manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
{
"fileformat": "VCFv4.2",
"FILTER": "<ID=PASS,Description=\"All filters passed\">",
"INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
"FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
"FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
"FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
"FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
"FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
"FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
"FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
"FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
"FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
"META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
"META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
"META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
"META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
"META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
"META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
"META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
"META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
"SAMPLE": "<ID=UKB-b:1853,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=461945,TotalCases=1065,StudyType=CaseControl>",
"contig": "<ID=1,length=249250621,assembly=GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=GRCh37>",
"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_41202_K920.vcf.gz --id UKB-b:1853 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41202_K920.txt.gz --cohort_cases 1065 --cohort_controls 461945 --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": "2019-09-12T20:27:55.102719",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1853/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1853/UKB-b-1853_raw.vcf.gz; Date=Thu Oct 17 12:36:34 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-1853/ukb-b-1853.vcf.gz; Date=Sun May 10 05:19:26 2020"
}
*********************************************************************
* 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-1853/UKB-b-1853_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1853/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-1853/UKB-b-1853_data.vcf.gz ...
Read summary statistics for 1533662 SNPs.
Dropped 136 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, 396356 SNPs remain.
After merging with regression SNP LD, 396356 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0015 (0.0014)
Lambda GC: 1.0429
Mean Chi^2: 1.0268
Intercept: 1.0105 (0.0115)
Ratio: 0.3915 (0.4288)
Analysis finished at Thu Oct 17 14:40:46 2019
Total time elapsed: 26.8s
{
"af_correlation": 0.601,
"inflation_factor": 1.0475,
"mean_EFFECT": 1.1747e-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": 12247,
"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": 396356,
"ldsc_nsnp_merge_regression_ld": 396356,
"ldsc_observed_scale_h2_beta": 0.0015,
"ldsc_observed_scale_h2_se": 0.0014,
"ldsc_intercept_beta": 1.0105,
"ldsc_intercept_se": 0.0115,
"ldsc_lambda_gc": 1.0429,
"ldsc_mean_chisq": 1.0268,
"ldsc_ratio": 0.3918
}
name | value |
---|---|
af_correlation | TRUE |
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 | FALSE |
ldsc_intercept_beta | FALSE |
n_clumped_hits | FALSE |
r2_sum1 | FALSE |
r2_sum2 | FALSE |
r2_sum3 | FALSE |
r2_sum4 | FALSE |
General metrics
af_correlation
: Correlation coefficient between AF
and AF_reference
.inflation_factor
(lambda
): Genomic inflation factor.mean_EFFECT
: Mean of EFFECT
size.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 below 5e-8
.n_mono
: Number of monomorphic (MAF == 1
or MAF == 0
) SNPs.n_ns
: Number of SNPs with nonsense values:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 0
or > 1
.n_mac
: Number of cases where MAC
(\(2 \times N \times MAF\)) is less than 6
.is_snpid_unique
: true
if the combination of ID
REF
ALT
is unique and therefore no duplication in snpid.n_miss_<*>
: Number of NA
observations 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 expect ratio_se_n
to 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.
ratio_diff
: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff
and the mean of diff2
(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.
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.
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.
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>
: r2
statistics under various assumptions
1
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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
: NOT is_snpid_unique
.mean_EFFECT_nonfinite
: mean(EFFECT)
is NA
, NaN
, or Inf
.mean_EFFECT_05
: abs(mean(EFFECT))
