manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_41245_1780.vcf.gz --id UKB-b:3389 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41245_1780.txt.gz --cohort_cases 1343 --cohort_controls 459767 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-13T13:15:43.669334",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3389/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3389/UKB-b-3389_raw.vcf.gz; Date=Thu Oct 17 12:41:32 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-3389/ukb-b-3389.vcf.gz; Date=Sat May 9 14:53:53 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/public/UKB-b-3389/UKB-b-3389_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3389/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:43:27 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3389/UKB-b-3389_data.vcf.gz ...
Read summary statistics for 2209735 SNPs.
Dropped 234 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 563221 SNPs remain.
After merging with regression SNP LD, 563221 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0026 (0.0012)
Lambda GC: 1.0431
Mean Chi^2: 1.037
Intercept: 1.0096 (0.0102)
Ratio: 0.2581 (0.2749)
Analysis finished at Thu Oct 17 14:43:56 2019
Total time elapsed: 29.1s{
"af_correlation": 0.73,
"inflation_factor": 1.0475,
"mean_EFFECT": 1.072e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 17498,
"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": 563221,
"ldsc_nsnp_merge_regression_ld": 563221,
"ldsc_observed_scale_h2_beta": 0.0026,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0096,
"ldsc_intercept_se": 0.0102,
"ldsc_lambda_gc": 1.0431,
"ldsc_mean_chisq": 1.037,
"ldsc_ratio": 0.2595
}
| name | value |
|---|---|
| name | value |
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | FALSE |
| 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 | 0 | 1.0000000 | 4 | 58 | 0 | 2209503 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 2209735 | 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 | 8.647441e+00 | 5.765231e+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 | 7.867576e+07 | 5.665900e+07 | 5687.0000000 | 3.177796e+07 | 6.918526e+07 | 1.147898e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.000000e-07 | 1.198000e-04 | -0.0005526 | -8.090000e-05 | 0.000000e+00 | 8.140000e-05 | 5.912000e-04 | ▁▂▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.178000e-04 | 5.200000e-06 | 0.0001083 | 1.136000e-04 | 1.164000e-04 | 1.213000e-04 | 2.282000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.938395e-01 | 2.902562e-01 | 0.0000003 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.938417e-01 | 2.902318e-01 | 0.0000003 | 2.401871e-01 | 4.905064e-01 | 7.456765e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.628342e-01 | 1.366167e-01 | 0.2606110 | 3.428730e-01 | 4.447540e-01 | 5.738220e-01 | 7.393890e-01 | ▇▆▅▅▃ |
| numeric | AF_reference | 17498 | 0.9920814 | NA | NA | NA | NA | NA | NA | NA | 4.432839e-01 | 1.672935e-01 | 0.0001997 | 3.130990e-01 | 4.315100e-01 | 5.650960e-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 | 49298 | rs200943160 | T | C | -0.0004880 | 0.0001993 | 0.0140001 | 0.0143427 | 0.623779 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0003007 | 0.0001975 | 0.1299999 | 0.1278401 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0001037 | 0.0001944 | 0.5900000 | 0.5938620 | 0.456862 | 0.4207270 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0001005 | 0.0001379 | 0.4700002 | 0.4659422 | 0.515668 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0002780 | 0.0001616 | 0.0850002 | 0.0854833 | 0.706756 | 0.6176120 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0000734 | 0.0001474 | 0.6200004 | 0.6183954 | 0.265365 | 0.0756789 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0002545 | 0.0001890 | 0.1800002 | 0.1782887 | 0.340385 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | -0.0000447 | 0.0001265 | 0.7199992 | 0.7237975 | 0.697214 | 0.6912940 | NA |
