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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/87a3fb40-bb9f-42c7-9f49-d300353fd60c/call-vcf/inputs/562856161/upload.txt.gz --id ieu-b-25 --json /data/cromwell-executions/qc/87a3fb40-bb9f-42c7-9f49-d300353fd60c/call-vcf/inputs/562856161/ieu-b-25_data.json --ref /data/cromwell-executions/qc/87a3fb40-bb9f-42c7-9f49-d300353fd60c/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/87a3fb40-bb9f-42c7-9f49-d300353fd60c/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-25/ieu-b-25.vcf.gz --rm_chr_prefix; 1.2.1",
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}
*********************************************************************
* 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 /data/cromwell-executions/qc/87a3fb40-bb9f-42c7-9f49-d300353fd60c/call-ldsc/inputs/562856161/ieu-b-25.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-25/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Thu Aug 20 16:17:07 2020
Reading summary statistics from /data/cromwell-executions/qc/87a3fb40-bb9f-42c7-9f49-d300353fd60c/call-ldsc/inputs/562856161/ieu-b-25.vcf.gz ...
Read summary statistics for 11913648 SNPs.
Dropped 37037 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1209999 SNPs remain.
After merging with regression SNP LD, 1209999 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0719 (0.0065)
Lambda GC: 1.2222
Mean Chi^2: 1.3256
Intercept: 0.9632 (0.009)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Aug 20 16:18:52 2020
Total time elapsed: 1.0m:45.08s
{
"af_correlation": 0.9644,
"inflation_factor": 1.1167,
"mean_EFFECT": 0.0002,
"n": 263956,
"n_snps": 11913711,
"n_clumped_hits": 23,
"n_p_sig": 2125,
"n_mono": 0,
"n_ns": 0,
"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": 241087,
"n_est": 253225.2598,
"ratio_se_n": 0.9795,
"mean_diff": -0.0002,
"ratio_diff": 2.3163,
"sd_y_est1": 2.0578,
"sd_y_est2": 2.0155,
"r2_sum1": 0.0354,
"r2_sum2": 0.0084,
"r2_sum3": 0.0087,
"r2_sum4": 0.0088,
"ldsc_nsnp_merge_refpanel_ld": 1209999,
"ldsc_nsnp_merge_regression_ld": 1209999,
"ldsc_observed_scale_h2_beta": 0.0719,
"ldsc_observed_scale_h2_se": 0.0065,
"ldsc_intercept_beta": 0.9632,
"ldsc_intercept_se": 0.009,
"ldsc_lambda_gc": 1.2222,
"ldsc_mean_chisq": 1.3256,
"ldsc_ratio": -0.113
}
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 | 9 | 0.9999992 | 3 | 23 | 0 | 11913337 | 0 | 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 |
character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.649378e+00 | 5.764328e+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 | 7.882161e+07 | 5.629131e+07 | 1.73000e+02 | 3.255890e+07 | 6.939964e+07 | 1.145542e+08 | 2.492385e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.736000e-04 | 3.836620e-02 | -4.29195e-01 | -1.053000e-02 | 3.900000e-05 | 1.065990e-02 | 4.622720e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.772490e-02 | 2.603750e-02 | 5.50530e-03 | 7.085800e-03 | 