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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/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-ldsc/inputs/562856220/ieu-b-42.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-42/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Sat Aug 22 00:02:22 2020
Reading summary statistics from /data/cromwell-executions/qc/4e410728-95ea-4c9e-8588-0cf8599c35ce/call-ldsc/inputs/562856220/ieu-b-42.vcf.gz ...
Read summary statistics for 14237418 SNPs.
Dropped 109203 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, 1220686 SNPs remain.
After merging with regression SNP LD, 1220686 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.4552 (0.0165)
Lambda GC: 1.5613
Mean Chi^2: 1.7348
Intercept: 1.0456 (0.0095)
Ratio: 0.0621 (0.013)
Analysis finished at Sat Aug 22 00:04:16 2020
Total time elapsed: 1.0m:54.38s
{
"af_correlation": 0.9595,
"inflation_factor": 1.1941,
"mean_EFFECT": 0.0626,
"n": 77096,
"n_snps": 14237637,
"n_clumped_hits": 81,
"n_p_sig": 12625,
"n_mono": 1693817,
"n_ns": 0,
"n_mac": 1655602,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 452238,
"n_est": 66851.2629,
"ratio_se_n": 0.9312,
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": 2.3558,
"sd_y_est2": 2.1937,
"r2_sum1": 0.2093,
"r2_sum2": 0.0377,
"r2_sum3": 0.0435,
"r2_sum4": 0.0437,
"ldsc_nsnp_merge_refpanel_ld": 1220686,
"ldsc_nsnp_merge_regression_ld": 1220686,
"ldsc_observed_scale_h2_beta": 0.4552,
"ldsc_observed_scale_h2_se": 0.0165,
"ldsc_intercept_beta": 1.0456,
"ldsc_intercept_se": 0.0095,
"ldsc_lambda_gc": 1.5613,
"ldsc_mean_chisq": 1.7348,
"ldsc_ratio": 0.0621
}
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 | 102 | 0.9999928 | 3 | 59 | 0 | 14211946 | 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 | 8.660667e+00 | 5.772339e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.874250e+07 | 5.627260e+07 | 828.0000 | 3.254248e+07 | 6.927169e+07 | 1.144739e+08 | 2.492395e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.262600e-02 | 5.499043e+00 | -707.2710 | -2.700200e-02 | 9.000000e-04 | 3.130500e-02 | 7.094110e+02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.933884e+01 | 6.411964e+02 | 0.0106 | 1.480000e-02 | 3.920000e-02 | 2.015000e-01 | 1.299000e+05 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.712639e-01 | 2.995100e-01 | 0.0000 | 2.051002e-01 | 4.610999e-01 | 7.306998e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.712637e-01 | 2.995123e-01 | 0.0000 | 2.051112e-01 | 4.610983e-01 | 7.306670e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.585929e-01 | 2.456719e-01 | 0.0000 | 4.000000e-03 | 2.600000e-02 | 2.160000e-01 | 1.000000e+00 | ▇▁▁▁▁ |
