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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30220_irnt/ukb-d-30220_irnt_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T13:33:40.672599",
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"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30220_irnt/ukb-d-30220_irnt.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30220_irnt/ukb-d-30220_irnt_data.vcf.gz; Date=Mon Nov 25 14:23:02 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-30220_irnt/ukb-d-30220_irnt.vcf.gz; Date=Sat May 9 18:07:53 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/dev/ukb-d-import/processed/ukb-d-30220_irnt/ukb-d-30220_irnt.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/ukb-d-import/processed/ukb-d-30220_irnt/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 14:54:53 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30220_irnt/ukb-d-30220_irnt.vcf.gz ...
Read summary statistics for 13586282 SNPs.
Dropped 12710 SNPs with duplicated rs numbers.
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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0448 (0.0046)
Lambda GC: 1.1721
Mean Chi^2: 1.3641
Intercept: 1.0543 (0.0103)
Ratio: 0.149 (0.0282)
Analysis finished at Mon Nov 25 14:57:16 2019
Total time elapsed: 2.0m:22.65s
{
"af_correlation": 0.9521,
"inflation_factor": 1.1144,
"mean_EFFECT": 0,
"n": 349861,
"n_snps": 13586282,
"n_clumped_hits": 109,
"n_p_sig": 12613,
"n_mono": 0,
"n_ns": 1251790,
"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": 569186,
"n_est": 351190.7542,
"ratio_se_n": 1.0019,
"mean_diff": -5.3896e-07,
"ratio_diff": 1.2592,
"sd_y_est1": 1.003,
"sd_y_est2": 1.0049,
"r2_sum1": 0.0282,
"r2_sum2": 0.0281,
"r2_sum3": 0.028,
"r2_sum4": 0.028,
"ldsc_nsnp_merge_refpanel_ld": 1283504,
"ldsc_nsnp_merge_regression_ld": 1283504,
"ldsc_observed_scale_h2_beta": 0.0448,
"ldsc_observed_scale_h2_se": 0.0046,
"ldsc_intercept_beta": 1.0543,
"ldsc_intercept_se": 0.0103,
"ldsc_lambda_gc": 1.1721,
"ldsc_mean_chisq": 1.3641,
"ldsc_ratio": 0.1491
}
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 | TRUE |
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 |
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 | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 0 | 1.0000000 | 3 | 94 | 0 | 13574236 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57080 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33337 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051329e+00 | 6.184984e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.902513e+07 | 5.591486e+07 | 3.02000e+02 | 3.293100e+07 | 7.013871e+07 | 1.148589e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.250000e-05 | 1.428920e-02 | -2.63462e-01 | -3.980800e-03 | 8.100000e-06 | 3.967000e-03 | 2.386860e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.007650e-02 | 9.720100e-03 | 1.97090e-03 | 2.868800e-03 | 5.286500e-03 | 1.448060e-02 | 4.933820e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.819028e-01 | 2.946865e-01 | 0.00000e+00 | 2.222798e-01 | 4.764425e-01 | 7.376783e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.819023e-01 | 2.946868e-01 | 0.00000e+00 | 2.222795e-01 | 4.764419e-01 | 7.376787e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.908059e-01 | 2.544033e-01 | 1.00000e-03 | 7.430400e-03 | 6.003370e-02 | 2.953180e-01 | 9.989990e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 569186 | 0.9581058 | NA | NA | NA | NA | NA | 1.963355e-01 | 2.471013e-01 | 0.00000e+00 | 5.591000e-03 | 8.426520e-02 | 3.081070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.498610e+05 | 0.000000e+00 | 3.49861e+05 | 3.498610e+05 | 3.498610e+05 | 3.498610e+05 | 3.498610e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0021225 | 0.0041983 | 0.6131603 | 0.6131593 | 0.1106490 | 0.1894970 | 349861 |
1 | 693731 | rs12238997 | A | G | 0.0044995 | 0.0039671 | 0.2567078 | 0.2567072 | 0.1158220 | 0.1417730 | 349861 |
1 | 707522 | rs371890604 | G | C | 0.0028805 | 0.0044614 | 0.5185146 | 0.5185146 | 0.0972503 | 0.1293930 | 349861 |