1.551780e-02 | 4.266510e-02 | 1.829490e-01 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.815233e-01 | 2.939862e-01 | 0.00000e+00 | 2.230001e-01 | 4.760001e-01 | 7.360003e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.815237e-01 | 2.939857e-01 | 0.00000e+00 | 2.222169e-01 | 4.755742e-01 | 7.356366e-01 | 9.999997e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.684694e-01 | 2.457111e-01 | 1.00000e-03 | 5.270000e-03 | 3.720000e-02 | 2.420000e-01 | 9.990000e-01 | ▇▁▁▁▁ |
numeric | AF_reference | 241087 | 0.9797639 | NA | NA | NA | NA | NA | 1.737977e-01 | 2.399675e-01 | 0.00000e+00 | 4.193300e-03 | 5.650960e-02 | 2.549920e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.260828e+05 | 4.420008e+04 | 2.64190e+04 | 2.003680e+05 | 2.500350e+05 | 2.597510e+05 | 2.639560e+05 | ▁▁▂▂▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 54676 | rs2462492 | C | T | -0.0040647 | 0.0069202 | 0.5569997 | 0.5569567 | 0.37200 | NA | 56929 |
1 | 55326 | rs3107975 | T | C | 0.0145564 | 0.0296514 | 0.6240006 | 0.6234846 | 0.00910 | 0.0459265 | 78220 |
1 | 79137 | rs143777184 | A | T | 0.0700055 | 0.0761109 | 0.3580000 | 0.3576863 | 0.00220 | 0.0413339 | 62961 |
1 | 86028 | rs114608975 | T | C | 0.0009764 | 0.0093093 | 0.9160001 | 0.9164704 | 0.09160 | 0.0277556 | 81864 |
1 | 91536 | rs6702460 | G | T | 0.0005392 | 0.0060814 | 0.9290000 | 0.9293548 | 0.44700 | 0.4207270 | 83832 |
1 | 234313 | rs8179466 | C | T | -0.0043619 | 0.0119158 | 0.7149999 | 0.7143195 | 0.07500 | NA | 61220 |
1 | 526736 | rs28863004 | C | G | 0.0230709 | 0.0240009 | 0.3359998 | 0.3364258 | 0.00945 | 0.1317890 | 91142 |
1 | 533198 | rs78497331 | C | T | 0.0275874 | 0.0478786 | 0.5639999 | 0.5644835 | 0.00405 | 0.0814696 | 66754 |
1 | 534192 | rs6680723 | C | T | -0.0043337 | 0.0084026 | 0.6060005 | 0.6060275 | 0.23600 | NA | 63438 |
1 | 544584 | rs576404767 | C | T | -0.0101225 | 0.0684012 | 0.8820000 | 0.8823529 | 0.00228 | 0.0003994 | 106048 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51226692 | rs150189434 | G | A | -0.1190920 | 0.0693378 | 0.0858005 | 0.0858765 | 0.00379 | 0.0155751 | 166256 |
22 | 51227766 | rs186062720 | T | C | 0.0137456 | 0.0553828 | 0.8039999 | 0.8039854 | 0.00225 | 0.0005990 | 139204 |
22 | 51229805 | rs9616985 | T | C | -0.0014901 | 0.0108388 | 0.8910000 | 0.8906542 | 0.07640 | 0.0730831 | 224158 |
22 | 51230673 | rs555680442 | G | C | 0.0151673 | 0.0598606 | 0.8000000 | 0.7999769 | 0.00174 | 0.0017971 | 139633 |
22 | 51232488 | rs376461333 | A | G | -0.0453464 | 0.0193358 | 0.0189998 | 0.0190167 | 0.01910 | NA | 134324 |
22 | 51234048 | rs141330630 | T | C | -0.0783230 | 0.0746780 | 0.2930003 | 0.2942658 | 0.00196 | 0.0095847 | 127634 |
22 | 51234159 | rs8138356 | T | A | 0.2011460 | 0.0920985 | 0.0290001 | 0.0289600 | 0.00209 | 0.0215655 | 94255 |
22 | 51237063 | rs3896457 | T | C | -0.0014461 | 0.0059787 | 0.8090000 | 0.8088826 | 0.28600 | 0.2050720 | 201630 |
