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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I9_NONRHEVALV/ukb-d-I9_NONRHEVALV_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T13:05:15.545245",
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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-I9_NONRHEVALV/ukb-d-I9_NONRHEVALV.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I9_NONRHEVALV/ukb-d-I9_NONRHEVALV_data.vcf.gz; Date=Mon Nov 25 13:50:12 2019",
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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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I9_NONRHEVALV/ukb-d-I9_NONRHEVALV.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-I9_NONRHEVALV/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 14:47:28 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-I9_NONRHEVALV/ukb-d-I9_NONRHEVALV.vcf.gz ...
Read summary statistics for 10080949 SNPs.
Dropped 7811 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, 1278650 SNPs remain.
After merging with regression SNP LD, 1278650 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -1.7911e-05 (0.0012)
Lambda GC: 1.0011
Mean Chi^2: 1.0109
Intercept: 1.011 (0.0059)
Ratio: 1.012 (0.5396)
Analysis finished at Mon Nov 25 14:48:59 2019
Total time elapsed: 1.0m:30.87s
{
"af_correlation": 0.942,
"inflation_factor": 1.0068,
"mean_EFFECT": 1.098e-06,
"n": 361194,
"n_snps": 10080949,
"n_clumped_hits": 1,
"n_p_sig": 3,
"n_mono": 0,
"n_ns": 1087834,
"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": 198954,
"n_est": 361260.3782,
"ratio_se_n": 1.0001,
"mean_diff": 0,
"ratio_diff": 46.7215,
"sd_y_est1": 0.0667,
"sd_y_est2": 0.0667,
"r2_sum1": 3.8102e-07,
"r2_sum2": 0.0001,
"r2_sum3": 0.0001,
"r2_sum4": 0.0001,
"ldsc_nsnp_merge_refpanel_ld": 1278650,
"ldsc_nsnp_merge_regression_ld": 1278650,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.011,
"ldsc_intercept_se": 0.0059,
"ldsc_lambda_gc": 1.0011,
"ldsc_mean_chisq": 1.0109,
"ldsc_ratio": 1.0092
}
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 | FALSE |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | TRUE |
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 | 10073692 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 98 | 0 | 48436 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 30250 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.080583e+00 | 6.177836e+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 | 7.876270e+07 | 5.608055e+07 | 3.02000e+02 | 3.249173e+07 | 6.967419e+07 | 1.147315e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.100000e-06 | 3.889000e-04 | -3.60640e-03 | -1.767000e-04 | -1.400000e-06 | 1.737000e-04 | 4.383700e-03 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.283000e-04 | 2.026000e-04 | 1.29100e-04 | 1.730000e-04 | 2.367000e-04 | 4.258000e-04 | 1.152900e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.981895e-01 | 2.892925e-01 | 0.00000e+00 | 2.470831e-01 | 4.985492e-01 | 7.486365e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.981890e-01 | 2.892928e-01 | 0.00000e+00 | 2.470825e-01 | 4.985480e-01 | 7.486356e-01 | 9.999998e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.527173e-01 | 2.629466e-01 | 7.78330e-03 | 3.710480e-02 | 1.467330e-01 | 4.034120e-01 | 9.922170e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 198954 | 0.9802644 | NA | NA | NA | NA | NA | 2.523997e-01 | 2.537952e-01 | 0.00000e+00 | 4.093450e-02 | 1.627400e-01 | 3.997600e-01 | 1.000000e+00 | ▇▃▂▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.611940e+05 | 0.000000e+00 | 3.61194e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0001060 | 0.0002749 | 0.6998243 | 0.6998250 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | 0.0000332 | 0.0002597 | 0.8982481 | 0.8982483 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | -0.0000254 | 0.0002920 | 0.9305630 | 0.9305627 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | 0.0004209 | 0.0006968 | 0.5458370 | 0.5458370 | 0.0156880 | 0.0045926 | 361194 |
1 | 730087 | rs148120343 | T | C | 0.0006105 | 0.0003619 | 0.0915693 | 0.0915685 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | 0.0000587 | 0.0002463 | 0.8115990 | 0.8115992 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | 0.0001028 | 0.0002628 | 0.6956487 | 0.6956484 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | 0.0000714 | 0.0002465 | 0.7719479 | 0.7719480 | 0.1209650 | 0.1525560 | 361194 |
1 | 749963 | rs529266287 | T | TAA | -0.0000396 | 0.0002430 | 0.8704469 | 0.8704465 | 0.8697420 | 0.7641770 | 361194 |
