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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_SCIATICA/ukb-d-M13_SCIATICA_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
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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-M13_SCIATICA/ukb-d-M13_SCIATICA.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_SCIATICA/ukb-d-M13_SCIATICA_data.vcf.gz; Date=Mon Nov 25 13:51:07 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-M13_SCIATICA/ukb-d-M13_SCIATICA.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_SCIATICA/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 15:00:52 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_SCIATICA/ukb-d-M13_SCIATICA.vcf.gz ...
Read summary statistics for 9530485 SNPs.
Dropped 7087 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, 1273500 SNPs remain.
After merging with regression SNP LD, 1273500 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0005 (0.0011)
Lambda GC: 1.0151
Mean Chi^2: 1.0129
Intercept: 1.0094 (0.0059)
Ratio: 0.7299 (0.4583)
Analysis finished at Mon Nov 25 15:02:30 2019
Total time elapsed: 1.0m:38.08s
{
"af_correlation": 0.939,
"inflation_factor": 1.0132,
"mean_EFFECT": 1.7198e-06,
"n": 361194,
"n_snps": 9530485,
"n_clumped_hits": 3,
"n_p_sig": 9,
"n_mono": 0,
"n_ns": 1052738,
"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": 190577,
"n_est": 361031.5725,
"ratio_se_n": 0.9998,
"mean_diff": 0,
"ratio_diff": 69.4898,
"sd_y_est1": 0.0566,
"sd_y_est2": 0.0566,
"r2_sum1": 9.1112e-07,
"r2_sum2": 0.0003,
"r2_sum3": 0.0003,
"r2_sum4": 0.0003,
"ldsc_nsnp_merge_refpanel_ld": 1273500,
"ldsc_nsnp_merge_regression_ld": 1273500,
"ldsc_observed_scale_h2_beta": 0.0005,
"ldsc_observed_scale_h2_se": 0.0011,
"ldsc_intercept_beta": 1.0094,
"ldsc_intercept_se": 0.0059,
"ldsc_lambda_gc": 1.0151,
"ldsc_mean_chisq": 1.0129,
"ldsc_ratio": 0.7287
}
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 | 9523934 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 98 | 0 | 46519 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 29458 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.079971e+00 | 6.174483e+00 | 1.00000e+00 | 4.00000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.871284e+07 | 5.611441e+07 | 3.02000e+02 | 3.24174e+07 | 6.958440e+07 | 1.147348e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.700000e-06 | 2.899000e-04 | -3.21600e-03 | -1.42100e-04 | 3.000000e-07 | 1.424000e-04 | 3.320600e-03 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.534000e-04 | 1.396000e-04 | 1.09600e-04 | 1.45400e-04 | 1.920000e-04 | 3.225000e-04 | 7.853000e-04 | ▇▂▂▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.981682e-01 | 2.889478e-01 | 0.00000e+00 | 2.47362e-01 | 4.971770e-01 | 7.484366e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.981678e-01 | 2.889480e-01 | 0.00000e+00 | 2.47361e-01 | 4.971767e-01 | 7.484360e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.657774e-01 | 2.627603e-01 | 1.08413e-02 | 4.74662e-02 | 1.653730e-01 | 4.224430e-01 | 9.891580e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 190577 | 0.9800034 | NA | NA | NA | NA | NA | 2.651590e-01 | 2.535605e-01 | 0.00000e+00 | 5.43131e-02 | 1.801120e-01 | 4.173320e-01 | 1.000000e+00 | ▇▃▂▂▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.611940e+05 | 0.000000e+00 | 3.61194e+05 | 3.61194e+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 | 0.0001126 | 0.0002334 | 0.6295845 | 0.6295863 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | -0.0000001 | 0.0002205 | 0.9997440 | 0.9997439 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | 0.0000835 | 0.0002479 | 0.7361901 | 0.7361902 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | -0.0002025 | 0.0005915 | 0.7321263 | 0.7321270 | 0.0156880 | 0.0045926 | 361194 |
1 | 730087 | rs148120343 | T | C | 0.0001866 | 0.0003072 | 0.5436295 | 0.5436292 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | 0.0000157 | 0.0002091 | 0.9400170 | 0.9400172 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | 0.0000353 | 0.0002231 | 0.8743480 | 0.8743475 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | 0.0000218 | 0.0002092 | 0.9171670 | 0.9171670 | 0.1209650 | 0.1525560 | 361194 |
1 | 749963 | rs529266287 | T | TAA | 0.0000738 | 0.0002063 | 0.7203806 | 0.7203803 | 0.8697420 | 0.7641770 | 361194 |
1 | 751343 | rs28544273 | T | A | -0.0000438 | 0.0002043 | 0.8301290 | 0.8301283 | 0.1229160 | 0.2426120 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0001401 | 0.0002416 | 0.5619828 | 0.5619821 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | -0.0000666 | 0.0002655 | 0.8019509 | 0.8019513 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | -0.0000455 | 0.0001278 | 0.7214895 | 0.7214903 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | -0.0000397 | 0.0001307 | 0.7615528 | 0.7615521 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | 0.0000039 | 0.0001201 | 0.9740160 | 0.9740155 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | -0.0000440 | 0.0001278 | 0.7304105 | 0.7304107 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | 0.0000853 | 0.0001334 | 0.5225165 | 0.5225163 