22 | 51239586 | rs535432390 | T | G | -0.0394083 | 0.0627827 | 0.5300002 | 0.5302047 | 0.00243 | 0.0001997 | 112757 |
23 | 91532627 | rs879949883 | G | A | -0.0065243 | 0.0067582 | 0.3339996 | 0.3343436 | 0.21900 | NA | 254385 |
1 54676 rs2462492 C T . PASS AF=0.372 ES:SE:LP:AF:SS:ID -0.00406472:0.00692023:0.254145:0.372:56929:rs2462492
1 55326 rs3107975 T C . PASS AF=0.0091 ES:SE:LP:AF:SS:ID 0.0145564:0.0296514:0.204815:0.0091:78220:rs3107975
1 79137 rs143777184 A T . PASS AF=0.0022 ES:SE:LP:AF:SS:ID 0.0700055:0.0761109:0.446117:0.0022:62961:rs143777184
1 86028 rs114608975 T C . PASS AF=0.0916 ES:SE:LP:AF:SS:ID 0.000976363:0.00930926:0.0381045:0.0916:81864:rs114608975
1 91536 rs1251109649 G T . PASS AF=0.447 ES:SE:LP:AF:SS:ID 0.000539154:0.00608137:0.0319843:0.447:83832:rs1251109649
1 234313 rs8179466 C T . PASS AF=0.075 ES:SE:LP:AF:SS:ID -0.00436191:0.0119158:0.145694:0.075:61220:rs8179466
1 526736 rs28863004 C G . PASS AF=0.00945 ES:SE:LP:AF:SS:ID 0.0230709:0.0240009:0.473661:0.00945:91142:rs28863004
1 533198 rs1557498752 C T . PASS AF=0.00405 ES:SE:LP:AF:SS:ID 0.0275874:0.0478786:0.248721:0.00405:66754:rs1557498752
1 534192 rs6680723 C T . PASS AF=0.236 ES:SE:LP:AF:SS:ID -0.00433367:0.00840262:0.217527:0.236:63438:rs6680723
1 544584 rs576404767 C T . PASS AF=0.00228 ES:SE:LP:AF:SS:ID -0.0101225:0.0684012:0.0545314:0.00228:106048:rs576404767
1 546697 rs12025928 A G . PASS AF=0.917 ES:SE:LP:AF:SS:ID 0.00902947:0.011696:0.356547:0.917:89785:rs12025928
1 565130 rs371431021 G A . PASS AF=0.0043 ES:SE:LP:AF:SS:ID 0.0302587:0.0386158:0.363512:0.0043:81591:rs371431021
1 565196 rs139723294 T C . PASS AF=0.00185 ES:SE:LP:AF:SS:ID 0.0102884:0.0427201:0.091515:0.00185:85698:rs139723294
1 565469 rs554127336 C T . PASS AF=0.0028 ES:SE:LP:AF:SS:ID -0.0621803:0.0590189:0.533132:0.0028:101311:rs554127336
1 566792 rs9283152 T C . PASS AF=0.00499 ES:SE:LP:AF:SS:ID 0.00821866:0.0453109:0.0675262:0.00499:81517:rs9283152
1 566875 rs2185539 C T . PASS AF=0.00211 ES:SE:LP:AF:SS:ID -0.0382939:0.0641807:0.258848:0.00211:65472:rs2185539
1 567006 rs565235853 G T . PASS AF=0.00179 ES:SE:LP:AF:SS:ID 0.0460053:0.0622034:0.337242:0.00179:123087:rs565235853
1 567540 rs146275198 A G . PASS AF=0.00156 ES:SE:LP:AF:SS:ID 0.113052:0.0840307:0.74958:0.00156:65034:rs146275198
1 567726 rs560688216 T C . PASS AF=0.00325 ES:SE:LP:AF:SS:ID 0.0432953:0.0654189:0.294136:0.00325:67905:rs560688216
1 567867 rs2000096 A G . PASS AF=0.0121 ES:SE:LP:AF:SS:ID 0.0309717:0.0333395:0.452225:0.0121:72584:rs2000096
1 568201 rs4098611 T C . PASS AF=0.00182 ES:SE:LP:AF:SS:ID 0.104507:0.054552:1.25649:0.00182:60595:rs4098611
1 568322 rs9699599 A G . PASS AF=0.00202 ES:SE:LP:AF:SS:ID 0.0361731:0.0739923:0.20412:0.00202:70350:rs9699599
1 568800 rs375217967 G A . PASS AF=0.0148 ES:SE:LP:AF:SS:ID 0.0173727:0.0139541:0.67162:0.0148:81013:rs375217967
1 569204 rs112660509 T C . PASS AF=0.0026 ES:SE:LP:AF:SS:ID 0.0066166:0.0122029:0.230623:0.0026:73100:rs112660509
