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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-30790_raw/ukb-d-30790_raw.vcf.gz; Date=Sun May 10 02:29:59 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-30790_raw/ukb-d-30790_raw.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-30790_raw/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 14:55:13 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30790_raw/ukb-d-30790_raw.vcf.gz ...
Read summary statistics for 13583853 SNPs.
Dropped 12709 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, 1283503 SNPs remain.
After merging with regression SNP LD, 1283503 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2024 (0.1841)
Lambda GC: 1.0162
Mean Chi^2: 2.6836
Intercept: 1.0047 (0.0105)
Ratio: 0.0028 (0.0062)
Analysis finished at Mon Nov 25 14:57:30 2019
Total time elapsed: 2.0m:17.07s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0103,
"mean_EFFECT": 0.0008,
"n": 273896,
"n_snps": 13583853,
"n_clumped_hits": 18,
"n_p_sig": 8414,
"n_mono": 0,
"n_ns": 1251716,
"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": 568583,
"n_est": 274967.4604,
"ratio_se_n": 1.002,
"mean_diff": -0.0008,
"ratio_diff": 810.8805,
"sd_y_est1": 49.6655,
"sd_y_est2": 49.7626,
"r2_sum1": 98.8161,
"r2_sum2": 0.0401,
"r2_sum3": 0.0399,
"r2_sum4": 0.0381,
"ldsc_nsnp_merge_refpanel_ld": 1283503,
"ldsc_nsnp_merge_regression_ld": 1283503,
"ldsc_observed_scale_h2_beta": 0.2024,
"ldsc_observed_scale_h2_se": 0.1841,
"ldsc_intercept_beta": 1.0047,
"ldsc_intercept_se": 0.0105,
"ldsc_lambda_gc": 1.0162,
"ldsc_mean_chisq": 2.6836,
"ldsc_ratio": 0.0028
}
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 | TRUE |
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 | 13571808 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57079 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33336 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051285e+00 | 6.184985e+00 | 1.00000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.902522e+07 | 5.591492e+07 | 302.00000 | 3.293025e+07 | 7.013957e+07 | 1.148595e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.763000e-04 | 8.568721e-01 | -45.90600 | -2.084700e-01 | -1.858000e-04 | 2.072200e-01 | 1.034200e+02 | ▁▇▁▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.636492e-01 | 5.436486e-01 | 0.11037 | 1.605400e-01 | 2.957500e-01 | 8.097900e-01 | 2.738000e+00 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.981497e-01 | 2.893725e-01 | 0.00000 | 2.468698e-01 | 4.978104e-01 | 7.488296e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.981492e-01 | 2.893728e-01 | 0.00000 | 2.468669e-01 | 4.978060e-01 | 7.488267e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.908360e-01 | 2.544079e-01 | 0.00100 | 7.439100e-03 | 6.007200e-02 | 2.953700e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 568583 | 0.9581427 | NA | NA | NA | NA | NA | 1.963564e-01 | 2.471036e-01 | 0.00000 | 5.591000e-03 | 8.426520e-02 | 3.081070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.738960e+05 | 0.000000e+00 | 273896.00000 | 2.738960e+05 | 2.738960e+05 | 2.738960e+05 | 2.738960e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.361460 | 0.23528 | 0.1244601 | 0.1244655 | 0.1103400 | 0.1894970 | 273896 |
1 | 693731 | rs12238997 | A | G | -0.284330 | 0.22208 | 0.2004398 | 0.2004381 | 0.1156800 | 0.1417730 | 273896 |
1 | 707522 | rs371890604 | G | C | -0.368630 | 0.24995 | 0.1402701 | 0.1402623 | 0.0970790 | 0.1293930 | 273896 |
1 | 717587 | rs144155419 | G | A | 0.127590 | 0.59553 | 0.8303500 | 0.8303551 | 0.0156870 | 0.0045926 | 273896 |
1 | 723329 | rs189787166 | A | T | 0.046987 | 1.74670 | 0.9785400 | 0.9785391 | 0.0017565 | 0.0003994 | 273896 |
