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_20002_1066.vcf.gz --id UKB-b:8315 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20002_1066.txt.gz --cohort_cases 1486 --cohort_controls 461447 --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": "2019-09-13T07:59:02.173834",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-8315/ukb-b-8315.vcf.gz; Date=Sun May 10 02:28:01 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-8315/UKB-b-8315_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8315/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:29 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8315/UKB-b-8315_data.vcf.gz ...
Read summary statistics for 2475858 SNPs.
Dropped 289 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, 626969 SNPs remain.
After merging with regression SNP LD, 626969 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -5.0321e-05 (0.0011)
Lambda GC: 0.9989
Mean Chi^2: 0.9981
Intercept: 0.9987 (0.0087)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Thu Oct 17 14:42:04 2019
Total time elapsed: 34.49sQC metrics
Metrics
Metrics
{
"af_correlation": 0.7656,
"inflation_factor": 1,
"mean_EFFECT": 7.6554e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"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": 19619,
"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": 626969,
"ldsc_nsnp_merge_regression_ld": 626969,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 0.9987,
"ldsc_intercept_se": 0.0087,
"ldsc_lambda_gc": 0.9989,
"ldsc_mean_chisq": 0.9981,
"ldsc_ratio": 0.6842
}
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 | FALSE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | TRUE |
| 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 | 4 | 58 | 0 | 2475572 | 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 | 2475858 | 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 | 8.652686e+00 | 5.765813e+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 | 7.855148e+07 | 5.661670e+07 | 5687.0000000 | 3.168376e+07 | 6.897948e+07 | 1.147407e+08 | 2.491917e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.000000e-07 | 1.251000e-04 | -0.0006437 | -8.330000e-05 | 8.000000e-07 | 8.490000e-05 | 5.935000e-04 | ▁▂▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.249000e-04 | 6.700000e-06 | 0.0001134 | 1.192000e-04 | 1.230000e-04 | 1.295000e-04 | 2.457000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.999482e-01 | 2.890128e-01 | 0.0000031 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.999481e-01 | 2.889871e-01 | 0.0000031 | 2.495346e-01 | 4.996020e-01 | 7.497053e-01 | 9.999994e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.542532e-01 | 1.504463e-01 | 0.2355320 | 3.220850e-01 | 4.322610e-01 | 5.750870e-01 | 7.644680e-01 | ▇▆▅▅▃ |
| numeric | AF_reference | 19619 | 0.9920759 | NA | NA | NA | NA | NA | NA | NA | 4.357580e-01 | 1.756891e-01 | 0.0001997 | 2.971250e-01 | 4.205270e-01 | 5.642970e-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 | 0.0003053 | 0.0002088 | 0.1400000 | 0.1437185 | 0.623763 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0000428 | 0.0002068 | 0.8400000 | 0.8359150 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0000512 | 0.0002037 | 0.8000000 | 0.8014921 | 0.456851 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0001405 | 0.0002326 | 0.5500004 | 0.5458360 | 0.240960 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0000502 | 0.0001444 | 0.7300002 | 0.7283310 | 0.515650 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0000143 | 0.0001693 | 0.9299999 | 0.9328061 | 0.706753 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | 0.0001726 | 0.0001382 | 0.2099999 | 0.2116844 | 0.761304 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0000611 | 0.0001544 | 0.6899999 | 0.6923476 | 0.265390 | 0.0756789 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0004124 | 0.0001980 | 0.0369999 | 0.0373083 | 0.340397 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | -0.0001408 | 0.0001325 | 0.2900000 | 0.2878106 | 0.697259 | 0.6912940 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | -3.34e-05 | 0.0001359 | 0.8100000 | 0.8059345 | 0.713658 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | -2.12e-05 | 0.0001352 | 0.8800001 | 0.8755613 | 0.695471 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | -2.99e-05 | 0.0001363 | 0.8300000 | 0.8264165 | 0.715505 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | -3.60e-06 | 0.0001264 | 0.9800000 | 0.9770728 | 0.381826 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | 1.32e-05 | 0.0001232 | 0.9100000 | 0.9145777 | 0.451063 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | 7.17e-05 | 0.0001272 | 0.5700002 | 0.5728636 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | 2.71e-05 | 0.0001440 | 0.8499999 | 0.8509041 | 0.254557 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | 6.03e-05 | 0.0001428 | 0.6700003 | 0.6727138 | 0.271547 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | 1.08e-05 | 0.0001357 | 0.9400001 | 0.9363592 | 0.331455 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | 5.91e-05 | 0.0001389 | 0.6700003 | 0.6704259 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID 0.000305261:0.000208785:0.853872:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -4.2841e-05:0.00020684:0.0757207:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID 5.1204e-05:0.000203662:0.09691:0.456851:rs6702460
