Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

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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_1040.vcf.gz --id UKB-b:19023 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41245_1040.txt.gz --cohort_cases 5479 --cohort_controls 456017 --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",
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}
 

LDSC

*********************************************************************
* 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-19023/UKB-b-19023_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19023/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:56 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19023/UKB-b-19023_data.vcf.gz ...
Read summary statistics for 5049616 SNPs.
Dropped 1484 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, 1122233 SNPs remain.
After merging with regression SNP LD, 1122233 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0049 (0.0012)
Lambda GC: 1.0762
Mean Chi^2: 1.0786
Intercept: 1.0318 (0.0077)
Ratio: 0.4045 (0.0983)
Analysis finished at Thu Oct 17 14:41:55 2019
Total time elapsed: 59.38s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9076,
    "inflation_factor": 1.0966,
    "mean_EFFECT": 1.1247e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 2,
    "n_p_sig": 3,
    "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": 43229,
    "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": 1122233,
    "ldsc_nsnp_merge_regression_ld": 1122233,
    "ldsc_observed_scale_h2_beta": 0.0049,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.0318,
    "ldsc_intercept_se": 0.0077,
    "ldsc_lambda_gc": 1.0762,
    "ldsc_mean_chisq": 1.0786,
    "ldsc_ratio": 0.4046
}
 

Flags

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

Definitions

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 SNPs
  • n_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:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 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.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • 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.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • 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.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) 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.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

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 > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