1 | 730087 | rs148120343 | T | C | -0.245660 | 0.30992 | 0.4279795 | 0.4279782 | 0.0562580 | 0.0127796 | 273896 |
1 | 731718 | rs142557973 | T | C | -0.327150 | 0.21060 | 0.1203200 | 0.1203231 | 0.1215900 | 0.1543530 | 273896 |
1 | 732032 | rs61770163 | A | C | -0.434660 | 0.22478 | 0.0531496 | 0.0531484 | 0.1210100 | 0.1555510 | 273896 |
1 | 734349 | rs141242758 | T | C | -0.313040 | 0.21070 | 0.1373599 | 0.1373547 | 0.1208200 | 0.1525560 | 273896 |
1 | 740284 | rs61770167 | C | T | -0.380390 | 0.96999 | 0.6949395 | 0.6949410 | 0.0057178 | 0.0023962 | 273896 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.12844 | 0.24376 | 0.5982504 | 0.5982549 | 0.056105 | 0.0309934 | 273896 |
23 | 154923374 | rs111332691 | T | A | -0.20871 | 0.26771 | 0.4356302 | 0.4356191 | 0.044659 | 0.0116556 | 273896 |
23 | 154925045 | rs509981 | C | T | 0.15840 | 0.12870 | 0.2184399 | 0.2184092 | 0.245450 | 0.3634440 | 273896 |
23 | 154925895 | rs538470 | C | T | 0.16876 | 0.13167 | 0.1999599 | 0.1999517 | 0.241770 | 0.3634440 | 273896 |
23 | 154927581 | rs644138 | G | A | 0.10817 | 0.12107 | 0.3716199 | 0.3716162 | 0.301950 | 0.4635760 | 273896 |
23 | 154929412 | rs557132 | C | T | 0.15204 | 0.12874 | 0.2376102 | 0.2376087 | 0.245320 | 0.3568210 | 273896 |
23 | 154929637 | rs35185538 | CT | C | 0.14498 | 0.13434 | 0.2805098 | 0.2804977 | 0.229550 | 0.3011920 | 273896 |
23 | 154929952 | rs4012982 | CAA | C | 0.12462 | 0.13535 | 0.3571799 | 0.3571945 | 0.239420 | 0.3165560 | 273896 |
23 | 154930230 | rs781880 | A | G | 0.14828 | 0.12873 | 0.2493699 | 0.2493752 | 0.245710 | 0.3618540 | 273896 |
23 | 154930487 | rs781879 | T | A | 0.63568 | 0.43923 | 0.1478199 | 0.1478241 | 0.019705 | 0.1263580 | 273896 |
1 692794 rs530212009 CA C . PASS AF=0.11034 ES:SE:LP:AF:SS:ID -0.36146:0.23528:0.90497:0.11034:273896:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11568 ES:SE:LP:AF:SS:ID -0.28433:0.22208:0.698016:0.11568:273896:rs12238997
1 707522 rs371890604 G C . PASS AF=0.097079 ES:SE:LP:AF:SS:ID -0.36863:0.24995:0.853035:0.097079:273896:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015687 ES:SE:LP:AF:SS:ID 0.12759:0.59553:0.0807388:0.015687:273896:rs144155419
1 723329 rs189787166 A T . PASS AF=0.0017565 ES:SE:LP:AF:SS:ID 0.046987:1.7467:0.00942142:0.0017565:273896:rs189787166
1 730087 rs148120343 T C . PASS AF=0.056258 ES:SE:LP:AF:SS:ID -0.24566:0.30992:0.368577:0.056258:273896:rs148120343
1 731718 rs58276399 T C . PASS AF=0.12159 ES:SE:LP:AF:SS:ID -0.32715:0.2106:0.919662:0.12159:273896:rs58276399
1 732032 rs61770163 A C . PASS AF=0.12101 ES:SE:LP:AF:SS:ID -0.43466:0.22478:1.2745:0.12101:273896:rs61770163
1 734349 rs141242758 T C . PASS AF=0.12082 ES:SE:LP:AF:SS:ID -0.31304:0.2107:0.86214:0.12082:273896:rs141242758
1 740284 rs61770167 C T . PASS AF=0.0057178 ES:SE:LP:AF:SS:ID -0.38039:0.96999:0.158053:0.0057178:273896:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0018548 ES:SE:LP:AF:SS:ID -0.16616:1.837:0.0324848:0.0018548:273896:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.86997 ES:SE:LP:AF:SS:ID 0.21797:0.2078:0.531357:0.86997:273896:rs529266287
1 750230 rs190826124 G C . PASS AF=0.0015055 ES:SE:LP:AF:SS:ID -2.6152:1.8974:0.774406:0.0015055:273896:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12273 ES:SE:LP:AF:SS:ID -0.31019:0.20576:0.88048:0.12273:273896:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.14258 ES:SE:LP:AF:SS:ID -0.30606:0.20333:0.878539:0.14258:273896:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12284 ES:SE:LP:AF:SS:ID -0.30794:0.20547:0.87309:0.12284:273896:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87109 ES:SE:LP:AF:SS:ID 0.26624:0.20022:0.736104:0.87109:273896:rs3115860