1 | 751343 | rs28544273 | T | A | 0.0000233 | 0.0002406 | 0.9228281 | 0.9228279 | 0.1229160 | 0.2426120 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 1.02e-05 | 0.0002846 | 0.9714890 | 0.9714893 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | 5.31e-05 | 0.0003128 | 0.8650761 | 0.8650760 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | 3.84e-05 | 0.0001505 | 0.7984380 | 0.7984383 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | 6.00e-05 | 0.0001539 | 0.6967083 | 0.6967078 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | 3.62e-05 | 0.0001415 | 0.7978960 | 0.7978957 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | 4.07e-05 | 0.0001505 | 0.7866237 | 0.7866229 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | 3.90e-05 | 0.0001571 | 0.8038629 | 0.8038627 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | 4.41e-05 | 0.0001583 | 0.7807302 | 0.7807297 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | 3.81e-05 | 0.0001505 | 0.8000870 | 0.8000861 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | -5.86e-04 | 0.0005163 | 0.2563770 | 0.2563766 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID 0.000105988:0.000274896:0.155011:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID 3.32145e-05:0.000259743:0.0466037:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID -2.54444e-05:0.000292005:0.0312542:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID 0.000420873:0.000696798:0.262937:0.015688:361194:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID 0.000610515:0.000361855:1.03825:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID 5.87187e-05:0.000246341:0.0906585:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID 0.000102796:0.00026277:0.15761:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID 7.1435e-05:0.000246474:0.112412:0.120965:361194:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID -3.96286e-05:0.000242984:0.0602577:0.869742:361194:rs529266287
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID 2.33117e-05:0.000240644:0.0348792:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID 6.57218e-05:0.000237863:0.106617:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID 2.67921e-05:0.000240309:0.0403729:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID 2.95479e-05:0.000234173:0.0459554:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID 1.16152e-05:0.000238054:0.0172382:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID -2.19318e-05:0.00023476:0.0335917:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID -0.000387536:0.000425909:0.440245:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID 2.70035e-05:0.000233929:0.0418658:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID 3.53623e-05:0.000234036:0.0555672:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID 2.70779e-05:0.000233921:0.0419883:0.870481:361194:rs3131967
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID 2.41883e-05:0.000233509:0.0373949:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID 5.19422e-06:0.000238265:0.00762015:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID 1.97459e-05:0.000232947:0.0303754:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID 6.66611e-06:0.000232735:0.0100388:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID 1.35968e-05:0.000233148:0.0206816:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID 1.3846e-05:0.000233164:0.021068:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID 1.38939e-05:0.000233172:0.0211419:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID 1.9256e-05:0.000233765:0.0294904:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID 3.78657e-05:0.000271649:0.0510294:0.0988442:361194:rs10157329
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID -8.31562e-07:0.000237249:0.00121642:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID 4.5691e-05:0.000232658:0.0734996:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID 2.37642e-05:0.000234917:0.0364842:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID 1.83484e-05:0.000234964:0.0279101:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -9.13058e-05:0.000281296:0.127557:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 4.66498e-06:0.000237641:0.00685575:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 4.66731e-06:0.000237641:0.00685928:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID 4.64074e-06:0.000237646:0.00681957:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID 1.66593e-05:0.000237781:0.0249613:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID 2.02618e-05:0.000237969:0.0305161:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID -5.34104e-06:0.000259062:0.00720312:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID -7.35374e-05:0.000232571:0.123865:0.855376:361194:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID 0.000134702:0.000229124:0.254456:0.838358:361194:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763351 ES:SE:LP:AF:SS:ID 0.000144203:0.000184402:0.362299:0.763351:361194:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105921 ES:SE:LP:AF:SS:ID -0.000260672:0.00025406:0.515868:0.105921:361194:rs12562034
1 769138 rs59306077 CAT C . PASS AF=0.128938 ES:SE:LP:AF:SS:ID 1.51538e-05:0.00023464:0.0229599:0.128938:361194:rs762168062
1 769223 rs60320384 C G . PASS AF=0.128608 ES:SE:LP:AF:SS:ID 2.48262e-06:0.000234423:0.00368538:0.128608:361194:rs60320384
1 769963 rs7518545 G A . PASS AF=0.105213 ES:SE:LP:AF:SS:ID -0.000246553:0.000255979:0.474361:0.105213:361194:rs7518545
1 770181 rs146076599 A G . PASS AF=0.009077 ES:SE:LP:AF:SS:ID -0.00137858:0.00090244:0.897535:0.009077:361194:rs146076599
1 770886 rs371458725 G A . PASS AF=0.104268 ES:SE:LP:AF:SS:ID -0.000236158:0.000258025:0.443626:0.104268:361194:rs371458725
1 771410 rs2519006 C T . PASS AF=0.830106 ES:SE:LP:AF:SS:ID -3.83768e-05:0.000228418:0.0621943:0.830106:361194:rs2519006
1 771823 rs2977605 T C . PASS AF=0.87012 ES:SE:LP:AF:SS:ID -7.04692e-06:0.000233374:0.0105898:0.87012:361194:rs2977605