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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-22610_0/ukb-d-22610_0.vcf.gz; Date=Sun May 10 12:07:50 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-22610_0/ukb-d-22610_0.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-22610_0/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 16:38:46 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22610_0/ukb-d-22610_0.vcf.gz ...
Read summary statistics for 13566574 SNPs.
Dropped 12683 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0158 (0.0047)
Lambda GC: 1.0268
Mean Chi^2: 1.0272
Intercept: 1.0002 (0.0057)
Ratio: 0.008 (0.208)
Analysis finished at Mon Nov 25 16:41:02 2019
Total time elapsed: 2.0m:15.85s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0181,
"mean_EFFECT": -0,
"n": 88638,
"n_snps": 13566574,
"n_clumped_hits": 0,
"n_p_sig": 3,
"n_mono": 0,
"n_ns": 1251219,
"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": 562992,
"n_est": 88961.4134,
"ratio_se_n": 1.0018,
"mean_diff": -0,
"ratio_diff": 12.8994,
"sd_y_est1": 0.2295,
"sd_y_est2": 0.23,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1283504,
"ldsc_nsnp_merge_regression_ld": 1283504,
"ldsc_observed_scale_h2_beta": 0.0158,
"ldsc_observed_scale_h2_se": 0.0047,
"ldsc_intercept_beta": 1.0002,
"ldsc_intercept_se": 0.0057,
"ldsc_lambda_gc": 1.0268,
"ldsc_mean_chisq": 1.0272,
"ldsc_ratio": 0.0074
}
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 | 1.0000000 | 3 | 94 | 0 | 13554555 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57045 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33332 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051324e+00 | 6.184975e+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 | 7.902468e+07 | 5.591663e+07 | 3.02000e+02 | 3.292804e+07 | 7.013432e+07 | 1.148619e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.290000e-05 | 6.377300e-03 | -8.96773e-02 | -1.659100e-03 | 1.630000e-05 | 1.721600e-03 | 7.070390e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.562600e-03 | 4.397000e-03 | 8.98800e-04 | 1.303600e-03 | 2.397800e-03 | 6.551400e-03 | 2.207030e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.966935e-01 | 2.895957e-01 | 0.00000e+00 | 2.450569e-01 | 4.961454e-01 | 7.471280e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.966917e-01 | 2.895968e-01 | 0.00000e+00 | 2.450534e-01 | 4.961442e-01 | 7.471276e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.910729e-01 | 2.544764e-01 | 1.00000e-03 | 7.499400e-03 | 6.030680e-02 | 2.957860e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 562992 | 0.9585015 | NA | NA | NA | NA | NA | 1.965265e-01 | 2.471471e-01 | 0.00000e+00 | 5.790700e-03 | 8.446490e-02 | 3.085060e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.863800e+04 | 0.000000e+00 | 8.86380e+04 | 8.863800e+04 | 8.863800e+04 | 8.863800e+04 | 8.863800e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0017553 | 0.0019044 | 0.3566794 | 0.3566758 | 0.1113450 | 0.1894970 | 88638 |
1 | 693731 | rs12238997 | A | G | -0.0021760 | 0.0018044 | 0.2278468 | 0.2278432 | 0.1163190 | 0.1417730 | 88638 |
1 | 707522 | rs371890604 | G | C | -0.0020244 | 0.0020279 | 0.3181427 | 0.3181417 | 0.0977362 | 0.1293930 | 88638 |
1 | 717587 | rs144155419 | G | A | 0.0028666 | 0.0048257 | 0.5524946 | 0.5524913 | 0.0158097 | 0.0045926 | 88638 |
1 | 723329 | rs189787166 | A | T | -0.0147232 | 0.0140751 | 0.2955432 | 0.2955399 | 0.0017813 | 0.0003994 | 88638 |
1 | 730087 | rs148120343 | T | C | -0.0022025 | 0.0025032 | 0.3789309 | 0.3789286 | 0.0567943 | 0.0127796 | 88638 |
1 | 731718 | rs142557973 | T | C | -0.0023503 | 0.0017121 | 0.1698431 | 0.1698374 | 0.1221780 | 0.1543530 | 88638 |
1 | 732032 | rs61770163 | A | C | -0.0018804 | 0.0018257 | 0.3030421 | 0.3030389 | 0.1218840 | 0.1555510 | 88638 |
