0.110698:0:0.968:rs372212855
1 72297 rs200651397 G GTAT . PASS AF=0 ES:SE:LP:AF:SI:ID 2.1587:1.14551:1.22548:0:0.891:rs200651397
1 72526 rs547237130 A G . PASS AF=0 ES:SE:LP:AF:SI:ID -0.026:0.0221279:0.619789:0:0.983:rs547237130
1 79277 rs543555199 C A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.1701:0.109995:0.91364:0:0.88:rs543555199
1 84139 rs183605470 A T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.05:0.0303082:1.00436:0:0.934:rs183605470
1 87647 rs146836579 T C . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0019:0.0360781:0.0186345:0:0.992:rs146836579
1 89567 rs545434463 G A . PASS AF=0.0001 ES:SE:LP:AF:SI:ID 0.0901:0.0946238:0.467246:0.0001:0.882:rs545434463
1 90051 rs7545609 C T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0046:0.0358847:0.0467237:0:0.992:rs7545609
1 92875 rs193157612 T C . PASS AF=0.0001 ES:SE:LP:AF:SI:ID -0.0528:0.0597665:0.423659:0.0001:0.863:rs193157612
1 95046 rs577360244 G A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0026:0.0450728:0.0204516:0:0.92:rs577360244
1 108230 rs9726668 C T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0187:0.0368676:0.213249:0:0.999:rs9726668
1 139016 rs562488749 T G . PASS AF=0 ES:SE:LP:AF:SI:ID 0.4237:0.469678:0.435334:0:0.951:rs562488749
1 139189 rs1208725433 G T . PASS AF=0 ES:SE:LP:AF:SI:ID 0.0062:4.94688:0.000434512:0:0.922:rs1208725433
1 139853 rs533633326 C T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.4518:0.775168:0.251812:0:0.879:rs533633326
1 231487 rs541748235 G A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.4933:1.15017:0.175224:0:0.891:rs541748235
1 231817 rs562060551 G A . PASS AF=0 ES:SE:LP:AF:SI:ID 2.9645:0.93935:2.79588:0:0.905:rs562060551
1 232241 rs541423180 G A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.4559:0.768452:0.257275:0:0.967:rs541423180
1 233364 rs570142352 C T . PASS AF=0 ES:SE:LP:AF:SI:ID 1.6125:1.03433:0.924453:0:0.979:rs570142352
1 235920 rs113244325 C T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.072:0.0881408:0.383:0:0.922:rs113244325
1 243570 rs528256103 G A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.1572:0.109738:0.818156:0:0.978:rs528256103
1 247827 rs559456774 G T . PASS AF=0 ES:SE:LP:AF:SI:ID 1.9179:0.579899:3.02595:0:0.992:rs559456774
1 250191 rs369328110 C A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.2293:0.52453:0.179142:0:1:rs369328110
1 250761 rs545120676 A G . PASS AF=0 ES:SE:LP:AF:SI:ID 0.0329:0.118338:0.107349:0:0.811:rs545120676
1 251688 rs566517303 C T . PASS AF=0 ES:SE:LP:AF:SI:ID 0.0295:1.02323:0.0101054:0:0.97:rs566517303
1 254186 rs148663102 T C . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0113:0.0999659:0.0409586:0:0.825:rs148663102
1 522224 rs564572333 G A . PASS AF=0.0114 ES:SE:LP:AF:SI:ID 0.0141:0.0211012:0.297569:0.0114:0.968:rs564572333
1 525215 rs555742707 G T . PASS AF=0.0038 ES:SE:LP:AF:SI:ID -0.0074:0.0340594:0.0819697:0.0038:0.964:rs555742707
1 526057 rs141459107 T C . PASS AF=0.0193 ES:SE:LP:AF:SI:ID 0.0274:0.0165744:1.00745:0.0193:0.948:rs141459107
1 526733 rs28760963 C T . PASS AF=0 ES:SE:LP:AF:SI:ID -0.7749:0.705437:0.565431:0:0.823:rs28760963
1 526832 rs192574259 G C . PASS AF=0.0425 ES:SE:LP:AF:SI:ID 0.0309:0.0107419:2.39577:0.0425:0.938:rs192574259
1 526889 rs542823434 C T . PASS AF=0.0104 ES:SE:LP:AF:SI:ID -0.0251:0.0230893:0.55752:0.0104:0.977:rs542823434
1 528642 rs76388980 G A . PASS AF=0.0084 ES:SE:LP:AF:SI:ID 0.0049:0.0236701:0.0777937:0.0084:0.953:rs76388980
1 529026 rs543513679 A G . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0158:0.548036:0.0101054:0:0.966:rs543513679
1 529821 rs563365870 C T . PASS AF=0.0017 ES:SE:LP:AF:SI:ID -0.0755:0.0572184:0.728158:0.0017:0.976:rs563365870
1 531294 rs551604754 C A . PASS AF=0.0144 ES:SE:LP:AF:SI:ID -0.0141:0.0186652:0.346787:0.0144:0.951:rs551604754
1 532124 rs1557498364 A C . PASS AF=0 ES:SE:LP:AF:SI:ID -0.0217:0.0865371:0.0958256:0:0.881:rs1557498364
1 532413 rs190029356 G A . PASS AF=0.01 ES:SE:LP:AF:SI:ID -0.0209:0.0218587:0.4698:0.01:0.951:rs190029356
1 532519 rs550891320 G A . PASS AF=0.0021 ES:SE:LP:AF:SI:ID 0.1012:0.0425542:1.75945:0.0021:0.929:rs550891320
1 534302 rs538439623 G A . PASS AF=0.0039 ES:SE:LP:AF:SI:ID -0.0102:0.0375679:0.104577:0.0039:0.981:rs538439623
1 534321 rs536226227 G A . PASS AF=0.0007 ES:SE:LP:AF:SI:ID 0.0343:0.0334383:0.5157:0.0007:0.981:rs536226227
1 534540 rs183186584 G T . PASS AF=0.0034 ES:SE:LP:AF:SI:ID 0.0167:0.03703:0.185752:0.0034:0.957:rs183186584
1 534743 rs560819266 G A . PASS AF=0 ES:SE:LP:AF:SI:ID -0.1689:0.41085:0.166853:0:0.921:rs560819266