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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"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_20004_1455.vcf.gz --id UKB-b:6235 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20004_1455.txt.gz --cohort_cases 18319 --cohort_controls 444614 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-13T01:16:03.178932",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-6235/ukb-b-6235.vcf.gz; Date=Sun May 10 03:34:23 2020"
}
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/public/UKB-b-6235/UKB-b-6235_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6235/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6235/UKB-b-6235_data.vcf.gz ...
Read summary statistics for 6807705 SNPs.
Dropped 4011 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1256871 SNPs remain.
After merging with regression SNP LD, 1256871 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0246 (0.0032)
Lambda GC: 1.188
Mean Chi^2: 1.2637
Intercept: 1.0422 (0.0105)
Ratio: 0.1599 (0.0399)
Analysis finished at Thu Oct 17 14:41:41 2019
Total time elapsed: 1.0m:22.43sQC metrics
Metrics
Metrics
{
"af_correlation": 0.934,
"inflation_factor": 1.1474,
"mean_EFFECT": 2.5562e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 46,
"n_p_sig": 3190,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 62536,
"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": 1256871,
"ldsc_nsnp_merge_regression_ld": 1256871,
"ldsc_observed_scale_h2_beta": 0.0246,
"ldsc_observed_scale_h2_se": 0.0032,
"ldsc_intercept_beta": 1.0422,
"ldsc_intercept_se": 0.0105,
"ldsc_lambda_gc": 1.188,
"ldsc_mean_chisq": 1.2637,
"ldsc_ratio": 0.16
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | FALSE |
| 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 | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 0 | 1.0000000 | 3 | 58 | 0 | 6803716 | 0 | NA | NA | 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 | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 6807705 | 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 | 8.664005e+00 | 5.764842e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.861135e+07 | 5.647029e+07 | 828.0000000 | 3.209983e+07 | 6.905312e+07 | 1.145044e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.600000e-06 | 8.003000e-04 | -0.0117709 | -4.369000e-04 | 1.200000e-06 | 4.382000e-04 | 4.375760e-02 | ▂▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.774000e-04 | 2.981000e-04 | 0.0003887 | 4.370000e-04 | 5.538000e-04 | 8.430000e-04 | 3.398500e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.747395e-01 | 2.954876e-01 | 0.0000000 | 2.099999e-01 | 4.700002e-01 | 7.300002e-01 | 1.000000e+00 | ▇▇▇▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.747381e-01 | 2.954605e-01 | 0.0000000 | 2.127086e-01 | 4.654688e-01 | 7.306182e-01 | 1.000000e+00 | ▇▇▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.822845e-01 | 2.589744e-01 | 0.0191060 | 6.578000e-02 | 1.885630e-01 | 4.412600e-01 | 9.808930e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 62536 | 0.9908139 | NA | NA | NA | NA | NA | NA | NA | 2.802893e-01 | 2.511094e-01 | 0.0000000 | 7.448080e-02 | 1.998800e-01 | 4.335060e-01 | 1.000000e+00 | ▇▃▂▂▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | 0.0005107 | 0.0007153 | 0.4799997 | 0.4752771 | 0.623763 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0005230 | 0.0007087 | 0.4600002 | 0.4605239 | 0.400401 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0007034 | 0.0011330 | 0.5300002 | 0.5347199 | 0.103556 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0007829 | 0.0006978 | 0.2599998 | 0.2619058 | 0.456851 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0013370 | 0.0013759 | 0.3300000 | 0.3311684 | 0.074508 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0015665 | 0.0007971 | 0.0490004 | 0.0493717 | 0.240960 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0010239 | 0.0009944 | 0.2999998 | 0.3031442 | 0.913473 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0000335 | 0.0006680 | 0.9599999 | 0.9600009 | 0.116325 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0006811 | 0.0009788 | 0.4899999 | 0.4865604 | 0.067285 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0001373 | 0.0004948 | 0.7800007 | 0.7813804 | 0.515650 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | 0.0011447 | 0.0005970 | 0.0549997 | 0.0551900 | 0.137953 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0017135 | 0.0007749 | 0.0269998 | 0.0270259 | 0.073747 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0015475 | 0.0010384 | 0.1400000 | 0.1361725 | 0.041955 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0026418 | 0.0010368 | 0.0109999 | 0.0108313 | 0.049731 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0017652 | 0.0007754 | 0.0230001 | 0.0228161 | 0.073238 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0001706 | 0.0009129 | 0.8499999 | 0.8517450 | 0.054459 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0001122 | 0.0009173 | 0.9000000 | 0.9026550 | 0.054088 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0016536 | 0.0007782 | 0.0340001 | 0.0335967 | 0.073073 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0013434 | 0.0018333 | 0.4600002 | 0.4637093 | 0.020043 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0008499 | 0.0004760 | 0.0739997 | 0.0741662 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID 0.0005107:0.000715347:0.318759:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -0.000522997:0.000708683:0.337242:0.400401:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103556 ES:SE:LP:AF:ID 0.000703417:0.00113305:0.275724:0.103556:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID -0.000782857:0.000697797:0.585027:0.456851:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074508 ES:SE:LP:AF:ID -0.00133701:0.00137586:0.481486:0.074508:rs8179466
