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/public/UKB-b-19937/UKB-b-19937_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19937/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:41:57 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19937/UKB-b-19937_data.vcf.gz ...
Read summary statistics for 3169802 SNPs.
Dropped 438 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, 784724 SNPs remain.
After merging with regression SNP LD, 784724 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0022 (0.0012)
Lambda GC: 1.0243
Mean Chi^2: 1.0264
Intercept: 1.0033 (0.009)
Ratio: 0.1238 (0.3389)
Analysis finished at Thu Oct 17 14:42:43 2019
Total time elapsed: 45.76s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8299,
    "inflation_factor": 1,
    "mean_EFFECT": 1.4753e-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": 25337,
    "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": 784724,
    "ldsc_nsnp_merge_regression_ld": 784724,
    "ldsc_observed_scale_h2_beta": 0.0022,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.0033,
    "ldsc_intercept_se": 0.009,
    "ldsc_lambda_gc": 1.0243,
    "ldsc_mean_chisq": 1.0264,
    "ldsc_ratio": 0.125
}
 

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 3169367 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 3169802 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 8.663056e+00 5.772732e+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 7.854225e+07 5.670661e+07 828.0000000 3.160086e+07 6.892371e+07 1.147871e+08 2.492013e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.000000e-07 1.515000e-04 -0.0008060 -1.012000e-04 1.000000e-07 1.012000e-04 8.344000e-04 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.494000e-04 1.270000e-05 0.0001307 1.383000e-04 1.455000e-04 1.584000e-04 3.233000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.968009e-01 2.902048e-01 0.0000005 2.399999e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.968021e-01 2.901782e-01 0.0000005 2.439263e-01 4.962672e-01 7.485579e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.283853e-01 1.823889e-01 0.1765010 2.683020e-01 3.949710e-01 5.699830e-01 8.234990e-01 ▇▆▅▃▃
numeric AF_reference 25337 0.9920068 NA NA NA NA NA NA NA 4.131712e-01 1.962315e-01 0.0000000 2.545930e-01 3.871810e-01 5.571090e-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 -0.0000315 0.0002406 0.9000000 0.8958859 0.623765 0.7821490 NA
1 54676 rs2462492 C T -0.0004752 0.0002384 0.0460002 0.0462120 0.400401 NA NA
1 91536 rs6702460 G T -0.0002223 0.0002347 0.3400001 0.3436058 0.456846 0.4207270 NA
1 534192 rs6680723 C T -0.0001256 0.0002681 0.6400000 0.6393006 0.240959 NA NA
1 706368 rs55727773 A G 0.0001678 0.0001664 0.3100002 0.3134095 0.515645 0.2751600 NA
1 763394 rs369924889 G A 0.0000402 0.0001951 0.8400000 0.8367954 0.706753 0.6176120 NA
1 768253 rs2977608 A C -0.0001402 0.0001593 0.3800004 0.3786344 0.761297 0.4894170 NA
1 776546 rs12124819 A G 0.0001266 0.0001779 0.4799997 0.4765994 0.265385 0.0756789 NA
1 798400 rs10900604 A G 0.0000846 0.0001699 0.6200004 0.6187103 0.206591 0.4105430 NA
1 798959 rs11240777 G A 0.0000847 0.0001700 0.6200004 0.6183612 0.206420 0.4099440 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51180501 rs5770999 T C -0.0000593 0.0001566 0.7099994 0.7050976 0.713656 0.6369810 NA
22 51181919 rs9616825 G C -0.0001267 0.0001558 0.4199997 0.4160122 0.695470 0.6194090 NA
22 51182485 rs6009961 A G -0.0000559 0.0001571 0.7199992 0.7222303 0.715502 0.6383790 NA
22 51186143 rs2879914 T C -0.0000434 0.0001457 0.7700005 0.7657760 0.381825 0.2733630 NA
22 51186228 rs3865766 C T -0.0000273 0.0001420 0.8499999 0.8477838 0.451061 0.4532750 NA
22 51197266 rs61290853 A G 0.0000199 0.0001466 0.8900000 0.8919018 0.386333 0.4229230 NA
22 51198027 rs34939255 A G -0.0000230 0.0001660 0.8900000 0.8896981 0.254562 0.0984425 NA
22 51211106 rs9628250 T C -0.0000382 0.0001645 0.8200001 0.8165036 0.271547 0.1671330 NA
22 51212875 rs2238837 A C -0.0000756 0.0001564 0.6300007 0.6285998 0.331457 0.3724040 NA
22 51237063 rs3896457 T C 0.0000123 0.0001601 0.9400001 0.9388325 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  -3.1486e-05:0.000240608:0.0457575:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -0.000475177:0.000238369:1.33724:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  -0.000222278:0.000234702:0.468521:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000125649:0.000268093:0.19382:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  0.000167773:0.000166426:0.508638:0.515645:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  4.01934e-05:0.000195119:0.0757207:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  -0.000140207:0.000159251:0.420216:0.761297:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  0.000126619:0.00017789:0.318759:0.265385:rs12124819