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | -0.0000272 | 0.0001344 | 0.8397560 | 0.8397563 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | -0.0000404 | 0.0001278 | 0.7517302 | 0.7517292 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | -0.0000202 | 0.0004383 | 0.9632739 | 0.9632739 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID 0.000112557:0.000233371:0.200946:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID -7.07702e-08:0.000220507:0.000111194:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID 8.35165e-05:0.000247895:0.13301:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID -0.000202483:0.000591541:0.135414:0.015688:361194:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID 0.00018657:0.000307195:0.264697:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID 1.57366e-05:0.000209129:0.0268643:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID 3.52771e-05:0.000223077:0.0583157:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID 2.17618e-05:0.000209242:0.0375516:0.120965:361194:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID 7.38377e-05:0.000206279:0.142438:0.869742:361194:rs529266287
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID -4.38282e-05:0.000204292:0.0808544:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID 2.77821e-05:0.000201932:0.0503315:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID -4.68969e-05:0.000204008:0.0871474:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID 5.33946e-05:0.000198799:0.103337:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID 0.000117013:0.000202093:0.24981:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID -3.19471e-05:0.000199298:0.0591619:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID -0.000417979:0.000361571:0.606113:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID 6.61627e-05:0.000198592:0.131347:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID 6.41914e-05:0.000198683:0.126894:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID 6.62646e-05:0.000198585:0.13158:0.870481:361194:rs3131967
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID 5.43951e-05:0.000198235:0.105806:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID -2.42364e-05:0.000202273:0.0435309:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID 4.78729e-05:0.000197758:0.0922018:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID 6.27105e-05:0.000197578:0.124393:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID 4.53884e-05:0.000197929:0.0869161:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID 4.54271e-05:0.000197943:0.0869898:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID 4.50858e-05:0.000197949:0.0862767:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID 5.53361e-05:0.000198453:0.107699:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID -0.000163323:0.000230614:0.319832:0.0988442:361194:rs10157329
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID 0.000120141:0.00020141:0.258973:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID 0.000119465:0.000197513:0.26338:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID 1.96795e-05:0.000199431:0.0355546:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID 9.0656e-05:0.000199471:0.187433:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -0.00031815:0.000238803:0.738088:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000102311:0.000201743:0.213206:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000102313:0.000201743:0.21321:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID 0.000102042:0.000201747:0.212537:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID 9.48807e-05:0.000201862:0.194951:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID -6.90509e-05:0.000202022:0.135191:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID 1.44294e-05:0.000219928:0.0233342:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID 6.87764e-05:0.000197439:0.138117:0.855376:361194:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID 0.000141266:0.000194513:0.330049:0.838358:361194:rs376645387
1 768253 rs2977608 A C . PASS AF=0.763351 ES:SE:LP:AF:SS:ID 0.000162728:0.000156546:0.524944:0.763351:361194:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105921 ES:SE:LP:AF:SS:ID -0.000223816:0.000215682:0.523741:0.105921:361194:rs12562034
1 769138 rs59306077 CAT C . PASS AF=0.128938 ES:SE:LP:AF:SS:ID -2.61926e-05:0.000199196:0.0479897:0.128938:361194:rs762168062
1 769223 rs60320384 C G . PASS AF=0.128608 ES:SE:LP:AF:SS:ID -1.8688e-05:0.000199012:0.0337714:0.128608:361194:rs60320384
1 769963 rs7518545 G A . PASS AF=0.105213 ES:SE:LP:AF:SS:ID -0.000223551:0.000217311:0.517678:0.105213:361194:rs7518545
1 770886 rs371458725 G A . PASS AF=0.104268 ES:SE:LP:AF:SS:ID -0.000234004:0.000219048:0.544551:0.104268:361194:rs371458725
1 771410 rs2519006 C T . PASS AF=0.830106 ES:SE:LP:AF:SS:ID -5.45583e-05:0.000193913:0.108775:0.830106:361194:rs2519006
1 771823 rs2977605 T C . PASS AF=0.87012 ES:SE:LP:AF:SS:ID 5.10433e-05:0.00019812:0.0987123:0.87012:361194:rs2977605
1 771967 rs59066358 G A . PASS AF=0.128668 ES:SE:LP:AF:SS:ID -1.75301e-05:0.000198919:0.0316217:0.128668:361194:rs59066358