| 1 | 831489 | rs4970385 | C | T | -0.0000919 | 0.0001242 | 0.4600002 | 0.4590597 | 0.705350 | 0.6491610 | NA |
| 1 | 831909 | rs9697642 | C | T | -0.0000906 | 0.0001242 | 0.4700002 | 0.4655919 | 0.705395 | 0.6485620 | 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 | 51174662 | rs1858748 | T | C | 0.0000221 | 0.0001333 | 0.8700001 | 0.8685524 | 0.737440 | 0.732827 | NA |
| 22 | 51180501 | rs5770999 | T | C | 0.0001194 | 0.0001297 | 0.3599996 | 0.3573801 | 0.713660 | 0.636981 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0000601 | 0.0001291 | 0.6400000 | 0.6413011 | 0.695490 | 0.619409 | NA |
| 22 | 51182485 | rs6009961 | A | G | 0.0001276 | 0.0001302 | 0.3300000 | 0.3267976 | 0.715505 | 0.638379 | NA |
| 22 | 51186143 | rs2879914 | T | C | -0.0001053 | 0.0001207 | 0.3800004 | 0.3828731 | 0.381816 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0000439 | 0.0001176 | 0.7099994 | 0.7086970 | 0.451059 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0000527 | 0.0001214 | 0.6600001 | 0.6642091 | 0.386346 | 0.422923 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0001224 | 0.0001363 | 0.3700002 | 0.3691925 | 0.271567 | 0.167133 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0000601 | 0.0001295 | 0.6400000 | 0.6423638 | 0.331445 | 0.372404 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0001097 | 0.0001326 | 0.4100001 | 0.4082031 | 0.297972 | 0.205072 | NA |
1 49298 rs10399793 T C . PASS AF=0.623779 ES:SE:LP:AF:ID -0.000487984:0.000199294:1.85387:0.623779:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.00030071:0.000197488:0.886057:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456862 ES:SE:LP:AF:ID 0.000103673:0.000194418:0.229148:0.456862:rs6702460
1 706368 rs12029736 A G . PASS AF=0.515668 ES:SE:LP:AF:ID -0.000100525:0.000137876:0.327902:0.515668:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706756 ES:SE:LP:AF:ID -0.000277979:0.000161642:1.07058:0.706756:rs3115847
1 776546 rs12124819 A G . PASS AF=0.265365 ES:SE:LP:AF:ID 7.34063e-05:0.000147365:0.207608:0.265365:rs12124819
1 814495 rs74461805 C A . PASS AF=0.340385 ES:SE:LP:AF:ID -0.00025446:0.000189043:0.744727:0.340385:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697214 ES:SE:LP:AF:ID -4.46937e-05:0.000126472:0.142668:0.697214:rs28444699
1 831489 rs4970385 C T . PASS AF=0.70535 ES:SE:LP:AF:ID -9.19446e-05:0.000124183:0.337242:0.70535:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705395 ES:SE:LP:AF:ID -9.06097e-05:0.000124179:0.327902:0.705395:rs9697642
1 832066 rs9697380 G C . PASS AF=0.70558 ES:SE:LP:AF:ID -9.1634e-05:0.000124185:0.337242:0.70558:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705609 ES:SE:LP:AF:ID -9.19197e-05:0.000124198:0.337242:0.705609:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730079 ES:SE:LP:AF:ID -4.53226e-05:0.000127583:0.142668:0.730079:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294424 ES:SE:LP:AF:ID 9.13795e-05:0.000124192:0.337242:0.294424:rs28765502
1 836896 rs28705752 T C . PASS AF=0.269537 ES:SE:LP:AF:ID 7.07391e-05:0.000126593:0.236572:0.269537:rs28705752