1 | 734349 | rs141242758 | T | C | -0.0022783 | 0.0017134 | 0.1836272 | 0.1836238 | 0.1214140 | 0.1525560 | 88638 |
1 | 740284 | rs61770167 | C | T | 0.0019835 | 0.0078522 | 0.8005720 | 0.8005715 | 0.0057548 | 0.0023962 | 88638 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | -0.0042774 | 0.0020029 | 0.0327122 | 0.0327093 | 0.0550976 | 0.0309934 | 88638 |
23 | 154923374 | rs111332691 | T | A | 0.0025130 | 0.0021730 | 0.2474862 | 0.2474826 | 0.0449751 | 0.0116556 | 88638 |
23 | 154925045 | rs509981 | C | T | -0.0001630 | 0.0010489 | 0.8764911 | 0.8764907 | 0.2446440 | 0.3634440 | 88638 |
23 | 154925895 | rs538470 | C | T | -0.0002911 | 0.0010722 | 0.7859990 | 0.7859992 | 0.2411540 | 0.3634440 | 88638 |
23 | 154927581 | rs644138 | G | A | -0.0012030 | 0.0009866 | 0.2227168 | 0.2227141 | 0.3001550 | 0.4635760 | 88638 |
23 | 154929412 | rs557132 | C | T | -0.0001611 | 0.0010492 | 0.8779660 | 0.8779651 | 0.2444980 | 0.3568210 | 88638 |
23 | 154929637 | rs35185538 | CT | C | -0.0001723 | 0.0010955 | 0.8750001 | 0.8750003 | 0.2289290 | 0.3011920 | 88638 |
23 | 154929952 | rs4012982 | CAA | C | -0.0006521 | 0.0011044 | 0.5548595 | 0.5548589 | 0.2384260 | 0.3165560 | 88638 |
23 | 154930230 | rs781880 | A | G | -0.0001422 | 0.0010488 | 0.8921459 | 0.8921458 | 0.2449550 | 0.3618540 | 88638 |
23 | 154930487 | rs781879 | T | A | 0.0004696 | 0.0035577 | 0.8949989 | 0.8949992 | 0.0196537 | 0.1263580 | 88638 |
1 692794 rs530212009 CA C . PASS AF=0.111345 ES:SE:LP:AF:SS:ID -0.00175531:0.00190439:0.447722:0.111345:88638:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116319 ES:SE:LP:AF:SS:ID -0.00217595:0.00180437:0.642357:0.116319:88638:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0977362 ES:SE:LP:AF:SS:ID -0.00202443:0.00202791:0.497378:0.0977362:88638:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0158097 ES:SE:LP:AF:SS:ID 0.00286661:0.00482569:0.257672:0.0158097:88638:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00178134 ES:SE:LP:AF:SS:ID -0.0147232:0.0140751:0.529379:0.00178134:88638:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0567943 ES:SE:LP:AF:SS:ID -0.00220254:0.00250325:0.42144:0.0567943:88638:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122178 ES:SE:LP:AF:SS:ID -0.0023503:0.00171214:0.769952:0.122178:88638:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121884 ES:SE:LP:AF:SS:ID -0.0018804:0.00182574:0.518497:0.121884:88638:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121414 ES:SE:LP:AF:SS:ID -0.0022783:0.00171342:0.736063:0.121414:88638:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00575478 ES:SE:LP:AF:SS:ID 0.00198352:0.00785218:0.0965996:0.00575478:88638:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00182996 ES:SE:LP:AF:SS:ID -0.00584923:0.0150188:0.156806:0.00182996:88638:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869087 ES:SE:LP:AF:SS:ID 0.00219224:0.00168504:0.713854:0.869087:88638:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00161171 ES:SE:LP:AF:SS:ID -0.00811028:0.0148064:0.23369:0.00161171:88638:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12356 ES:SE:LP:AF:SS:ID -0.0017416:0.00167054:0.527001:0.12356:88638:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.1431 ES:SE:LP:AF:SS:ID -0.00163509:0.00165348:0.491166:0.1431:88638:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123692 ES:SE:LP:AF:SS:ID -0.00168937:0.00166814:0.50697:0.123692:88638:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87006 ES:SE:LP:AF:SS:ID 0.0018097:0.00162552:0.575803:0.87006:88638:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874702 ES:SE:LP:AF:SS:ID 0.00154907:0.00165191:0.457952:0.874702:88638:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129376 ES:SE:LP:AF:SS:ID -0.00176191:0.00163047:0.553041:0.129376:88638:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0357522 