1   798400  rs10900604  A   G   .   PASS    AF=0.206591 ES:SE:LP:AF:ID  8.45502e-05:0.000169889:0.207608:0.206591:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.20642  ES:SE:LP:AF:ID  8.46702e-05:0.000169961:0.207608:0.20642:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  -0.000144973:0.000161681:0.431798:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  -0.000136972:0.000161953:0.39794:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  -0.000123927:0.000228199:0.229148:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  0.000174597:0.000152677:0.60206:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  0.000153324:0.000149914:0.508638:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  0.000152232:0.000149909:0.508638:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  0.000153884:0.000149916:0.522879:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  0.000153346:0.000149932:0.508638:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  0.000203757:0.000154017:0.721246:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  -0.000149216:0.000149925:0.49485:0.294377:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236703 ES:SE:LP:AF:ID  -0.000187006:0.000159618:0.619789:0.236703:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236691 ES:SE:LP:AF:ID  -0.000186722:0.00015962:0.619789:0.236691:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.23975  ES:SE:LP:AF:ID  -0.000202097:0.000159108:0.69897:0.23975:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236693 ES:SE:LP:AF:ID  -0.00018671:0.000159618:0.619789:0.236693:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.212421 ES:SE:LP:AF:ID  -0.0002504:0.000165902:0.886057:0.212421:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.212316 ES:SE:LP:AF:ID  -0.000246899:0.000165931:0.853872:0.212316:rs28385272
1   834832  rs4411087   G   C   .   PASS    AF=0.237178 ES:SE:LP:AF:ID  -0.000188182:0.000159496:0.619789:0.237178:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.212962 ES:SE:LP:AF:ID  -0.000256892:0.000165695:0.920819:0.212962:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.212924 ES:SE:LP:AF:ID  -0.00025582:0.000165729:0.920819:0.212924:rs28570054
1   835499  rs4422948   A   G   .   PASS    AF=0.241162 ES:SE:LP:AF:ID  -0.000193321:0.000158383:0.657577:0.241162:rs4422948
1   836529  rs28731045  C   G   .   PASS    AF=0.213543 ES:SE:LP:AF:ID  -0.000261891:0.000165485:0.958607:0.213543:rs28731045
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  -0.000221189:0.000152827:0.823909:0.269511:rs28705752
1   836924  rs72890788  G   A   .   PASS    AF=0.213513 ES:SE:LP:AF:ID  -0.000260309:0.000165505:0.920819:0.213513:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.214587 ES:SE:LP:AF:ID  -0.000242212:0.000165186:0.853872:0.214587:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  -0.00026941:0.000157294:1.06048:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  -0.000230649:0.000152935:0.886057:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  0.000118356:0.000138283:0.408935:0.400124:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237102 ES:SE:LP:AF:ID  -0.000343008:0.000160621:1.48149:0.237102:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.215391 ES:SE:LP:AF:ID  -0.000250695:0.000165297:0.886057:0.215391:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.235323 ES:SE:LP:AF:ID  -0.000249985:0.000163027:0.886057:0.235323:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  -0.000157013:0.000171659:0.443698:0.362606:rs11516185
1   844300  rs61769713  C   G   .   PASS    AF=0.818811 ES:SE:LP:AF:ID  -5.06338e-05:0.000176423:0.113509:0.818811:rs61769713
1   845283  rs7366404   G   T   .   PASS    AF=0.814497 ES:SE:LP:AF:ID  -2.10175e-05:0.000174868:0.0457575:0.814497:rs7366404
1   845635  rs117086422 C   T   .   PASS    AF=0.205429 ES:SE:LP:AF:ID  -0.000187747:0.000168108:0.585027:0.205429:rs117086422
1   845938  rs57760052  G   A   .   PASS    AF=0.210864 ES:SE:LP:AF:ID  -0.000198313:0.00016649:0.638272:0.210864:rs57760052
1   846078  rs28612348  C   T   .   PASS    AF=0.196785 ES:SE:LP:AF:ID  -0.000167371:0.000170684:0.481486:0.196785:rs28612348
1   846338  rs4970334   A   G   .   PASS    AF=0.813828 ES:SE:LP:AF:ID  -2.59675e-05:0.000174719:0.0555173:0.813828:rs4970334
1   846398  rs58781670  G   A   .   PASS    AF=0.204447 ES:SE:LP:AF:ID  -0.000208122:0.000168682:0.657577:0.204447:rs58781670
1   846489  rs4970333   T   C   .   PASS    AF=0.81392  ES:SE:LP:AF:ID  -2.60479e-05:0.00017484:0.0555173:0.81392:rs4970333
1   846808  rs4475691   C   T   .   PASS    AF=0.198378 ES:SE:LP:AF:ID  -0.00019797:0.000170198:0.619789:0.198378:rs4475691