> 0.5.mean_EFFECT_01
: abs(mean(EFFECT))
> 0.1.mean_chisq
: ldsc_mean_chisq
> 1.3 or ldsc_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<*>
> 0.5Plots
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 | 1533528 | 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 | 1533662 | 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 | 8.672012e+00 | 5.767869e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.857657e+07 | 5.656498e+07 | 1.23330e+04 | 3.171473e+07 | 6.909216e+07 | 1.145685e+08 | 2.491722e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.000000e-07 | 1.034000e-04 | -4.66500e-04 | -7.090000e-05 | -1.000000e-07 | 7.020000e-05 | 5.138000e-04 | ▁▃▇▂▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.022000e-04 | 2.800000e-06 | 9.61000e-05 | 1.003000e-04 | 1.015000e-04 | 1.036000e-04 | 1.899000e-04 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.939247e-01 | 2.890923e-01 | 3.50000e-06 | 2.399999e-01 | 4.899999e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.939283e-01 | 2.890634e-01 | 3.50000e-06 | 2.431738e-01 | 4.901886e-01 | 7.441244e-01 | 9.999978e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.813645e-01 | 9.837250e-02 | 3.28639e-01 | 3.948542e-01 | 4.719860e-01 | 5.628208e-01 | 6.713610e-01 | ▇▇▆▅▅ |
numeric | AF_reference | 12247 | 0.9920145 | NA | NA | NA | NA | NA | NA | NA | 4.598552e-01 | 1.464307e-01 | 1.99700e-04 | 3.502400e-01 | 4.536740e-01 | 5.644970e-01 | 1.000000e+00 | ▁▆▇▃▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 49298 | rs200943160 | T | C | -0.0001614 | 0.0001768 | 0.3599996 | 0.3611656 | 0.623765 | 0.782149 | NA |
1 | 54676 | rs2462492 | C | T | -0.0000439 | 0.0001752 | 0.8000000 | 0.8021660 | 0.400401 | NA | NA |
1 | 91536 | rs6702460 | G | T | -0.0003010 | 0.0001725 | 0.0810009 | 0.0809273 | 0.456846 | 0.420727 | NA |
1 | 706368 | rs55727773 | A | G | -0.0000857 | 0.0001223 | 0.4799997 | 0.4835056 | 0.515645 | 0.275160 | NA |
1 | 814495 | rs74461805 | C | A | -0.0000447 | 0.0001677 | 0.7899998 | 0.7899136 | 0.340396 | NA | NA |
1 | 840753 | rs4970382 | T | C | -0.0001208 | 0.0001016 | 0.2300001 | 0.2345553 | 0.400124 | 0.468850 | NA |
1 | 843405 | rs11516185 | A | G | -0.0001447 | 0.0001261 | 0.2500000 | 0.2513629 | 0.362606 | 0.375399 | NA |
1 | 850218 | rs6664536 | T | A | 0.0000664 | 0.0001013 | 0.5099998 | 0.5125115 | 0.590331 | 0.345248 | NA |
1 | 850371 | rs6679046 | G | T | 0.0000562 | 0.0001019 | 0.5800000 | 0.5809848 | 0.603723 | 0.508786 | NA |
1 | 850780 | rs6657440 | C | T | 0.0000587 | 0.0001019 | 0.5600000 | 0.5646782 | 0.603942 | 0.560304 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51158499 | rs8136930 | T | G | -0.0000772 | 0.0001000 | 0.4400003 | 0.4398891 | 0.461636 | 0.544728 | NA |
22 | 51161019 | rs5770994 | C | T | 0.0000779 | 0.0000997 | 0.4299995 | 0.4346398 | 0.482204 | 0.425719 | NA |
22 | 51163039 | rs715584 | G | T | -0.0000717 | 0.0001012 | 0.4799997 | 0.4787937 | 0.426975 | 0.473642 | NA |
22 | 51164109 | rs5770995 | G | C | -0.0000813 | 0.0001006 | 0.4199997 | 0.4191013 | 0.452705 | 0.510982 | NA |
22 | 51164115 | rs5770996 | C | T | -0.0000811 | 0.0001005 | 0.4199997 | 0.4197907 | 0.456917 | 0.514776 | NA |
22 | 51174048 | rs9628245 | G | C | -0.0000553 | 0.0001136 | 0.6300007 | 0.6263214 | 0.380135 | 0.433107 | NA |
22 | 51186143 | rs2879914 | T | C | 0.0000222 | 0.0001071 | 0.8400000 | 0.8360700 | 0.381825 | 0.273363 | NA |
22 | 51186228 | rs3865766 | C | T | -0.0000659 | 0.0001043 | 0.5300002 | 0.5273785 | 0.451061 | 0.453275 | NA |
22 | 51197266 | rs61290853 | A | G | -0.0002087 | 0.0001077 | 0.0530005 | 0.0527541 | 0.386333 | 0.422923 | NA |
22 | 51212875 | rs2238837 | A | C | -0.0000680 | 0.0001149 | 0.5500004 | 0.5542217 | 0.331457 | 0.372404 | NA |
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID -0.000161447:0.000176803:0.443698:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -4.38847e-05:0.000175157:0.09691:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID -0.000301005:0.000172463:1.09151:0.456846:rs6702460
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID -8.56877e-05:0.000122293:0.318759:0.515645:rs12029736
1 814495 rs74461805 C A . PASS AF=0.340396 ES:SE:LP:AF:ID -4.46751e-05:0.000167685:0.102373:0.340396:rs74461805