ES:SE:LP:AF:SS:ID -0.00419896:0.0029802:0.799005:0.0357522:88638:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869698 ES:SE:LP:AF:SS:ID 0.00176791:0.00162412:0.558519:0.869698:88638:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869776 ES:SE:LP:AF:SS:ID 0.00181074:0.00162483:0.576585:0.869776:88638:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869694 ES:SE:LP:AF:SS:ID 0.00177093:0.00162405:0.559842:0.869694:88638:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00531348 ES:SE:LP:AF:SS:ID -0.00134692:0.0081062:0.0614643:0.00531348:88638:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00527862 ES:SE:LP:AF:SS:ID -0.00153841:0.00812609:0.0706608:0.00527862:88638:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00567028 ES:SE:LP:AF:SS:ID -0.0021741:0.00798319:0.104928:0.00567028:88638:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869688 ES:SE:LP:AF:SS:ID 0.00170794:0.00162074:0.534653:0.869688:88638:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126767 ES:SE:LP:AF:SS:ID -0.00183165:0.0016543:0.571527:0.126767:88638:rs61768170
1 756604 rs3131962 A G . PASS AF=0.869215 ES:SE:LP:AF:SS:ID 0.00171282:0.0016165:0.538596:0.869215:88638:rs3131962
1 757640 rs3115853 G A . PASS AF=0.86859 ES:SE:LP:AF:SS:ID 0.00166318:0.00161543:0.518245:0.86859:88638:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869368 ES:SE:LP:AF:SS:ID 0.00169876:0.00161801:0.532003:0.869368:88638:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869374 ES:SE:LP:AF:SS:ID 0.00170116:0.00161811:0.532963:0.869374:88638:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869376 ES:SE:LP:AF:SS:ID 0.00170315:0.00161813:0.533795:0.869376:88638:rs3131956
1 758626 rs3131954 C T . PASS AF=0.86985 ES:SE:LP:AF:SS:ID 0.001741:0.00162245:0.547841:0.86985:88638:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0990386 ES:SE:LP:AF:SS:ID -0.00171251:0.00188809:0.438414:0.0990386:88638:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00651513 ES:SE:LP:AF:SS:ID 0.00145755:0.00726878:0.0751663:0.00651513:88638:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873831 ES:SE:LP:AF:SS:ID 0.00138102:0.00164641:0.396229:0.873831:88638:rs3115851
1 761732 rs2286139 C T . PASS AF=0.863222 ES:SE:LP:AF:SS:ID 0.00218522:0.00161496:0.754428:0.863222:88638:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868644 ES:SE:LP:AF:SS:ID 0.00144545:0.00163103:0.425389:0.868644:88638:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865523 ES:SE:LP:AF:SS:ID 0.0014003:0.00163143:0.40814:0.865523:88638:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0993726 ES:SE:LP:AF:SS:ID -0.00192765:0.00195312:0.489904:0.0993726:88638:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870804 ES:SE:LP:AF:SS:ID 0.00152025:0.00164997:0.447509:0.870804:88638:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870804 ES:SE:LP:AF:SS:ID 0.00152023:0.00164997:0.447498:0.870804:88638:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870801 ES:SE:LP:AF:SS:ID 0.00152101:0.00164998:0.4478:0.870801:88638:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871168 ES:SE:LP:AF:SS:ID 0.00144063:0.00165074:0.417007:0.871168:88638:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126371 ES:SE:LP:AF:SS:ID -0.00151107:0.00165238:0.443133:0.126371:88638:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105855 ES:SE:LP:AF:SS:ID -0.00245321:0.00179694:0.763992:0.105855:88638:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854488 ES:SE:LP:AF:SS:ID 0.00109544:0.00161417:0.30332:0.854488:88638:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00169447 ES:SE:LP:AF:SS:ID -0.0117282:0.014118:0.391332:0.00169447:88638:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.839146 ES:SE:LP:AF:SS:ID -0.000358083:0.00159457:0.0849597:0.839146:88638:rs376645387