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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}

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/dev/ukb-d-import/processed/ukb-d-20118_8/ukb-d-20118_8.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-20118_8/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 16:28:53 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20118_8/ukb-d-20118_8.vcf.gz ...
Read summary statistics for 12863830 SNPs.
Dropped 11667 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, 1283338 SNPs remain.
After merging with regression SNP LD, 1283338 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0042 (0.0012)
Lambda GC: 1.0275
Mean Chi^2: 1.0212
Intercept: 0.9914 (0.0062)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:31:13 2019
Total time elapsed: 2.0m:20.03s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9509,
    "inflation_factor": 1.024,
    "mean_EFFECT": -6.4708e-06,
    "n": 357712,
    "n_snps": 12863830,
    "n_clumped_hits": 0,
    "n_p_sig": 3,
    "n_mono": 0,
    "n_ns": 1223012,
    "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": 404867,
    "n_est": 358767.5088,
    "ratio_se_n": 1.0015,
    "mean_diff": -0,
    "ratio_diff": 79.0133,
    "sd_y_est1": 0.1479,
    "sd_y_est2": 0.1481,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283338,
    "ldsc_nsnp_merge_regression_ld": 1283338,
    "ldsc_observed_scale_h2_beta": 0.0042,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 0.9914,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.0275,
    "ldsc_mean_chisq": 1.0212,
    "ldsc_ratio": -0.4057
}

Flags

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

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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 94 0 12852813 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 55475 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32849 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.060118e+00 6.185840e+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 7.896713e+07 5.593906e+07 3.02000e+02 3.282594e+07 7.003992e+07 1.148081e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -6.500000e-06 1.704600e-03 -1.72051e-02 -5.226000e-04 -1.030000e-05 4.930000e-04 2.653740e-02 ▁▇▃▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.262200e-03 1.142800e-03 2.87600e-04 4.105000e-04 7.052000e-04 1.784400e-03 6.160300e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.965900e-01 2.891536e-01 0.00000e+00 2.455253e-01 4.948989e-01 7.469904e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.965895e-01 2.891539e-01 0.00000e+00 2.455249e-01 4.948982e-01 7.469912e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.009451e-01 2.567567e-01 1.57150e-03 1.031460e-02 7.334680e-02 3.154400e-01 9.984280e-01 ▇▂▁▁▁
numeric AF_reference 404867 0.9685267 NA NA NA NA NA 2.042029e-01 2.487898e-01 0.00000e+00 7.587900e-03 9.524760e-02 3.228830e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.577120e+05 0.000000e+00 3.57712e+05 3.577120e+05 3.577120e+05 3.577120e+05 3.577120e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0001230 0.0006122 0.8408180 0.8408184 0.1107240 0.1894970 357712
1 693731 rs12238997 A G -0.0004470 0.0005785 0.4397694 0.4397684 0.1158980 0.1417730 357712
1 707522 rs371890604 G C -0.0001357 0.0006504 0.8346940 0.8346944 0.0973675 0.1293930 357712
1 717587 rs144155419 G A -0.0009270 0.0015526 0.5504590 0.5504572 0.0156859 0.0045926 357712
1 723329 rs189787166 A T 0.0002672 0.0045708 0.9533810 0.9533809 0.0017396 0.0003994 357712
1 730087 rs148120343 T C -0.0007008 0.0008058 0.3844236 0.3844230 0.0565115 0.0127796 357712
1 731718 rs142557973 T C -0.0004053 0.0005487 0.4600722 0.4600712 0.1218030 0.1543530 357712
1 732032 rs61770163 A C -0.0005808 0.0005853 0.3210687 0.3210679 0.1212390 0.1555510 357712
1 734349 rs141242758 T C -0.0004144 0.0005490 0.4503063 0.4503058 0.1210310 0.1525560 357712
1 740284 rs61770167 C T 0.0001629 0.0025073 0.9481979 0.9481980 0.0058047 0.0023962 357712
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0002292 0.0006341 0.7177745 0.7177747 0.0561556 0.0309934 357712
23 154923374 rs111332691 T A 0.0008095 0.0006972 0.2456298 0.2456290 0.0447734 0.0116556 357712
23 154925045 rs509981 C T -0.0001769 0.0003353 0.5977932 0.5977936 0.2456140 0.3634440 357712
23 154925895 rs538470 C T -0.0002185 0.0003430 0.5240660 0.5240644 0.2419220 0.3634440 357712
23 154927581 rs644138 G A -0.0002225 0.0003153 0.4803746 0.4803744 0.3021610 0.4635760 357712
23 154929412 rs557132 C T -0.0001853 0.0003354 0.5806708 0.5806718 0.2454660 0.3568210 357712
23 154929637 rs35185538 CT C -0.0001186 0.0003501 0.7347998 0.7348002 0.2296840 0.3011920 357712
23 154929952 rs4012982 CAA C -0.0001508 0.0003528 0.6690938 0.6690934 0.2394310 0.3165560 357712
23 154930230 rs781880 A G -0.0001946 0.0003354 0.5617758 0.5617756 0.2458740 0.3618540 357712
23 154930487 rs781879 T A -0.0019586 0.0011508 0.0887544 0.0887511 0.0195614 0.1263580 357712