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 3 58 0 5048143 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 5049616 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 8.671186e+00 5.766661e+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 7.855750e+07 5.663020e+07 828.0000000 3.187945e+07 6.895760e+07 1.145711e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.100000e-06 3.109000e-04 -0.0019322 -1.968000e-04 3.000000e-07 1.988000e-04 2.357000e-03 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.928000e-04 6.680000e-05 0.0002176 2.362000e-04 2.688000e-04 3.354000e-04 8.355000e-04 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.883137e-01 2.914740e-01 0.0000000 2.300001e-01 4.799997e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.883145e-01 2.914490e-01 0.0000000 2.336635e-01 4.838489e-01 7.404867e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.497389e-01 2.393349e-01 0.0638810 1.436210e-01 2.834250e-01 5.163320e-01 9.361170e-01 ▇▅▃▂▂
numeric AF_reference 43229 0.9914392 NA NA NA NA NA NA NA 3.432870e-01 2.358325e-01 0.0000000 1.485620e-01 2.857430e-01 5.057910e-01 1.000000e+00 ▇▆▅▃▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0004791 0.0004004 0.2300001 0.2314307 0.623779 0.7821490 NA
1 54676 rs2462492 C T -0.0001651 0.0003967 0.6800001 0.6772006 0.400421 NA NA
1 86028 rs114608975 T C -0.0008213 0.0006343 0.2000000 0.1953235 0.103549 0.0277556 NA
1 91536 rs6702460 G T -0.0001832 0.0003906 0.6400000 0.6389669 0.456872 0.4207270 NA
1 234313 rs8179466 C T 0.0023570 0.0007701 0.0022000 0.0022073 0.074513 NA NA
1 534192 rs6680723 C T -0.0007527 0.0004461 0.0920005 0.0915684 0.240950 NA NA
1 546697 rs12025928 A G -0.0000815 0.0005565 0.8800001 0.8836007 0.913469 NA NA
1 693731 rs12238997 A G 0.0002154 0.0003739 0.5600000 0.5645776 0.116330 0.1417730 NA
1 705882 rs72631875 G A -0.0008686 0.0005478 0.1100001 0.1128577 0.067305 0.0315495 NA
1 706368 rs55727773 A G -0.0000507 0.0002770 0.8499999 0.8546831 0.515673 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51213613 rs34726907 C T -0.0000162 0.0003428 0.9599999 0.9622423 0.127813 0.1727240 NA
22 51216564 rs9616970 T C -0.0000217 0.0003413 0.9500000 0.9492701 0.128325 0.1563500 NA
22 51217954 rs9616974 G A 0.0001011 0.0004331 0.8200001 0.8154991 0.073303 0.0621006 NA
22 51218224 rs9616975 C A 0.0000974 0.0004333 0.8200001 0.8222300 0.073323 0.0619010 NA
22 51218377 rs2519461 G C 0.0000985 0.0004328 0.8200001 0.8199880 0.073611 0.0826677 NA
22 51219006 rs28729663 G A 0.0000246 0.0003341 0.9400001 0.9412166 0.137949 0.2052720 NA
22 51219387 rs9616832 T C 0.0000819 0.0004336 0.8499999 0.8502698 0.073736 0.0654952 NA
22 51221731 rs115055839 T C 0.0000964 0.0004339 0.8200001 0.8241332 0.073226 0.0625000 NA
22 51229805 rs9616985 T C 0.0000737 0.0004355 0.8700001 0.8656254 0.073063 0.0730831 NA
22 51237063 rs3896457 T C 0.0005636 0.0002664 0.0340001 0.0343529 0.298009 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623779 ES:SE:LP:AF:ID  -0.000479113:0.000400368:0.638272:0.623779:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400421 ES:SE:LP:AF:ID  -0.000165147:0.000396715:0.167491:0.400421:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103549 ES:SE:LP:AF:ID  -0.000821349:0.000634251:0.69897:0.103549:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456872 ES:SE:LP:AF:ID  -0.000183225:0.000390552:0.19382:0.456872:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074513 ES:SE:LP:AF:ID  0.00235702:0.000770062:2.65758:0.074513:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24095  ES:SE:LP:AF:ID  -0.000752699:0.000446128:1.03621:0.24095:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913469 ES:SE:LP:AF:ID  -8.14818e-05:0.000556546:0.0555173:0.913469:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.11633  ES:SE:LP:AF:ID  0.000215378:0.000373884:0.251812:0.11633:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067305 ES:SE:LP:AF:ID  -0.000868552:0.000547817:0.958607:0.067305:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515673 ES:SE:LP:AF:ID  -5.07257e-05:0.000276968:0.0705811:0.515673:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.1012   ES:SE:LP:AF:ID  6.65684e-05:0.000456986:0.0555173:0.1012:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.843191 ES:SE:LP:AF:ID  0.000322817:0.000324016:0.49485:0.843191:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.12232  ES:SE:LP:AF:ID  8.76244e-05:0.000354662:0.09691:0.12232:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121563 ES:SE:LP:AF:ID  7.9107e-05:0.000354811:0.0861861:0.121563:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132343 ES:SE:LP:AF:ID  -0.00024595:0.000349712:0.318759:0.132343:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.838931 ES:SE:LP:AF:ID  0.000195405:0.000313785:0.275724:0.838931:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83856  ES:SE:LP:AF:ID  0.000216247:0.000313447:0.309804:0.83856:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869769 ES:SE:LP:AF:ID  -4.87621e-05:0.000336341:0.0555173:0.869769:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129885 ES:SE:LP:AF:ID  6.97666e-05:0.000337022:0.0757207:0.129885:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.86911  ES:SE:LP:AF:ID  -2.97355e-05:0.00033568:0.0315171:0.86911:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869207 ES:SE:LP:AF:ID  -3.8338e-05:0.000335812:0.0409586:0.869207:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869113 ES:SE:LP:AF:ID  -3.19068e-05:0.000335674:0.0362122:0.869113:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838012 ES:SE:LP:AF:ID  0.000209384:0.000312578:0.30103:0.838012:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838643 ES:SE:LP:AF:ID  0.000226949:0.000313456:0.327902:0.838643:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.839761 ES:SE:LP:AF:ID  0.000180129:0.0003177:0.244125:0.839761:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869393 ES:SE:LP:AF:ID  -6.9898e-05:0.000335288:0.0809219:0.869393:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868942 ES:SE:LP:AF:ID  -8.5935e-05:0.000334445:0.09691:0.868942:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867892 ES:SE:LP:AF:ID  -7.76836e-05:0.000333802:0.0861861:0.867892:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869085 ES:SE:LP:AF:ID  -8.67583e-05:0.000334719:0.09691:0.869085:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869094 ES:SE:LP:AF:ID  -8.71269e-05:0.000334745:0.102373:0.869094:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869102 ES:SE:LP:AF:ID  -8.68493e-05:0.000334753:0.09691:0.869102:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869577 ES:SE:LP:AF:ID  -7.17508e-05:0.000335669:0.0809219:0.869577:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.838293 ES:SE:LP:AF:ID  0.000191513:0.000311984:0.267606:0.838293:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838414 ES:SE:LP:AF:ID  0.000189448:0.000312205:0.267606:0.838414:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862248 ES:SE:LP:AF:ID  1.34855e-06:0.000333539:-0:0.862248:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.706757 ES:SE:LP:AF:ID  -0.000102034:0.000324715:0.124939:0.706757:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.105135 ES:SE:LP:AF:ID  0.000294148:0.000374077:0.366532:0.105135:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.761327 ES:SE:LP:AF:ID  -0.000137692:0.000265039:0.221849:0.761327:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.10646  ES:SE:LP:AF:ID  0.000164347:0.000365335:0.187087:0.10646:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.129582 ES:SE:LP:AF:ID  0.000157222:0.000336828:0.19382:0.129582:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.868905 ES:SE:LP:AF:ID  -0.000117365:0.000335034:0.136677:0.868905:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129684 ES:SE:LP:AF:ID  0.000154389:0.000336611:0.187087:0.129684:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.868915 ES:SE:LP:AF:ID  -0.000110646:0.000335041:0.130768:0.868915:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.265358 ES:SE:LP:AF:ID  0.000125223:0.000296038:0.173925:0.265358:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.870033 ES:SE:LP:AF:ID  -4.02163e-05:0.00033572:0.0457575:0.870033:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.095124 ES:SE:LP:AF:ID  0.000103395:0.000389138:0.102373:0.095124:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.128586 ES:SE:LP:AF:ID  8.67512e-05:0.000337041:0.09691:0.128586:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128884 ES:SE:LP:AF:ID  7.29994e-05:0.000336468:0.0809219:0.128884:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.868774 ES:SE:LP:AF:ID  7.97641e-08:0.000334823:-0:0.868774:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.10187  ES:SE:LP:AF:ID  0.000206525:0.000379409:0.229148:0.10187:rs61768199