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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIANAS/ukb-d-M13_DORSALGIANAS_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T13:07:07.936457",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"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-M13_DORSALGIANAS/ukb-d-M13_DORSALGIANAS.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIANAS/ukb-d-M13_DORSALGIANAS_data.vcf.gz; Date=Mon Nov 25 13:56:21 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-M13_DORSALGIANAS/ukb-d-M13_DORSALGIANAS.vcf.gz; Date=Sat May 9 16:20:39 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-M13_DORSALGIANAS/ukb-d-M13_DORSALGIANAS.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-M13_DORSALGIANAS/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 14:57:54 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIANAS/ukb-d-M13_DORSALGIANAS.vcf.gz ...
Read summary statistics for 10546672 SNPs.
Dropped 8449 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, 1280867 SNPs remain.
After merging with regression SNP LD, 1280867 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0039 (0.0014)
Lambda GC: 1.0292
Mean Chi^2: 1.0283
Intercept: 0.9999 (0.0065)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 14:59:39 2019
Total time elapsed: 1.0m:45.17s
{
"af_correlation": 0.9442,
"inflation_factor": 1.0217,
"mean_EFFECT": 4.4317e-07,
"n": 361194,
"n_snps": 10546672,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1114384,
"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": 207569,
"n_est": 361427.5007,
"ratio_se_n": 1.0003,
"mean_diff": 5.0177e-06,
"ratio_diff": 15.5163,
"sd_y_est1": 0.0766,
"sd_y_est2": 0.0766,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1280867,
"ldsc_nsnp_merge_regression_ld": 1280867,
"ldsc_observed_scale_h2_beta": 0.0039,
"ldsc_observed_scale_h2_se": 0.0014,
"ldsc_intercept_beta": 0.9999,
"ldsc_intercept_se": 0.0065,
"ldsc_lambda_gc": 1.0292,
"ldsc_mean_chisq": 1.0283,
"ldsc_ratio": -0.0035
}
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 | 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 | 1.000000 | 3 | 94 | 0 | 10538792 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.000000 | 1 | 100 | 0 | 49835 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.000000 | 1 | 342 | 0 | 30799 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | 9.075309e+00 | 6.178523e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.879762e+07 | 5.605012e+07 | 3.02000e+02 | 3.256543e+07 | 6.974348e+07 | 1.147409e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.000000e-07 | 4.964000e-04 | -4.63040e-03 | -2.136000e-04 | -2.400000e-06 | 2.106000e-04 | 5.624300e-03 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.106000e-04 | 2.760000e-04 | 1.48300e-04 | 2.007000e-04 | 2.836000e-04 | 5.405000e-04 | 1.545400e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.967254e-01 | 2.895346e-01 | 2.00000e-07 | 2.450867e-01 | 4.953800e-01 | 7.475599e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.967250e-01 | 2.895349e-01 | 2.00000e-07 | 2.450858e-01 | 4.953799e-01 | 7.475597e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | 2.424295e-01 | 2.625552e-01 | 5.90180e-03 | 3.009490e-02 | 1.318890e-01 | 3.879890e-01 | 9.940980e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 207569 | 0.980319 | NA | NA | NA | NA | NA | 2.423459e-01 | 2.535116e-01 | 0.00000e+00 | 3.115020e-02 | 1.487620e-01 | 3.851840e-01 | 1.000000e+00 | ▇▂▂▁▁ |
numeric | N | 0 | 1.000000 | 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 | 0.0002436 | 0.0003159 | 0.4404950 | 0.4404937 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | 0.0001175 | 0.0002985 | 0.6938395 | 0.6938385 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | 0.0000380 | 0.0003355 | 0.9099059 | 0.9099062 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | 0.0009271 | 0.0008006 | 0.2468982 | 0.2468977 | 0.0156880 | 0.0045926 | 361194 |
1 | 730087 | rs148120343 | T | C | -0.0003543 | 0.0004158 | 0.3941913 | 0.3941902 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | 0.0001306 | 0.0002831 | 0.6444126 | 0.6444119 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | 0.0001298 | 0.0003019 | 0.6673567 | 0.6673568 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | 0.0001192 | 0.0002832 | 0.6738233 | 0.6738229 | 0.1209650 | 0.1525560 | 361194 |
1 | 749963 | rs529266287 | T | TAA | -0.0002794 | 0.0002792 | 0.3169013 | 0.3168999 | 0.8697420 | 0.7641770 | 361194 |