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110724 ES:SE:LP:AF:SS:ID   -0.000122966:0.000612238:0.075298:0.110724:357712:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.115898 ES:SE:LP:AF:SS:ID   -0.000446971:0.00057854:0.356775:0.115898:357712:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0973675    ES:SE:LP:AF:SS:ID   -0.000135726:0.000650388:0.0784727:0.0973675:357712:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0156859    ES:SE:LP:AF:SS:ID   -0.000926989:0.00155255:0.259275:0.0156859:357712:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00173965   ES:SE:LP:AF:SS:ID   0.000267219:0.00457084:0.0207335:0.00173965:357712:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0565115    ES:SE:LP:AF:SS:ID   -0.000700834:0.000805764:0.41519:0.0565115:357712:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121803 ES:SE:LP:AF:SS:ID   -0.000405338:0.000548696:0.337174:0.121803:357712:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121239 ES:SE:LP:AF:SS:ID   -0.000580786:0.000585313:0.493402:0.121239:357712:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121031 ES:SE:LP:AF:SS:ID   -0.000414437:0.000548992:0.346492:0.121031:357712:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00580468   ES:SE:LP:AF:SS:ID   0.000162899:0.0025073:0.023101:0.00580468:357712:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00187759   ES:SE:LP:AF:SS:ID   -0.00039357:0.00474381:0.0297094:0.00187759:357712:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869658 ES:SE:LP:AF:SS:ID   0.000547707:0.000541202:0.5065:0.869658:357712:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123001 ES:SE:LP:AF:SS:ID   -0.000606453:0.000535982:0.588626:0.123001:357712:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142797 ES:SE:LP:AF:SS:ID   -0.000362393:0.00052978:0.30632:0.142797:357712:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123117 ES:SE:LP:AF:SS:ID   -0.000558296:0.000535236:0.527375:0.123117:357712:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870799 ES:SE:LP:AF:SS:ID   0.000437026:0.000521566:0.395686:0.870799:357712:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875387 ES:SE:LP:AF:SS:ID   0.000446349:0.000530225:0.398054:0.875387:357712:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128727 ES:SE:LP:AF:SS:ID   -0.000444787:0.000522861:0.40346:0.128727:357712:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363491    ES:SE:LP:AF:SS:ID   -0.000536311:0.000949016:0.242612:0.0363491:357712:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87039  ES:SE:LP:AF:SS:ID   0.000411699:0.000521021:0.367113:0.87039:357712:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870496 ES:SE:LP:AF:SS:ID   0.000402351:0.000521261:0.356364:0.870496:357712:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870389 ES:SE:LP:AF:SS:ID   0.00040848:0.000521003:0.363486:0.870389:357712:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00505015   ES:SE:LP:AF:SS:ID   0.000567203:0.00267374:0.0798772:0.00505015:357712:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00501698   ES:SE:LP:AF:SS:ID   0.000550789:0.00268089:0.0771599:0.00501698:357712:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558678   ES:SE:LP:AF:SS:ID   -0.00280081:0.00259106:0.553278:0.00558678:357712:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870472 ES:SE:LP:AF:SS:ID   0.000464823:0.000520091:0.430082:0.870472:357712:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126072 ES:SE:LP:AF:SS:ID   -0.000459747:0.000530689:0.413058:0.126072:357712:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870038 ES:SE:LP:AF:SS:ID   0.00046106:0.000518847:0.42689:0.870038:357712:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869322 ES:SE:LP:AF:SS:ID   0.000471505:0.00051836:0.440057:0.869322:357712:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87019  ES:SE:LP:AF:SS:ID   0.000472855:0.000519285:0.440676:0.87019:357712:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870196 ES:SE:LP:AF:SS:ID   0.000472404:0.000519322:0.440087:0.870196:357712:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870205 ES:SE:LP:AF:SS:ID   0.000471521:0.000519339:0.438996:0.870205:357712:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870648 ES:SE:LP:AF:SS:ID   0.000465014:0.000520657:0.429705:0.870648:357712:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0989131    ES:SE:LP:AF:SS:ID   -0.00048426:0.000605033:0.37316:0.0989131:357712:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00648077   ES:SE:LP:AF:SS:ID   -0.00193208:0.00234041:0.388201:0.00648077:357712:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874551 ES:SE:LP:AF:SS:ID   0.000526183:0.000528431:0.4957:0.874551:357712:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863924 ES:SE:LP:AF:SS:ID   0.000507516:0.000518181:0.484954:0.863924:357712:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869335 ES:SE:LP:AF:SS:ID   0.00052573:0.000523227:0.501687:0.869335:357712:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866284 ES:SE:LP:AF:SS:ID   0.00052713:0.000523328:0.503335:0.866284:357712:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0988419    ES:SE:LP:AF:SS:ID   -0.000921602:0.0006266:0.849716:0.0988419:357712:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871475 ES:SE:LP:AF:SS:ID   0.000508205:0.000529296:0.472398:0.871475:357712:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871475 ES:SE:LP:AF:SS:ID   0.000508165:0.000529296:0.472348:0.871475:357712:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871474 ES:SE:LP:AF:SS:ID   0.000508047:0.000529306:0.472192:0.871474:357712:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871846 ES:SE:LP:AF:SS:ID   0.000495942:0.000529608:0.45711:0.871846:357712:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125652 ES:SE:LP:AF:SS:ID   -0.000515133:0.00053002:0.480047:0.125652:357712:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10551  ES:SE:LP:AF:SS:ID   -0.000408034:0.00057695:0.319278:0.10551:357712:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855281 ES:SE:LP:AF:SS:ID   0.000488714:0.000517997:0.461625:0.855281:357712:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00166014   ES:SE:LP:AF:SS:ID   4.14538e-05:0.00458067:0.00314742:0.00166014:357712:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838262 ES:SE:LP:AF:SS:ID   7.39938e-05:0.000510403:0.0531873:0.838262:357712:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763181 ES:SE:LP:AF:SS:ID   0.000375363:0.00041073:0.442765:0.763181:357712:rs2977608