1 | 717587 | rs144155419 | G | A | -0.0012651 | 0.0106308 | 0.9052731 | 0.9052735 | 0.0157178 | 0.0045926 | 349861 |
1 | 723329 | rs189787166 | A | T | 0.0459074 | 0.0315573 | 0.1457451 | 0.1457436 | 0.0017201 | 0.0003994 | 349861 |
1 | 730087 | rs148120343 | T | C | 0.0068113 | 0.0055244 | 0.2175981 | 0.2175972 | 0.0564796 | 0.0127796 | 349861 |
1 | 731718 | rs142557973 | T | C | 0.0027096 | 0.0037622 | 0.4713972 | 0.4713959 | 0.1217450 | 0.1543530 | 349861 |
1 | 732032 | rs61770163 | A | C | 0.0036490 | 0.0040137 | 0.3632829 | 0.3632831 | 0.1211440 | 0.1555510 | 349861 |
1 | 734349 | rs141242758 | T | C | 0.0026136 | 0.0037642 | 0.4874870 | 0.4874866 | 0.1209740 | 0.1525560 | 349861 |
1 | 740284 | rs61770167 | C | T | -0.0029404 | 0.0172208 | 0.8644250 | 0.8644245 | 0.0057855 | 0.0023962 | 349861 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0091888 | 0.0043446 | 0.0344326 | 0.0344324 | 0.0561652 | 0.0309934 | 349861 |
23 | 154923374 | rs111332691 | T | A | -0.0026452 | 0.0047764 | 0.5797049 | 0.5797043 | 0.0447935 | 0.0116556 | 349861 |
23 | 154925045 | rs509981 | C | T | -0.0007799 | 0.0022986 | 0.7343938 | 0.7343944 | 0.2454440 | 0.3634440 | 349861 |
23 | 154925895 | rs538470 | C | T | -0.0014124 | 0.0023512 | 0.5480132 | 0.5480120 | 0.2417890 | 0.3634440 | 349861 |
23 | 154927581 | rs644138 | G | A | -0.0031267 | 0.0021614 | 0.1480079 | 0.1480066 | 0.3020040 | 0.4635760 | 349861 |
23 | 154929412 | rs557132 | C | T | -0.0007434 | 0.0022993 | 0.7464436 | 0.7464440 | 0.2452990 | 0.3568210 | 349861 |
23 | 154929637 | rs35185538 | CT | C | -0.0005170 | 0.0023999 | 0.8294320 | 0.8294317 | 0.2295300 | 0.3011920 | 349861 |
23 | 154929952 | rs4012982 | CAA | C | -0.0014519 | 0.0024183 | 0.5482694 | 0.5482676 | 0.2392530 | 0.3165560 | 349861 |
23 | 154930230 | rs781880 | A | G | -0.0008333 | 0.0022989 | 0.7169981 | 0.7169975 | 0.2457090 | 0.3618540 | 349861 |
23 | 154930487 | rs781879 | T | A | -0.0268481 | 0.0078915 | 0.0006686 | 0.0006685 | 0.0195209 | 0.1263580 | 349861 |
1 692794 rs530212009 CA C . PASS AF=0.110649 ES:SE:LP:AF:SS:ID 0.00212252:0.00419828:0.212426:0.110649:349861:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.115822 ES:SE:LP:AF:SS:ID 0.00449954:0.00396712:0.590561:0.115822:349861:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0972503 ES:SE:LP:AF:SS:ID 0.00288047:0.00446144:0.285239:0.0972503:349861:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157178 ES:SE:LP:AF:SS:ID -0.00126509:0.0106308:0.0432204:0.0157178:349861:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00172013 ES:SE:LP:AF:SS:ID 0.0459074:0.0315573:0.836406:0.00172013:349861:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0564796 ES:SE:LP:AF:SS:ID 0.00681133:0.00552445:0.662345:0.0564796:349861:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121745 ES:SE:LP:AF:SS:ID 0.00270958:0.00376221:0.326613:0.121745:349861:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121144 ES:SE:LP:AF:SS:ID 0.00364899:0.00401373:0.439755:0.121144:349861:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120974 ES:SE:LP:AF:SS:ID 0.00261355:0.00376423:0.312037:0.120974:349861:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00578551 ES:SE:LP:AF:SS:ID -0.00294036:0.0172208:0.0632727:0.00578551:349861:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00188271 ES:SE:LP:AF:SS:ID -0.00288883:0.0325222:0.0318815:0.00188271:349861:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869759 ES:SE:LP:AF:SS:ID -0.0033218:0.00371133:0.430901:0.869759:349861:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00153174 ES:SE:LP:AF:SS:ID 0.00193494:0.0335773:0.0204307:0.00153174:349861:rs190826124
1 751343 rs28544273 T A . PASS AF=0.122895 ES:SE:LP:AF:SS:ID 0.00302647:0.00367531:0.386955:0.122895:349861:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142708 ES:SE:LP:AF:SS:ID 0.00371737:0.00363292:0.514005:0.142708:349861:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123012 ES:SE:LP:AF:SS:ID 0.00306101:0.00367017:0.393331:0.123012:349861:rs28527770