1 569543 rs538153094 G A . PASS AF=0.00145 ES:SE:LP:AF:SS:ID 0.00802521:0.0319986:0.0958256:0.00145:78482:rs538153094
1 569604 rs9645429 G A . PASS AF=0.00122 ES:SE:LP:AF:SS:ID 0.0366699:0.0467978:0.363512:0.00122:80002:rs9645429
1 569624 rs6594035 T C . PASS AF=0.0127 ES:SE:LP:AF:SS:ID 0.0436797:0.033902:0.703335:0.0127:55632:rs6594035
1 603515 rs190065153 C A . PASS AF=0.003 ES:SE:LP:AF:SS:ID -0.0409762:0.086578:0.196543:0.003:74355:rs190065153
1 603516 rs182349900 C A . PASS AF=0.00303 ES:SE:LP:AF:SS:ID -0.0405629:0.0874802:0.191789:0.00303:73517:rs182349900
1 693731 rs12238997 A G . PASS AF=0.122 ES:SE:LP:AF:SS:ID 0.0189452:0.00853249:1.5784:0.122:190193:rs12238997
1 705882 rs72631875 G A . PASS AF=0.0671 ES:SE:LP:AF:SS:ID -0.0142258:0.011938:0.630784:0.0671:126102:rs72631875
1 705942 rs544671234 A T . PASS AF=0.00176 ES:SE:LP:AF:SS:ID -0.00772927:0.0667708:0.0419142:0.00176:97047:rs544671234
1 713092 rs4565649 G A . PASS AF=0.00624 ES:SE:LP:AF:SS:ID 0.00861835:0.0685639:0.0457575:0.00624:104173:rs4565649
1 713977 rs74512038 C T . PASS AF=0.00621 ES:SE:LP:AF:SS:ID 0.0304419:0.0703965:0.177178:0.00621:89602:rs74512038
1 714277 rs138660747 C A . PASS AF=0.00698 ES:SE:LP:AF:SS:ID -0.0615096:0.0372957:1.00305:0.00698:113104:rs138660747
1 714596 rs149887893 T C . PASS AF=0.0378 ES:SE:LP:AF:SS:ID -0.0265501:0.0192615:0.774691:0.0378:117773:rs149887893
1 715205 rs141090730 C G . PASS AF=0.00668 ES:SE:LP:AF:SS:ID 0.0261346:0.0665971:0.158641:0.00668:103637:rs141090730
1 715265 rs12184267 C T . PASS AF=0.0408 ES:SE:LP:AF:SS:ID -0.0235141:0.0169258:0.785156:0.0408:156175:rs12184267
1 715367 rs12184277 A G . PASS AF=0.0411 ES:SE:LP:AF:SS:ID -0.0220653:0.0168737:0.721246:0.0411:157297:rs12184277
1 717474 rs141784362 C T . PASS AF=0.0061 ES:SE:LP:AF:SS:ID 0.0190829:0.0688594:0.106793:0.0061:104056:rs141784362
1 717485 rs12184279 C A . PASS AF=0.0406 ES:SE:LP:AF:SS:ID -0.0296267:0.0185895:0.954677:0.0406:126642:rs12184279
1 717587 rs144155419 G A . PASS AF=0.0152 ES:SE:LP:AF:SS:ID 0.00251738:0.0251738:0.0362122:0.0152:154135:rs144155419
1 718336 rs188996809 T C . PASS AF=0.00157 ES:SE:LP:AF:SS:ID -0.0905102:0.0621627:0.838632:0.00157:106402:rs188996809
1 720381 rs116801199 G T . PASS AF=0.0422 ES:SE:LP:AF:SS:ID -0.0230564:0.0167711:0.772113:0.0422:159101:rs116801199
1 720583 rs551231909 G A . PASS AF=0.00548 ES:SE:LP:AF:SS:ID -0.0733158:0.0743643:0.489455:0.00548:101040:rs551231909
1 720984 rs564367954 T G . PASS AF=0.00106 ES:SE:LP:AF:SS:ID 0.0611793:0.10225:0.259637:0.00106:58813:rs564367954
1 721290 rs12565286 G C . PASS AF=0.0424 ES:SE:LP:AF:SS:ID -0.0212817:0.0167205:0.692504:0.0424:159403:rs12565286
1 722559 rs150361918 T C . PASS AF=0.00713 ES:SE:LP:AF:SS:ID 0.032644:0.0654189:0.209012:0.00713:101728:rs150361918
1 722603 rs138029171 T C . PASS AF=0.0053 ES:SE:LP:AF:SS:ID 0.0441755:0.0736258:0.261219:0.0053:102766:rs138029171
1 722670 rs116030099 T C . PASS AF=0.0981 ES:SE:LP:AF:SS:ID -0.00691384:0.00933962:0.338187:0.0981:143914:rs116030099