manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/def6ca9d-c661-4752-a5cd-ca4cc91dc39b/call-vcf/inputs/-261043391/upload.txt.gz --id ieu-b-4975 --json /data/cromwell-executions/qc/def6ca9d-c661-4752-a5cd-ca4cc91dc39b/call-vcf/inputs/-261043391/ieu-b-4975_data.json --ref /data/cromwell-executions/qc/def6ca9d-c661-4752-a5cd-ca4cc91dc39b/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/def6ca9d-c661-4752-a5cd-ca4cc91dc39b/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4975/ieu-b-4975.vcf.gz --alias alias.txt --cohort_cases 4836 --cohort_controls 481648; 1.3.0",
"file_date": "2022-04-23T01:35:04.181290",
"bcftools_viewVersion": "1.9+htslib-1.9",
"bcftools_viewCommand": "view -h /data/cromwell-executions/qc/def6ca9d-c661-4752-a5cd-ca4cc91dc39b/call-report/inputs/-261043391/ieu-b-4975.vcf.gz; Date=Sat Apr 23 02:04:43 2022"
}
*********************************************************************
* 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/def6ca9d-c661-4752-a5cd-ca4cc91dc39b/call-ldsc/inputs/-261043391/ieu-b-4975.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4975/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Sat Apr 23 01:51:59 2022
Reading summary statistics from /data/cromwell-executions/qc/def6ca9d-c661-4752-a5cd-ca4cc91dc39b/call-ldsc/inputs/-261043391/ieu-b-4975.vcf.gz ...
Read summary statistics for 12242512 SNPs.
Dropped 231394 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
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] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1220578 SNPs remain.
After merging with regression SNP LD, 1220578 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0032 (0.001)
Lambda GC: 1.0402
Mean Chi^2: 1.0388
Intercept: 1.0083 (0.0067)
Ratio: 0.2132 (0.1714)
Analysis finished at Sat Apr 23 01:54:06 2022
Total time elapsed: 2.0m:6.87s{
"af_correlation": 0.95,
"inflation_factor": 1.0306,
"mean_EFFECT": -0.0001,
"n": "-Inf",
"n_snps": 12243512,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1279896,
"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": 404169,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NaN",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1220578,
"ldsc_nsnp_merge_regression_ld": 1220578,
"ldsc_observed_scale_h2_beta": 0.0032,
"ldsc_observed_scale_h2_se": 0.001,
"ldsc_intercept_beta": 1.0083,
"ldsc_intercept_se": 0.0067,
"ldsc_lambda_gc": 1.0402,
"ldsc_mean_chisq": 1.0388,
"ldsc_ratio": 0.2139
}
| name | value |
|---|---|
| name | value |
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| 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 betweenAFandAF_reference.inflation_factor(lambda): Genomic inflation factor.mean_EFFECT: Mean ofEFFECTsize.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 below5e-8.n_mono: Number of monomorphic (MAF == 1orMAF == 0) SNPs.n_ns: Number of SNPs with nonsense values:- alleles other than
A, C, G or T. - P-values
< 0or> 1. - negative or infinite standard errors (
<= 0or= Infinity). - infinite beta estimates or allele frequencies
< 0or> 1.
- alleles other than
n_mac: Number of cases whereMAC(2×N×MAF) is less than6.is_snpid_unique:trueif the combination ofIDREFALTis unique and therefore no duplication in snpid.n_miss_<*>: Number ofNAobservations for<*>column.
se_n metrics
n_est: Estimated sample size value, ˆn.ratio_se_n: ratio_se_n=√ˆn√n. We expectratio_se_nto 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: mean_diff=∑j^βstdj−βjn_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.- ^βstdj=√z2j/(z2j+n−2)2×MAFj×(1−MAFj)×sign(zj),
- zj=βjsej,
- and βj is the reported effect size.
ratio_diff: ratio_diff=|mean_diffmean_diff2|, absolute ratio between the mean ofdiffand the mean ofdiff2(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.- mean_diff2=∑j^βstdj−β′jn_snps
- β′j=βj^sd2y
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.- ^sd1y=√n×median(sej)C,
- C=median(1√2×MAFj×(1−MAFj)),
- and sej is the reported standard error.
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.- ^sd2y=median(^sdj),
- ^sdj=βj^βstdj,
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>:r2statistics under various assumptions1: r2=∑j2×β2j×MAFj×(1−MAFj)var1, var1=1.2: r2=∑j2×β2j×MAFj×(1−MAFj)var2, var2=^sd1y2,3: r2=∑j2×β2j×MAFj×(1−MAFj)var3, var3=^sd2y2,4: r2=∑jFjFj+n−2, F=β2jse2j.