1 | 751343 | rs28544273 | T | A | 0.0001509 | 0.0002765 | 0.5851309 | 0.5851313 | 0.1229160 | 0.2426120 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0000303 | 0.0003270 | 0.9262050 | 0.9262052 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | 0.0008381 | 0.0003594 | 0.0196929 | 0.0196923 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | 0.0003254 | 0.0001729 | 0.0598508 | 0.0598492 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | 0.0003370 | 0.0001769 | 0.0567518 | 0.0567514 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | 0.0002860 | 0.0001626 | 0.0786412 | 0.0786418 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | 0.0003261 | 0.0001730 | 0.0593649 | 0.0593648 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | 0.0004200 | 0.0001805 | 0.0199986 | 0.0199976 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | 0.0003406 | 0.0001819 | 0.0612097 | 0.0612090 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | 0.0003329 | 0.0001729 | 0.0542300 | 0.0542283 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | 0.0008140 | 0.0005933 | 0.1700772 | 0.1700761 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID 0.000243644:0.000315863:0.356059:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID 0.000117486:0.000298452:0.158741:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID 3.79666e-05:0.000335522:0.0410035:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID 0.000927074:0.000800639:0.607482:0.015688:361194:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID -0.000354265:0.000415783:0.404293:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID 0.00013064:0.000283053:0.190836:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID 0.000129763:0.00030193:0.175642:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID 0.000119203:0.000283205:0.171454:0.120965:361194:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID -0.000279432:0.000279195:0.499076:0.869742:361194:rs529266287
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID 0.000150946:0.000276506:0.232747:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID 0.000158368:0.000273311:0.250039:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID 0.000146286:0.000276121:0.224566:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID -7.80039e-05:0.000269071:0.112443:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID -0.000116224:0.00027353:0.173338:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID 0.000126163:0.000269746:0.193825:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID 7.67922e-05:0.000489381:0.0578381:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID -8.24669e-05:0.000268791:0.119763:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID -8.8081e-05:0.000268914:0.128861:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID -8.34153e-05:0.000268781:0.121307:0.870481:361194:rs3131967
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID -9.73121e-05:0.000268308:0.144578:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID 0.000186201:0.000273773:0.304148:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID -0.000111125:0.000267663:0.168759:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID -0.000111861:0.000267419:0.170228:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID -0.00010777:0.000267893:0.162745:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID -0.000107844:0.000267912:0.162859:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID -0.000108261:0.00026792:0.163578:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID -9.27278e-05:0.000268603:0.136721:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID 2.13819e-05:0.000312133:0.0243908:0.0988442:361194:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00647588 ES:SE:LP:AF:SS:ID 0.00157429:0.00120734:0.716113:0.00647588:361194:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID -0.000132528:0.000272606:0.20283:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID -9.75993e-05:0.00026733:0.145667:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID -0.000107469:0.000269926:0.160821:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID -7.45664e-05:0.000269981:0.106571:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID 0.000134422:0.000323217:0.169096:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID -0.000111763:0.000273056:0.166014:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID -0.00011176:0.000273056:0.166009:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID -0.000111757:0.000273062:0.166:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID -0.000117113:0.000273217:0.175106:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID 0.000164228:0.000273433:0.261143:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID 0.000101044:0.000297669:0.134144:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID -0.000177715:0.00026723:0.29582:0.855376:361194:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID -0.000201048:0.000263269:0.351571:0.838358:361194:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763351 ES:SE:LP:AF:SS:ID -0.000152032:0.000211883:0.325095:0.763351:361194:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105921 ES:SE:LP:AF:SS:ID 0.000154552:0.000291923:0.224382:0.105921:361194:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00768395 ES:SE:LP:AF:SS:ID 0.000423786:0.00108463:0.157388:0.00768395:361194:rs12562811
1 769138 rs59306077 CAT C . PASS AF=0.128938 ES:SE:LP:AF:SS:ID 0.000161871:0.000269608:0.261027:0.128938:361194:rs762168062
1 769223 rs60320384 C G . PASS AF=0.128608 ES:SE:LP:AF:SS:ID 0.0001592:0.000269359:0.256099:0.128608:361194:rs60320384
1 769963 rs7518545 G A . PASS AF=0.105213 ES:SE:LP:AF:SS:ID 0.000181253:0.000294128:0.269429:0.105213:361194:rs7518545
1 770181 rs146076599 A G . PASS AF=0.009077 ES:SE:LP:AF:SS:ID -0.000271389:0.00103693:0.100434:0.009077:361194:rs146076599
1 770377 rs112563271 A T . PASS AF=0.00769858 ES:SE:LP:AF:SS:ID 0.000478034:0.00108944:0.179921:0.00769858:361194:rs112563271