1 753405 rs3115860 C A . PASS AF=0.870893 ES:SE:LP:AF:SS:ID -0.00170812:0.00357641:0.198645:0.870893:349861:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875492 ES:SE:LP:AF:SS:ID -0.00234776:0.00363579:0.285291:0.875492:349861:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID 0.00241362:0.00358532:0.300315:0.128631:349861:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363487 ES:SE:LP:AF:SS:ID 0.00298608:0.00650784:0.189535:0.0363487:349861:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870486 ES:SE:LP:AF:SS:ID -0.001846:0.00357265:0.217984:0.870486:349861:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870587 ES:SE:LP:AF:SS:ID -0.00176562:0.00357422:0.206687:0.870587:349861:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID -0.00184734:0.0035725:0.218183:0.870481:349861:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00504546 ES:SE:LP:AF:SS:ID 0.000436122:0.0183438:0.00831683:0.00504546:349861:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00501229 ES:SE:LP:AF:SS:ID 0.00129064:0.0183927:0.0250018:0.00501229:349861:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00558051 ES:SE:LP:AF:SS:ID 0.00205228:0.0177734:0.0418792:0.00558051:349861:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870566 ES:SE:LP:AF:SS:ID -0.00143967:0.00356624:0.163399:0.870566:349861:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125972 ES:SE:LP:AF:SS:ID 0.00250519:0.00363915:0.308739:0.125972:349861:rs61768170
1 756604 rs3131962 A G . PASS AF=0.87013 ES:SE:LP:AF:SS:ID -0.00162822:0.00355765:0.188967:0.87013:349861:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869408 ES:SE:LP:AF:SS:ID -0.00171125:0.00355427:0.20053:0.869408:349861:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870284 ES:SE:LP:AF:SS:ID -0.00159199:0.00356073:0.183887:0.870284:349861:rs4951929
1 757936 rs4951862 C A . PASS AF=0.87029 ES:SE:LP:AF:SS:ID -0.00159465:0.00356099:0.18423:0.87029:349861:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870299 ES:SE:LP:AF:SS:ID -0.00159058:0.0035611:0.183676:0.870299:349861:rs3131956
1 758626 rs3131954 C T . PASS AF=0.87074 ES:SE:LP:AF:SS:ID -0.00152259:0.00357016:0.174081:0.87074:349861:rs3131954
1 759293 rs10157329 T A . PASS AF=0.098799 ES:SE:LP:AF:SS:ID 0.00350608:0.00415:0.399897:0.098799:349861:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00647255 ES:SE:LP:AF:SS:ID 0.00960488:0.0160567:0.259861:0.00647255:349861:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874649 ES:SE:LP:AF:SS:ID -0.00233215:0.00362351:0.284144:0.874649:349861:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864035 ES:SE:LP:AF:SS:ID -0.00249715:0.00355327:0.316776:0.864035:349861:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869419 ES:SE:LP:AF:SS:ID -0.00183043:0.00358779:0.214724:0.869419:349861:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866376 ES:SE:LP:AF:SS:ID -0.0021756:0.0035886:0.264123:0.866376:349861:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987125 ES:SE:LP:AF:SS:ID 0.00204591:0.00429772:0.197881:0.0987125:349861:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871561 ES:SE:LP:AF:SS:ID -0.00269955:0.00362948:0.340077:0.871561:349861:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871561 ES:SE:LP:AF:SS:ID -0.00269947:0.00362947:0.340066:0.871561:349861:rs3131950
1 762601 rs3131949 T C . PASS AF=0.87156 ES:SE:LP:AF:SS:ID -0.00267681:0.00362955:0.336472:0.87156:349861:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871932 ES:SE:LP:AF:SS:ID -0.00259679:0.00363161:0.323692:0.871932:349861:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125555 ES:SE:LP:AF:SS:ID 0.0030756:0.00363444:0.400749:0.125555:349861:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105385 ES:SE:LP:AF:SS:ID 0.00363882:0.00395743:0.446311:0.105385:349861:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855372 ES:SE:LP:AF:SS:ID -0.0015221:0.00355228:0.17503:0.855372:349861:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00164253 ES:SE:LP:AF:SS:ID 0.0454406:0.0316121:0.822192:0.00164253:349861:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.838283 ES:SE:LP:AF:SS:ID -0.00422725:0.00349881:0.644026:0.838283:349861:rs376645387