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 χ2 statistics.ldsc_ratio: ldsc_intercept_beta−1ldsc_mean_chisq−1, the proportion of the inflation in the mean χ2 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 h2 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: NOTis_snpid_unique.mean_EFFECT_nonfinite:mean(EFFECT)isNA,NaN, orInf.mean_EFFECT_05:abs(mean(EFFECT))> 0.5.mean_EFFECT_01:abs(mean(EFFECT))> 0.1.mean_chisq:ldsc_mean_chisq> 1.3 orldsc_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<*>> 0.5
Plots
- Manhattan plot
- Red line: −log5×10−810
- Blue line: −log5×10−510
- QQ plot
- AF plot
- P-Z plot
- beta_std plot: Scatter plot between ^βstdj and βj
| skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
| character | ID | 566 | 0.9999538 | 3 | 58 | 0 | 12193987 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 101 | 0 | 56052 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 662 | 0 | 34526 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 12243512 | 0.0000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.635978e+00 | 5.758638e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.869391e+07 | 5.629933e+07 | 302.0000000 | 3.250308e+07 | 6.911919e+07 | 1.143452e+08 | 2.492405e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.158000e-04 | 1.298556e-01 | -24.9223000 | -2.971360e-02 | -2.914000e-04 | 2.916850e-02 | 3.775480e+01 | ▁▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.373300e-02 | 1.307314e-01 | 0.0203787 | 2.471970e-02 | 3.996140e-02 | 9.225570e-02 | 3.717770e+01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.954148e-01 | 2.898443e-01 | 0.0000001 | 2.433677e-01 | 4.935157e-01 | 7.468373e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.954148e-01 | 2.898443e-01 | 0.0000001 | 2.433676e-01 | 4.935160e-01 | 7.468381e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.127953e-01 | 2.602011e-01 | 0.0000054 | 1.457930e-02 | 8.849620e-02 | 3.382510e-01 | 9.999950e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 404169 | 0.9669891 | NA | NA | NA | NA | NA | NA | NA | 2.160786e-01 | 2.512172e-01 | 0.0000000 | 1.357830e-02 | 1.106230e-01 | 3.426520e-01 | 1.000000e+00 | ▇▂▁▁▁ |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
| 1 | 10177 | rs367896724 | A | AC | -0.0323308 | 0.0315004 | 0.3047214 | 0.3047212 | 0.3989060 | 0.4253190 | NA |
| 1 | 10352 | rs555500075 | T | TA | 0.0223642 | 0.0324044 | 0.4900936 | 0.4900940 | 0.3932360 | 0.4375000 | NA |
| 1 | 11008 | rs575272151 | C | G | 0.0727434 | 0.0539258 | 0.1773520 | 0.1773519 | 0.0862242 | 0.0880591 | NA |
| 1 | 11012 | rs544419019 | C | G | 0.0727434 | 0.0539258 | 0.1773520 | 0.1773519 | 0.0862242 | 0.0880591 | NA |
| 1 | 13110 | rs540538026 | G | A | 0.0110579 | 0.0716371 | 0.8773262 | 0.8773259 | 0.0586843 | 0.0267572 | NA |
| 1 | 13116 | rs62635286 | T | G | 0.0554946 | 0.0423964 | 0.1905527 | 0.1905526 | 0.1891810 | 0.0970447 | NA |
| 1 | 13118 | rs200579949 | A | G | 0.0554946 | 0.0423964 | 0.1905527 | 0.1905526 | 0.1891810 | 0.0970447 | NA |
| 1 | 13273 | rs531730856 | G | C | -0.0421430 | 0.0496190 | 0.3956963 | 0.3956966 | 0.1341340 | 0.0950479 | NA |
| 1 | 14464 | rs546169444 | A | T | -0.0233188 | 0.0451889 | 0.6058331 | 0.6058339 | 0.1568980 | 0.0958466 | NA |
| 1 | 14599 | rs531646671 | T | A | 0.0603314 | 0.0410845 | 0.1419760 | 0.1419763 | 0.1915570 | 0.1475640 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