1 534192 rs6680723 C T . PASS AF=0.24096 ES:SE:LP:AF:ID -0.00156651:0.000797057:1.3098:0.24096:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913473 ES:SE:LP:AF:ID 0.00102392:0.000994373:0.522879:0.913473:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116325 ES:SE:LP:AF:ID -3.35005e-05:0.000667974:0.0177288:0.116325:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067285 ES:SE:LP:AF:ID -0.000681067:0.00097884:0.309804:0.067285:rs72631875
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID 0.000137318:0.000494803:0.107905:0.51565:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033004 ES:SE:LP:AF:ID 0.000236031:0.00124744:0.0705811:0.033004:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036621 ES:SE:LP:AF:ID 5.87824e-05:0.00113307:0.0177288:0.036621:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036737 ES:SE:LP:AF:ID 6.43869e-05:0.00112878:0.0222764:0.036737:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036437 ES:SE:LP:AF:ID -0.000123152:0.00113692:0.0409586:0.036437:rs12184279
1 720381 rs116801199 G T . PASS AF=0.036976 ES:SE:LP:AF:ID 9.3712e-05:0.00112432:0.0315171:0.036976:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037072 ES:SE:LP:AF:ID 5.26515e-05:0.00112047:0.0177288:0.037072:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101199 ES:SE:LP:AF:ID -0.00048803:0.000816394:0.259637:0.101199:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959096 ES:SE:LP:AF:ID 0.000328082:0.00108067:0.119186:0.959096:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031451 ES:SE:LP:AF:ID 0.00157714:0.00196174:0.376751:0.031451:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053254 ES:SE:LP:AF:ID -0.000828587:0.00156065:0.221849:0.053254:rs865924913
1 726794 rs28454925 C G . PASS AF=0.03659 ES:SE:LP:AF:ID 6.26023e-05:0.00112773:0.0177288:0.03659:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036907 ES:SE:LP:AF:ID 9.52204e-05:0.00111746:0.0315171:0.036907:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843212 ES:SE:LP:AF:ID -3.33601e-05:0.000578885:0.0222764:0.843212:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055911 ES:SE:LP:AF:ID -4.97956e-05:0.000937305:0.0177288:0.055911:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122307 ES:SE:LP:AF:ID 0.000109702:0.00063364:0.0655015:0.122307:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025713 ES:SE:LP:AF:ID -0.000349319:0.00155862:0.0861861:0.025713:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121549 ES:SE:LP:AF:ID 0.000110138:0.000633906:0.0655015:0.121549:rs141242758
1 736289 rs79010578 T A . PASS AF=0.13233 ES:SE:LP:AF:ID 8.83633e-05:0.000624777:0.05061:0.13233:rs79010578
1 752478 rs146277091 G A . PASS AF=0.036821 ES:SE:LP:AF:ID 0.000168305:0.00110616:0.0555173:0.036821:rs146277091
1 752566 rs3094315 G A . PASS AF=0.838951 ES:SE:LP:AF:ID -0.000122791:0.000560609:0.0809219:0.838951:rs3094315
1 752721 rs3131972 A G . PASS AF=0.83858 ES:SE:LP:AF:ID -0.000117198:0.000560006:0.0809219:0.83858:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869781 ES:SE:LP:AF:ID -1.20099e-05:0.000600908:0.00877392:0.869781:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129871 ES:SE:LP:AF:ID 9.13661e-05:0.000602139:0.0555173:0.129871:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037332 ES:SE:LP:AF:ID -2.03027e-05:0.0010874:0.00436481:0.037332:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037576 ES:SE:LP:AF:ID 5.27846e-06:0.00108053:-0:0.037576:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869123 ES:SE:LP:AF:ID -2.47618e-06:0.000599732:-0:0.869123:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869221 ES:SE:LP:AF:ID 2.29394e-06:0.00059997:-0:0.869221:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037534 ES:SE:LP:AF:ID -5.38685e-05:0.00108521:0.0177288:0.037534:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869126 ES:SE:LP:AF:ID -3.82881e-06:0.00059972:0.00436481:0.869126:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838033 ES:SE:LP:AF:ID -9.27199e-05:0.000558451:0.0604807:0.838033:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037547 ES:SE:LP:AF:ID -0.000128617:0.00108674:0.0409586:0.037547:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838664 ES:SE:LP:AF:ID -7.50653e-05:0.000560021:0.05061:0.838664:rs3131966
1 755775 rs3131965 A G . PASS AF=0.839777 ES:SE:LP:AF:ID -8.23989e-05:0.000567595:0.0555173:0.839777:rs3131965
1 755890 rs3115858 A T . PASS AF=0.869405 ES:SE:LP:AF:ID 4.61677e-06:0.000599026:0.00436481:0.869405:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868952 ES:SE:LP:AF:ID 2.64005e-05:0.000597519:0.0177288:0.868952:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867905 ES:SE:LP:AF:ID 4.58242e-05:0.000596374:0.0268721:0.867905:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869095 ES:SE:LP:AF:ID 9.4707e-06:0.000598008:0.00436481:0.869095:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869104 ES:SE:LP:AF:ID 9.16152e-06:0.000598054:0.00436481:0.869104:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869112 ES:SE:LP:AF:ID 1.73373e-05:0.000598068:0.00877392:0.869112:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869589 ES:SE:LP:AF:ID -1.21604e-05:0.00059971:0.00877392:0.869589:rs3131954