1 753425 rs3131970 T C . PASS AF=0.87567 ES:SE:LP:AF:SS:ID 0.25752:0.20353:0.686639:0.87567:273896:rs3131970
1 753541 rs2073813 G A . PASS AF=0.12844 ES:SE:LP:AF:SS:ID -0.27428:0.20073:0.764926:0.12844:273896:rs2073813
1 754105 rs12184325 C T . PASS AF=0.036444 ES:SE:LP:AF:SS:ID -0.055949:0.36372:0.0566292:0.036444:273896:rs12184325
1 754182 rs3131969 A G . PASS AF=0.87069 ES:SE:LP:AF:SS:ID 0.27461:0.20002:0.770088:0.87069:273896:rs3131969
1 754192 rs3131968 A G . PASS AF=0.87078 ES:SE:LP:AF:SS:ID 0.28407:0.20011:0.807656:0.87078:273896:rs3131968
1 754334 rs3131967 T C . PASS AF=0.87068 ES:SE:LP:AF:SS:ID 0.27573:0.20001:0.774613:0.87068:273896:rs3131967
1 754433 rs150578204 G A . PASS AF=0.0050575 ES:SE:LP:AF:SS:ID -1.3769:1.0248:0.746977:0.0050575:273896:rs150578204
1 754458 rs142682604 G T . PASS AF=0.0050247 ES:SE:LP:AF:SS:ID -1.3729:1.0275:0.741099:0.0050247:273896:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0055754 ES:SE:LP:AF:SS:ID 0.10637:0.99499:0.0386406:0.0055754:273896:rs184270342
1 755890 rs3115858 A T . PASS AF=0.87077 ES:SE:LP:AF:SS:ID 0.26364:0.19965:0.728949:0.87077:273896:rs3115858
1 756434 rs61768170 G C . PASS AF=0.12579 ES:SE:LP:AF:SS:ID -0.29171:0.20371:0.817728:0.12579:273896:rs61768170
1 756604 rs3131962 A G . PASS AF=0.87033 ES:SE:LP:AF:SS:ID 0.26855:0.19917:0.750704:0.87033:273896:rs3131962
1 757640 rs3115853 G A . PASS AF=0.86961 ES:SE:LP:AF:SS:ID 0.29358:0.199:0.853438:0.86961:273896:rs3115853
1 757734 rs4951929 C T . PASS AF=0.87048 ES:SE:LP:AF:SS:ID 0.26927:0.19934:0.752616:0.87048:273896:rs4951929
1 757936 rs4951862 C A . PASS AF=0.87049 ES:SE:LP:AF:SS:ID 0.26987:0.19935:0.754907:0.87049:273896:rs4951862
1 758144 rs3131956 A G . PASS AF=0.8705 ES:SE:LP:AF:SS:ID 0.27041:0.19936:0.757036:0.8705:273896:rs3131956
1 758626 rs3131954 C T . PASS AF=0.87095 ES:SE:LP:AF:SS:ID 0.26291:0.19987:0.724988:0.87095:273896:rs3131954
1 759293 rs10157329 T A . PASS AF=0.098586 ES:SE:LP:AF:SS:ID -0.3317:0.2325:0.813383:0.098586:273896:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.0064586 ES:SE:LP:AF:SS:ID 0.37382:0.89875:0.169116:0.0064586:273896:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.87485 ES:SE:LP:AF:SS:ID 0.26635:0.20284:0.723171:0.87485:273896:rs3115851
1 761732 rs2286139 C T . PASS AF=0.86421 ES:SE:LP:AF:SS:ID 0.28762:0.19894:0.829005:0.86421:273896:rs2286139
1 761752 rs1057213 C T . PASS AF=0.86961 ES:SE:LP:AF:SS:ID 0.28399:0.20085:0.803078:0.86961:273896:rs1057213
1 762273 rs3115849 G A . PASS AF=0.86652 ES:SE:LP:AF:SS:ID 0.31246:0.20089:0.921326:0.86652:273896:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0985 ES:SE:LP:AF:SS:ID -0.24837:0.24063:0.519993:0.0985:273896:rs12095200
1 762589 rs3115848 G C . PASS AF=0.87171 ES:SE:LP:AF:SS:ID 0.28859:0.20319:0.808186:0.87171:273896:rs3115848
1 762592 rs3131950 C G . PASS AF=0.87171 ES:SE:LP:AF:SS:ID 0.28859:0.20319:0.808214:0.87171:273896:rs3131950
1 762601 rs3131949 T C . PASS AF=0.87171 ES:SE:LP:AF:SS:ID 0.28832:0.20319:0.807126:0.87171:273896:rs3131949
1 762632 rs3131948 T A . PASS AF=0.8721 ES:SE:LP:AF:SS:ID 0.28446:0.2033:0.791129:0.8721:273896:rs3131948
1 764191 rs7515915 T G . PASS AF=0.12536 ES:SE:LP:AF:SS:ID -0.30741:0.20346:0.883359:0.12536:273896:rs7515915
1 766007 rs61768174 A C . PASS AF=0.10523 ES:SE:LP:AF:SS:ID -0.2884:0.22164:0.713993:0.10523:273896:rs61768174
1 766105 rs2519015 T A . PASS AF=0.85567 ES:SE:LP:AF:SS:ID 0.20246:0.1989:0.510421:0.85567:273896:rs2519015
1 767393 rs538667473 A C . PASS AF=0.0016731 ES:SE:LP:AF:SS:ID -0.45291:1.7517:0.0990978:0.0016731:273896:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.8384 ES:SE:LP:AF:SS:ID 0.14901:0.19575:0.35014:0.8384:273896:rs376645387