| 22 | 51233182 | rs4040317 | G | A | 0.0003831 | 0.0257492 | 0.9881298 | 0.9881298 | 0.3200860 | 0.2633790 | NA |
| 22 | 51233300 | rs9616839 | C | T | -0.0177812 | 0.0257050 | 0.4891004 | 0.4891001 | 0.3343140 | 0.3146960 | NA |
| 22 | 51233312 | rs62240043 | A | G | -0.0150203 | 0.0270683 | 0.5789606 | 0.5789605 | 0.2729950 | 0.2134580 | NA |
| 22 | 51233347 | rs62240044 | T | C | -0.0150203 | 0.0270683 | 0.5789606 | 0.5789605 | 0.2729950 | 0.2134580 | NA |
| 22 | 51234799 | rs191117135 | G | A | -0.1237770 | 0.0959773 | 0.1971710 | 0.1971727 | 0.0156550 | 0.0059904 | NA |
| 22 | 51235959 | rs200189535 | T | C | 0.0386893 | 0.0315152 | 0.2195831 | 0.2195824 | 0.1953500 | 0.1996810 | NA |
| 22 | 51235979 | rs62240045 | G | A | 0.0207079 | 0.0350983 | 0.5551930 | 0.5551925 | 0.2637980 | 0.2400160 | NA |
| 22 | 51236013 | rs200507571 | A | AT | 0.0040989 | 0.0271754 | 0.8801087 | 0.8801088 | 0.2513400 | 0.1487620 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0023652 | 0.0249073 | 0.9243463 | 0.9243462 | 0.2979820 | 0.2050720 | NA |
| 22 | 51237712 | rs370652263 | G | A | -0.0206406 | 0.0499033 | 0.6791583 | 0.6791583 | 0.0553522 | 0.0690895 | NA |
1 10177 rs1264289758 A AC . PASS AF=0.398906 ES:SE:LP:AF:ID -0.0323308:0.0315004:0.516097:0.398906:rs1264289758
1 10352 rs1557426776 T TA . PASS AF=0.393236 ES:SE:LP:AF:ID 0.0223642:0.0324044:0.309721:0.393236:rs1557426776
1 11008 rs575272151 C G . PASS AF=0.0862242 ES:SE:LP:AF:ID 0.0727434:0.0539258:0.751164:0.0862242:rs575272151
1 11012 rs544419019 C G . PASS AF=0.0862242 ES:SE:LP:AF:ID 0.0727434:0.0539258:0.751164:0.0862242:rs544419019
1 13110 rs540538026 G A . PASS AF=0.0586843 ES:SE:LP:AF:ID 0.0110579:0.0716371:0.0568389:0.0586843:rs540538026
1 13116 rs62635286 T G . PASS AF=0.189181 ES:SE:LP:AF:ID 0.0554946:0.0423964:0.719985:0.189181:rs62635286
1 13118 rs62028691 A G . PASS AF=0.189181 ES:SE:LP:AF:ID 0.0554946:0.0423964:0.719985:0.189181:rs62028691
1 13273 rs531730856 G C . PASS AF=0.134134 ES:SE:LP:AF:ID -0.042143:0.049619:0.402638:0.134134:rs531730856
1 14464 rs546169444 A T . PASS AF=0.156898 ES:SE:LP:AF:ID -0.0233188:0.0451889:0.217647:0.156898:rs546169444
1 14599 rs707680 T A . PASS AF=0.191557 ES:SE:LP:AF:ID 0.0603314:0.0410845:0.847785:0.191557:rs707680
1 14604 rs1418508701 A G . PASS AF=0.191557 ES:SE:LP:AF:ID 0.0603314:0.0410845:0.847785:0.191557:rs1418508701
1 14930 rs6682385 A G . PASS AF=0.473819 ES:SE:LP:AF:ID 0.033742:0.0319107:0.5371:0.473819:rs6682385
1 14933 rs199856693 G A . PASS AF=0.0450802 ES:SE:LP:AF:ID 0.0680383:0.0782621:0.414937:0.0450802:rs199856693
1 15211 rs3982632 T G . PASS AF=0.741355 ES:SE:LP:AF:ID 0.0394773:0.0368743:0.546143:0.741355:rs3982632
1 15820 rs1316988498 G T . PASS AF=0.275124 ES:SE:LP:AF:ID -0.00398007:0.0378109:0.0380251:0.275124:rs1316988498
1 15903 rs557514207 G GC . PASS AF=0.41884 ES:SE:LP:AF:ID -0.0144411:0.0312093:0.191407:0.41884:rs557514207
1 28590 rs1344649620 T TTGG . PASS AF=0.956571 ES:SE:LP:AF:ID -0.00301214:0.0888358:0.0119088:0.956571:rs1344649620
1 30923 rs1165072081 G T . PASS AF=0.910221 ES:SE:LP:AF:ID 0.0768874:0.0588553:0.718005:0.910221:rs1165072081
1 47159 rs540662756 T C . PASS AF=0.0627121 ES:SE:LP:AF:ID -0.062045:0.0668878:0.451469:0.0627121:rs540662756