1 840753 rs4970382 T C . PASS AF=0.400124 ES:SE:LP:AF:ID -0.000120788:0.000101613:0.638272:0.400124:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362606 ES:SE:LP:AF:ID -0.000144686:0.000126138:0.60206:0.362606:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590331 ES:SE:LP:AF:ID 6.63551e-05:0.000101316:0.29243:0.590331:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603723 ES:SE:LP:AF:ID 5.62351e-05:0.000101885:0.236572:0.603723:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603942 ES:SE:LP:AF:ID 5.86682e-05:0.000101871:0.251812:0.603942:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589686 ES:SE:LP:AF:ID 7.08104e-05:0.000101481:0.309804:0.589686:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589665 ES:SE:LP:AF:ID 7.01222e-05:0.000101436:0.309804:0.589665:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607671 ES:SE:LP:AF:ID 2.69179e-05:0.000102098:0.102373:0.607671:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607829 ES:SE:LP:AF:ID 2.53237e-05:0.000102112:0.09691:0.607829:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610316 ES:SE:LP:AF:ID 9.90868e-06:0.000102213:0.0362122:0.610316:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603283 ES:SE:LP:AF:ID 5.48152e-05:0.00010191:0.229148:0.603283:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610337 ES:SE:LP:AF:ID 9.58723e-06:0.000102215:0.0315171:0.610337:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389936 ES:SE:LP:AF:ID -1.25424e-05:0.000102234:0.0457575:0.389936:rs28534711
1 856108 rs28742275 A G . PASS AF=0.38992 ES:SE:LP:AF:ID -1.24548e-05:0.000102239:0.0457575:0.38992:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350356 ES:SE:LP:AF:ID -2.38739e-05:0.000105028:0.0861861:0.350356:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610552 ES:SE:LP:AF:ID 5.74045e-05:0.000102788:0.236572:0.610552:rs2880024
1 875770 rs4970379 A G . PASS AF=0.600085 ES:SE:LP:AF:ID 8.43159e-05:0.000103643:0.376751:0.600085:rs4970379
1 881627 rs2272757 G A . PASS AF=0.652393 ES:SE:LP:AF:ID 4.60645e-05:0.000104697:0.180456:0.652393:rs2272757
1 891059 rs13303065 C T . PASS AF=0.652432 ES:SE:LP:AF:ID 4.07653e-05:0.000104681:0.154902:0.652432:rs13303065
1 891945 rs13303106 A G . PASS AF=0.652494 ES:SE:LP:AF:ID 4.02258e-05:0.000104803:0.154902:0.652494:rs13303106
1 903245 rs28690976 A G . PASS AF=0.566938 ES:SE:LP:AF:ID 9.89511e-05:0.000104092:0.468521:0.566938:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386681 ES:SE:LP:AF:ID -0.000173603:0.000103809:1.02687:0.386681:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571408 ES:SE:LP:AF:ID -0.000197287:0.000100536:1.30103:0.571408:rs3829740
1 912049 rs7367995 T C . PASS AF=0.585249 ES:SE:LP:AF:ID -5.85907e-06:0.000101555:0.0222764:0.585249:rs7367995
1 913889 rs2340596 G A . PASS AF=0.59921 ES:SE:LP:AF:ID 1.06725e-05:0.00010172:0.0362122:0.59921:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602516 ES:SE:LP:AF:ID -1.65561e-05:0.000102028:0.0604807:0.602516:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600074 ES:SE:LP:AF:ID 8.77002e-06:0.000101832:0.0315171:0.600074:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584289 ES:SE:LP:AF:ID 5.48449e-06:0.000101262:0.0177288:0.584289:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589102 ES:SE:LP:AF:ID -1.70134e-05:0.000101416:0.0604807:0.589102:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584202 ES:SE:LP:AF:ID 1.37659e-05:0.000101214:0.05061:0.584202:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589327 ES:SE:LP:AF:ID -6.11177e-06:0.000101338:0.0222764:0.589327:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583926 ES:SE:LP:AF:ID -3.36392e-05:0.000104801:0.124939:0.583926:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567888 ES:SE:LP:AF:ID -4.62418e-05:0.000101129:0.187087:0.567888:rs13303278
1 924528 rs34712273 C A . PASS AF=0.578491 ES:SE:LP:AF:ID -5.01157e-05:0.000101419:0.207608:0.578491:rs34712273
1 930533 rs3128110 C G . PASS AF=0.386082 ES:SE:LP:AF:ID 7.16762e-05:0.000102714:0.309804:0.386082:rs3128110
1 930567 rs3121574 A G . PASS AF=0.386124 ES:SE:LP:AF:ID 7.11702e-05:0.000102717:0.309804:0.386124:rs3121574
1 930751 rs3128111 C G . PASS AF=0.385079 ES:SE:LP:AF:ID 6.41263e-05:0.000102779:0.275724:0.385079:rs3128111
1 931166 rs2710880 A G . PASS AF=0.386765 ES:SE:LP:AF:ID 7.06224e-05:0.000102734:0.309804:0.386765:rs2710880
1 931362 rs2799060 G A . PASS AF=0.385571 ES:SE:LP:AF:ID 6.28416e-05:0.000102784:0.267606:0.385571:rs2799060
1 933790 rs9442392 G A . PASS AF=0.578604 ES:SE:LP:AF:ID -3.35263e-05:0.000101385:0.130768:0.578604:rs9442392
1 936111 rs1936360 C T . PASS AF=0.573545 ES:SE:LP:AF:ID -1.54397e-06:0.000101361:0.00436481:0.573545:rs1936360
1 940005 rs2799056 A G . PASS AF=0.399264 ES:SE:LP:AF:ID 7.46806e-05:0.000102359:0.327902:0.399264:rs2799056
1 940096 rs4503294 C T . PASS AF=0.565308 ES:SE:LP:AF:ID -4.25239e-05:0.000101071:0.173925:0.565308:rs4503294
1 941284 rs3128116 C T . PASS AF=0.397398 ES:SE:LP:AF:ID 7.85477e-05:0.000102381:0.356547:0.397398:rs3128116
1 941334 rs57683598 G A . PASS AF=0.397402 ES:SE:LP:AF:ID 7.8415e-05:0.000102387:0.356547:0.397402:rs57683598