numeric | AF_reference | 452238 | 0.9682364 | NA | NA | NA | NA | NA | 1.655272e-01 | 2.391206e-01 | 0.0000 | 5.391400e-03 | 4.492810e-02 | 2.318290e-01 | 1.000000e+00 | ▇▁▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.709600e+04 | 0.000000e+00 | 77096.0000 | 7.709600e+04 | 7.709600e+04 | 7.709600e+04 | 7.709600e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 10611 | rs189107123 | C | G | 0.078502 | 0.0818 | 0.3366999 | 0.3372152 | 0.021 | NA | 77096 |
1 | 13302 | rs75241669 | C | T | 0.006698 | 0.0299 | 0.8220000 | 0.8227469 | 0.137 | NA | 77096 |
1 | 13327 | rs2691329 | G | C | 0.007204 | 0.0538 | 0.8936001 | 0.8934790 | 0.040 | NA | 77096 |
1 | 13980 | rs2592732 | T | C | -0.042504 | 0.0725 | 0.5577005 | 0.5576994 | 0.022 | NA | 77096 |
1 | 30923 | rs806731 | G | T | 0.000500 | 0.0223 | 0.9812000 | 0.9821117 | 0.728 | 0.8724040 | 77096 |
1 | 51476 | rs2531249 | T | C | -0.029102 | 0.1084 | 0.7883009 | 0.7883386 | 0.008 | NA | 77096 |
1 | 51479 | rs116400033 | T | A | -0.016201 | 0.0235 | 0.4890002 | 0.4905689 | 0.215 | 0.1281950 | 77096 |
1 | 52058 | rs1199236530 | G | C | 0.036602 | 0.0472 | 0.4378002 | 0.4380643 | 0.049 | NA | 77096 |
1 | 52144 | rs190291950 | T | A | -0.077702 | 0.0959 | 0.4177996 | 0.4178023 | 0.015 | 0.0009984 | 77096 |
1 | 52238 | rs2691277 | T | G | -0.005803 | 0.0418 | 0.8891000 | 0.8895863 | 0.951 | 0.9217250 | 77096 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51233300 | rs9616839 | C | T | 0.029297 | 0.0161 | 0.0679595 | 0.0688063 | 0.272 | 0.3146960 | 77096 |
22 | 51234048 | rs141330630 | T | C | 0.711494 | 0.7451 | 0.3396002 | 0.3396296 | 0.001 | 0.0095847 | 77096 |
22 | 51234159 | rs8138356 | T | A | 0.119799 | 0.1138 | 0.2921999 | 0.2924715 | 0.001 | 0.0215655 | 77096 |
22 | 51234677 | rs189571549 | A | C | 0.094399 | 0.1029 | 0.3587996 | 0.3589405 | 0.001 | 0.0227636 | 77096 |
22 | 51234799 | rs191117135 | G | A | -0.019499 | 0.0936 | 0.8351000 | 0.8349770 | 0.013 | 0.0059904 | 77096 |
22 | 51237063 | rs3896457 | T | C | 0.017095 | 0.0165 | 0.3008999 | 0.3001739 | 0.255 | 0.2050720 | 77096 |
22 | 51237069 | rs183661957 | T | C | 4.556380 | 3.2500 | 0.1609000 | 0.1609263 | 0.000 | 0.0029952 | 77096 |
22 | 51238249 | rs149733995 | A | C | 0.034995 | 0.0290 | 0.2267003 | 0.2275384 | 0.067 | NA | 77096 |
22 | 51242613 | rs140611932 | A | C | 4.556380 | 3.2500 | 0.1609000 | 0.1609263 | 0.000 | NA | 77096 |
22 | 51243297 | rs1555938782 | A | T | -0.045403 | 0.0241 | 0.0599998 | 0.0595728 | 0.148 | NA | 77096 |
1 10611 rs189107123 C G . PASS AF=0.021 ES:SE:LP:AF:SS:NC:ID 0.078502:0.0818:0.472757:0.021:77096:33640:rs189107123
1 13302 rs75241669 C T . PASS AF=0.137 ES:SE:LP:AF:SS:NC:ID 0.006698:0.0299:0.0851282:0.137:77096:33640:rs75241669