1 49298 rs10399793 T C . PASS AF=0.623768 ES:SE:LP:AF:ID 0.0428102:0.0374186:0.597588:0.623768:rs10399793
1 49554 rs539322794 A G . PASS AF=0.0929554 ES:SE:LP:AF:ID -0.0365296:0.0577975:0.277886:0.0929554:rs539322794
1 51479 rs116400033 T A . PASS AF=0.21326 ES:SE:LP:AF:ID -0.00486564:0.0400415:0.0441761:0.21326:rs116400033
1 54490 rs141149254 G A . PASS AF=0.154391 ES:SE:LP:AF:ID 0.0410552:0.0449594:0.442304:0.154391:rs141149254
1 54676 rs2462492 C T . PASS AF=0.400396 ES:SE:LP:AF:ID 0.0411843:0.0370622:0.574347:0.400396:rs2462492
1 54712 rs573184866 T TTTTC . PASS AF=0.585268 ES:SE:LP:AF:ID 0.0499079:0.0293264:1.05163:0.585268:rs573184866
1 54716 rs1166278911 C T . PASS AF=0.417371 ES:SE:LP:AF:ID -0.0139974:0.0338484:0.167992:0.417371:rs1166278911
1 55545 rs28396308 C T . PASS AF=0.253777 ES:SE:LP:AF:ID -0.0254274:0.0381216:0.296909:0.253777:rs28396308
1 58814 rs114420996 G A . PASS AF=0.0899979 ES:SE:LP:AF:ID -0.0942361:0.0582191:0.976651:0.0899979:rs114420996
1 59040 rs62637815 T C . PASS AF=0.0887883 ES:SE:LP:AF:ID -0.0607331:0.0585174:0.523845:0.0887883:rs62637815
1 60351 rs62637817 A G . PASS AF=0.0809837 ES:SE:LP:AF:ID -0.0947897:0.0606252:0.928388:0.0809837:rs62637817
1 62777 rs3844233 A T . PASS AF=0.438273 ES:SE:LP:AF:ID -0.0438018:0.0322057:0.759927:0.438273:rs3844233
1 63268 rs28664618 T C . PASS AF=0.382186 ES:SE:LP:AF:ID -0.0142047:0.0345745:0.166734:0.382186:rs28664618
1 63671 rs80011619 G A . PASS AF=0.158756 ES:SE:LP:AF:ID -0.0279496:0.0440537:0.279187:0.158756:rs80011619
1 63735 rs61158452 CCTA C . PASS AF=0.315972 ES:SE:LP:AF:ID -0.0114915:0.0343042:0.132159:0.315972:rs61158452
1 64931 rs62639104 G A . PASS AF=0.0795793 ES:SE:LP:AF:ID -0.0948794:0.0613737:0.913209:0.0795793:rs62639104
1 68082 rs367789441 T C . PASS AF=0.0707801 ES:SE:LP:AF:ID 0.0839783:0.0618572:0.75799:0.0707801:rs367789441
1 69428 rs140739101 T G . PASS AF=0.0329199 ES:SE:LP:AF:ID -0.0867576:0.0944316:0.445832:0.0329199:rs140739101
1 69761 rs200505207 A T . PASS AF=0.0738738 ES:SE:LP:AF:ID 0.0383373:0.0609494:0.276259:0.0738738:rs200505207
1 69897 rs200676709 T C . PASS AF=0.751218 ES:SE:LP:AF:ID 0.00747651:0.0389294:0.0717574:0.751218:rs200676709
1 74790 rs13328700 C G . PASS AF=0.0340921 ES:SE:LP:AF:ID -0.163266:0.089357:1.16953:0.0340921:rs13328700
1 74792 rs1335672253 G A . PASS AF=0.0340921 ES:SE:LP:AF:ID -0.163266:0.089357:1.16953:0.0340921:rs1335672253
1 76838 rs563953605 T G . PASS AF=0.0771356 ES:SE:LP:AF:ID -0.0462436:0.0626301:0.336963:0.0771356:rs563953605
1 76854 rs367666799 A G . PASS AF=0.0775037 ES:SE:LP:AF:ID -0.109023:0.059858:1.16398:0.0775037:rs367666799
1 77866 rs563593912 C T . PASS AF=0.0769408 ES:SE:LP:AF:ID -0.045062:0.0626418:0.326133:0.0769408:rs563593912
1 77874 rs62641297 G A . PASS AF=0.0769408 ES:SE:LP:AF:ID -0.045062:0.0626418:0.326133:0.0769408:rs62641297
1 81260 rs571136476 C T . PASS AF=0.0414632 ES:SE:LP:AF:ID -0.0109094:0.0870607:0.0456223:0.0414632:rs571136476
1 81587 rs536406113 C T . PASS AF=0.0609432 ES:SE:LP:AF:ID 0.0639308:0.0659243:0.478645:0.0609432:rs536406113
1 82163 rs139113303 G A . PASS AF=0.0754482 ES:SE:LP:AF:ID -0.0844403:0.0606667:0.785258:0.0754482:rs139113303
1 82609 rs149189449 C G . PASS AF=0.0754758 ES:SE:LP:AF:ID -0.0846105:0.0606536:0.787753:0.0754758:rs149189449
1 83514 rs201754587 C T . PASS AF=0.352798 ES:SE:LP:AF:ID -0.00481449:0.0348395:0.0505662:0.352798:rs201754587