1 534192 rs6680723 C T . PASS AF=0.24096 ES:SE:LP:AF:ID -0.000140513:0.000232633:0.259637:0.24096:rs6680723
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID 5.01624e-05:0.000144416:0.136677:0.51565:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID -1.42756e-05:0.000169313:0.0315171:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761304 ES:SE:LP:AF:ID 0.000172592:0.00013819:0.677781:0.761304:rs2977608
1 776546 rs12124819 A G . PASS AF=0.26539 ES:SE:LP:AF:ID 6.10758e-05:0.00015436:0.161151:0.26539:rs12124819
1 814495 rs74461805 C A . PASS AF=0.340397 ES:SE:LP:AF:ID -0.000412356:0.000198022:1.4318:0.340397:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697259 ES:SE:LP:AF:ID -0.00014082:0.000132482:0.537602:0.697259:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705403 ES:SE:LP:AF:ID -0.000177004:0.000130086:0.769551:0.705403:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705448 ES:SE:LP:AF:ID -0.000173927:0.000130081:0.744727:0.705448:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705634 ES:SE:LP:AF:ID -0.000176155:0.000130087:0.744727:0.705634:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705662 ES:SE:LP:AF:ID -0.000176603:0.000130101:0.769551:0.705662:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730134 ES:SE:LP:AF:ID -0.000186237:0.000133646:0.79588:0.730134:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294371 ES:SE:LP:AF:ID 0.000176229:0.000130095:0.744727:0.294371:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236696 ES:SE:LP:AF:ID 0.000212938:0.000138507:0.920819:0.236696:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236684 ES:SE:LP:AF:ID 0.000218861:0.000138508:0.958607:0.236684:rs28752186
1 833641 rs28594623 T C . PASS AF=0.239743 ES:SE:LP:AF:ID 0.000245781:0.000138064:1.12494:0.239743:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236686 ES:SE:LP:AF:ID 0.000218748:0.000138507:0.958607:0.236686:rs28484835
1 834832 rs4411087 G C . PASS AF=0.237171 ES:SE:LP:AF:ID 0.000213006:0.000138401:0.920819:0.237171:rs4411087
1 835499 rs4422948 A G . PASS AF=0.241155 ES:SE:LP:AF:ID 0.000242632:0.000137435:1.11351:0.241155:rs4422948
1 836896 rs28705752 T C . PASS AF=0.269503 ES:SE:LP:AF:ID 0.000141127:0.000132614:0.537602:0.269503:rs28705752
1 838555 rs4970383 C A . PASS AF=0.246197 ES:SE:LP:AF:ID 0.000122776:0.00013649:0.431798:0.246197:rs4970383
1 839103 rs28562941 A G . PASS AF=0.27001 ES:SE:LP:AF:ID 0.000142333:0.000132708:0.552842:0.27001:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400106 ES:SE:LP:AF:ID 0.000244925:0.000119993:1.38722:0.400106:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237094 ES:SE:LP:AF:ID 0.000152341:0.000139378:0.568636:0.237094:rs1574243
1 843405 rs11516185 A G . PASS AF=0.362599 ES:SE:LP:AF:ID 3.58021e-05:0.000148959:0.091515:0.362599:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590333 ES:SE:LP:AF:ID -0.000230181:0.000119642:1.26761:0.590333:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603726 ES:SE:LP:AF:ID -0.000249519:0.000120313:1.42022:0.603726:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603944 ES:SE:LP:AF:ID -0.000251229:0.000120296:1.4318:0.603944:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589688 ES:SE:LP:AF:ID -0.000225223:0.000119836:1.22185:0.589688:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589667 ES:SE:LP:AF:ID -0.000225723:0.000119782:1.22185:0.589667:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607674 ES:SE:LP:AF:ID -0.000253496:0.000120565:1.4437:0.607674:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607833 ES:SE:LP:AF:ID -0.000252548:0.000120582:1.4437:0.607833:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610318 ES:SE:LP:AF:ID -0.000265994:0.0001207:1.55284:0.610318:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603286 ES:SE:LP:AF:ID -0.000240482:0.000120343:1.33724:0.603286:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610338 ES:SE:LP:AF:ID -0.00027144:0.000120702:1.60206:0.610338:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389935 ES:SE:LP:AF:ID 0.000258481:0.000120725:1.49485:0.389935:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389918 ES:SE:LP:AF:ID 0.000258888:0.000120731:1.49485:0.389918:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350351 ES:SE:LP:AF:ID 0.000238226:0.000124026:1.25964:0.350351:rs4040605
1 862866 rs3892970 C T . PASS AF=0.763121 ES:SE:LP:AF:ID -0.000109838:0.000139104:0.366532:0.763121:rs3892970
1 864938 rs2340587 G A . PASS AF=0.760005 ES:SE:LP:AF:ID -7.89882e-05:0.000138073:0.244125:0.760005:rs2340587
1 866893 rs2880024 T C . PASS AF=0.610554 ES:SE:LP:AF:ID -0.000125203:0.00012138:0.522879:0.610554:rs2880024
1 868418 rs28546443 C T . PASS AF=0.297865 ES:SE:LP:AF:ID 2.75014e-06:0.000133363:0.00877392:0.297865:rs28546443
1 870645 rs28576697 T C . PASS AF=0.291287 ES:SE:LP:AF:ID 7.90941e-05:0.0001323:0.259637:0.291287:rs28576697
1 871334 rs4072383 G T . PASS AF=0.720619 ES:SE:LP:AF:ID -4.16238e-05:0.000131481:0.124939:0.720619:rs4072383
1 872352 rs1806780 G C . PASS AF=0.267526 ES:SE:LP:AF:ID 5.32413e-05:0.000133264:0.161151:0.267526:rs1806780
1 873558 rs1110052 G T . PASS AF=0.715253 ES:SE:LP:AF:ID -9.12708e-05:0.000130436:0.318759:0.715253:rs1110052
1 875770 rs4970379 A G . PASS AF=0.600084 ES:SE:LP:AF:ID -0.000156986:0.00012239:0.69897:0.600084:rs4970379