1 13327 rs2691329 G C . PASS AF=0.04 ES:SE:LP:AF:SS:NC:ID 0.007204:0.0538:0.0488568:0.04:77096:33640:rs2691329
1 13980 rs2592732 T C . PASS AF=0.022 ES:SE:LP:AF:SS:NC:ID -0.042504:0.0725:0.253599:0.022:77096:33640:rs2592732
1 30923 rs1165072081 G T . PASS AF=0.728 ES:SE:LP:AF:SS:NC:ID 0.0005:0.0223:0.00824246:0.728:77096:33640:rs1165072081
1 51476 rs2531249 T C . PASS AF=0.008 ES:SE:LP:AF:SS:NC:ID -0.029102:0.1084:0.103308:0.008:77096:33640:rs2531249
1 51479 rs116400033 T A . PASS AF=0.215 ES:SE:LP:AF:SS:NC:ID -0.016201:0.0235:0.310691:0.215:77096:33640:rs116400033
1 52058 rs1199236530 G C . PASS AF=0.049 ES:SE:LP:AF:SS:NC:ID 0.036602:0.0472:0.358724:0.049:77096:33640:rs1199236530
1 52144 rs190291950 T A . PASS AF=0.015 ES:SE:LP:AF:SS:NC:ID -0.077702:0.0959:0.379032:0.015:77096:33640:rs190291950
1 52238 rs2691277 T G . PASS AF=0.951 ES:SE:LP:AF:SS:NC:ID -0.005803:0.0418:0.0510494:0.951:77096:33640:rs2691277
1 54353 rs140052487 C A . PASS AF=0.001 ES:SE:LP:AF:SS:NC:ID 1.5385:1.139:0.752518:0.001:77096:33640:rs140052487
1 54421 rs146477069 A G . PASS AF=0.024 ES:SE:LP:AF:SS:NC:ID 0.024703:0.0429:0.24849:0.024:77096:33640:rs146477069
1 54490 rs141149254 G A . PASS AF=0.153 ES:SE:LP:AF:SS:NC:ID -0.009505:0.0261:0.145694:0.153:77096:33640:rs141149254
1 54676 rs2462492 C T . PASS AF=0.181 ES:SE:LP:AF:SS:NC:ID 0.022202:0.0245:0.436756:0.181:77096:33640:rs2462492
1 54753 rs1472236223 T G . PASS AF=0.025 ES:SE:LP:AF:SS:NC:ID 0.045604:0.0609:0.342562:0.025:77096:33640:rs1472236223
1 55164 rs3091274 C A . PASS AF=0.958 ES:SE:LP:AF:SS:NC:ID -0.006099:0.0452:0.0495378:0.958:77096:33640:rs3091274
1 55299 rs10399749 C T . PASS AF=0.129 ES:SE:LP:AF:SS:NC:ID 0.009505:0.0246:0.155834:0.129:77096:33640:rs10399749
1 55326 rs3107975 T C . PASS AF=0.009 ES:SE:LP:AF:SS:NC:ID -0.036197:0.0587:0.26946:0.009:77096:33640:rs3107975
1 55394 rs2949420 T A . PASS AF=0.016 ES:SE:LP:AF:SS:NC:ID -0.063004:0.082:0.354087:0.016:77096:33640:rs2949420
1 55816 rs3020699 G A . PASS AF=0.011 ES:SE:LP:AF:SS:NC:ID -0.054604:0.1224:0.183427:0.011:77096:33640:rs3020699
1 55850 rs191890754 C G . PASS AF=0.007 ES:SE:LP:AF:SS:NC:ID -0.0305:0.145:0.0790944:0.007:77096:33640:rs191890754
1 55852 rs184233019 G C . PASS AF=0.001 ES:SE:LP:AF:SS:NC:ID 0.748899:0.615:0.650917:0.001:77096:33640:rs184233019
1 57952 rs2691334 A C . PASS AF=0.913 ES:SE:LP:AF:SS:NC:ID -0.070002:0.0336:1.42911:0.913:77096:33640:rs2691334
1 58814 rs114420996 G A . PASS AF=0.061 ES:SE:LP:AF:SS:NC:ID -0.040301:0.033:0.652865:0.061:77096:33640:rs114420996
1 59040 rs62637815 T C . PASS AF=0.057 ES:SE:LP:AF:SS:NC:ID -0.0256:0.0396:0.286174:0.057:77096:33640:rs62637815
1 60726 rs2531295 C A . PASS AF=0.034 ES:SE:LP:AF:SS:NC:ID 0.009098:0.0444:0.0766523:0.034:77096:33640:rs2531295