1 839103 rs28562941 A G . PASS AF=0.270039 ES:SE:LP:AF:ID 9.07236e-05:0.000126682:0.327902:0.270039:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400164 ES:SE:LP:AF:ID 9.24539e-05:0.000114551:0.376751:0.400164:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362585 ES:SE:LP:AF:ID 8.18579e-05:0.000142192:0.251812:0.362585:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590329 ES:SE:LP:AF:ID -3.50501e-05:0.000114214:0.119186:0.590329:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603723 ES:SE:LP:AF:ID -1.15698e-05:0.000114856:0.0362122:0.603723:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603947 ES:SE:LP:AF:ID -3.53132e-06:0.00011484:0.00877392:0.603947:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589685 ES:SE:LP:AF:ID -3.77257e-05:0.000114399:0.130768:0.589685:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589666 ES:SE:LP:AF:ID -3.76189e-05:0.000114348:0.130768:0.589666:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607671 ES:SE:LP:AF:ID -2.11913e-05:0.000115095:0.0705811:0.607671:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607829 ES:SE:LP:AF:ID -2.18559e-05:0.00011511:0.0705811:0.607829:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610322 ES:SE:LP:AF:ID -1.0531e-05:0.000115223:0.0315171:0.610322:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603285 ES:SE:LP:AF:ID -8.03894e-06:0.000114884:0.0268721:0.603285:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610343 ES:SE:LP:AF:ID -1.07263e-05:0.000115225:0.0315171:0.610343:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389932 ES:SE:LP:AF:ID 1.14541e-05:0.000115247:0.0362122:0.389932:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389916 ES:SE:LP:AF:ID 1.17426e-05:0.000115253:0.0362122:0.389916:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350359 ES:SE:LP:AF:ID -3.60704e-05:0.000118404:0.119186:0.350359:rs4040605
1 866893 rs2880024 T C . PASS AF=0.61053 ES:SE:LP:AF:ID -1.4249e-05:0.000115874:0.0457575:0.61053:rs2880024
1 868418 rs28546443 C T . PASS AF=0.297908 ES:SE:LP:AF:ID -1.22173e-05:0.00012731:0.0362122:0.297908:rs28546443
1 870645 rs28576697 T C . PASS AF=0.291301 ES:SE:LP:AF:ID 3.55971e-06:0.000126293:0.00877392:0.291301:rs28576697
1 871334 rs4072383 G T . PASS AF=0.720599 ES:SE:LP:AF:ID 2.6506e-05:0.000125511:0.0809219:0.720599:rs4072383
1 872352 rs1806780 G C . PASS AF=0.267549 ES:SE:LP:AF:ID -6.71508e-05:0.000127213:0.221849:0.267549:rs1806780
1 873558 rs1110052 G T . PASS AF=0.715235 ES:SE:LP:AF:ID 2.59204e-05:0.000124517:0.0757207:0.715235:rs1110052
1 875770 rs4970379 A G . PASS AF=0.600067 ES:SE:LP:AF:ID 0.000113217:0.000116843:0.481486:0.600067:rs4970379
1 881627 rs2272757 G A . PASS AF=0.652403 ES:SE:LP:AF:ID 0.000199222:0.000118033:1.04096:0.652403:rs2272757
1 891059 rs13303065 C T . PASS AF=0.652441 ES:SE:LP:AF:ID 0.000193979:0.000118014:1:0.652441:rs13303065
1 891945 rs13303106 A G . PASS AF=0.652502 ES:SE:LP:AF:ID 0.000196487:0.000118151:1.01773:0.652502:rs13303106
1 900505 rs28705211 G C . PASS AF=0.271781 ES:SE:LP:AF:ID -0.000194693:0.000127725:0.886057:0.271781:rs28705211
1 903245 rs28690976 A G . PASS AF=0.56696 ES:SE:LP:AF:ID 0.000142551:0.00011736:0.657577:0.56696:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386684 ES:SE:LP:AF:ID 1.88375e-05:0.000117018:0.0604807:0.386684:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571429 ES:SE:LP:AF:ID -1.93015e-05:0.00011333:0.0655015:0.571429:rs3829740
1 910394 rs28477686 C T . PASS AF=0.324455 ES:SE:LP:AF:ID -0.00014484:0.000122843:0.619789:0.324455:rs28477686
1 912049 rs7367995 T C . PASS AF=0.585258 ES:SE:LP:AF:ID 0.000132422:0.000114488:0.60206:0.585258:rs7367995
1 913889 rs2340596 G A . PASS AF=0.599234 ES:SE:LP:AF:ID 0.000133667:0.000114677:0.619789:0.599234:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602534 ES:SE:LP:AF:ID 0.000103415:0.000115022:0.431798:0.602534:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600092 ES:SE:LP:AF:ID 0.00013027:0.000114803:0.585027:0.600092:rs13303368