1 61442 rs2531261 A G . PASS AF=0.988 ES:SE:LP:AF:SS:NC:ID -0.060003:0.0707:0.402086:0.988:77096:33640:rs2531261
1 61462 rs56992750 T A . PASS AF=0 ES:SE:LP:AF:SS:NC:ID -0.067904:0.1326:0.215525:0:77096:33640:rs56992750
1 61743 rs184286948 G C . PASS AF=0.003 ES:SE:LP:AF:SS:NC:ID 0.071204:1.224:0.0206338:0.003:77096:33640:rs184286948
1 61987 rs76735897 A G . PASS AF=0.387 ES:SE:LP:AF:SS:NC:ID 0.018704:0.0199:0.458421:0.387:77096:33640:rs76735897
1 61989 rs77573425 G C . PASS AF=0.387 ES:SE:LP:AF:SS:NC:ID 0.018596:0.0199:0.455064:0.387:77096:33640:rs77573425
1 63671 rs80011619 G A . PASS AF=0.115 ES:SE:LP:AF:SS:NC:ID -0.011203:0.0263:0.17412:0.115:77096:33640:rs80011619
1 64649 rs181431124 A C . PASS AF=0.025 ES:SE:LP:AF:SS:NC:ID 0.007004:0.0702:0.0360234:0.025:77096:33640:rs181431124
1 66162 rs201684885 A T . PASS AF=0.376 ES:SE:LP:AF:SS:NC:ID 0.0044:0.0202:0.0821795:0.376:77096:33640:rs201684885
1 66176 rs1491257206 T A . PASS AF=0.001 ES:SE:LP:AF:SS:NC:ID -0.042302:0.1267:0.131767:0.001:77096:33640:rs1491257206
1 66219 rs1557435148 A T . PASS AF=0.009 ES:SE:LP:AF:SS:NC:ID -0.048104:0.0831:0.249723:0.009:77096:33640:rs1557435148
1 66331 rs1557435418 A C . PASS AF=0 ES:SE:LP:AF:SS:NC:ID 0.201602:0.2541:0.369064:0:77096:33640:rs1557435418
1 66442 rs1227875005 T A . PASS AF=0.015 ES:SE:LP:AF:SS:NC:ID 0.001399:0.0701:0.00713733:0.015:77096:33640:rs1227875005
1 66457 rs1227875005 T A . PASS AF=0.011 ES:SE:LP:AF:SS:NC:ID 0.169498:0.0942:1.14249:0.011:77096:33640:rs1227875005
1 66507 rs1268339504 T A . PASS AF=0.094 ES:SE:LP:AF:SS:NC:ID -0.050904:0.0323:0.938171:0.094:77096:33640:rs1268339504
1 67181 rs28503582 A G . PASS AF=0 ES:SE:LP:AF:SS:NC:ID 0.022102:0.1223:0.0673233:0:77096:33640:rs28503582
1 69511 rs2691305 A G . PASS AF=0.695 ES:SE:LP:AF:SS:NC:ID 0.005495:0.02:0.105352:0.695:77096:33640:rs2691305
1 73841 rs143773730 C T . PASS AF=0.227 ES:SE:LP:AF:SS:NC:ID 0.045499:0.0224:1.37551:0.227:77096:33640:rs143773730
1 77462 rs2462497 G A . PASS AF=0.067 ES:SE:LP:AF:SS:NC:ID 0.030801:0.0372:0.389659:0.067:77096:33640:rs2462497
1 77874 rs62641297 G A . PASS AF=0.042 ES:SE:LP:AF:SS:NC:ID 0.004699:0.0396:0.0430636:0.042:77096:33640:rs62641297
1 77961 rs78385339 G A . PASS AF=0.026 ES:SE:LP:AF:SS:NC:ID 0.007601:0.0445:0.063436:0.026:77096:33640:rs78385339
1 79033 rs2462495 A G . PASS AF=0.971 ES:SE:LP:AF:SS:NC:ID 0.022604:0.0466:0.20211:0.971:77096:33640:rs2462495
1 79050 rs2949413 G T . PASS AF=0.935 ES:SE:LP:AF:SS:NC:ID 0.005296:0.0345:0.0563571:0.935:77096:33640:rs2949413
1 79137 rs143777184 A T . PASS AF=0 ES:SE:LP:AF:SS:NC:ID 0.312398:0.2165:0.826814:0:77096:33640:rs143777184
1 79772 rs147215883 C G . PASS AF=0.087 ES:SE:LP:AF:SS:NC:ID 0.021397:0.0354:0.263843:0.087:77096:33640:rs147215883