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-6834/UKB-b-6834_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6834/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-6834/UKB-b-6834_data.vcf.gz ...
Read summary statistics for 3339191 SNPs.
Dropped 493 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, 820956 SNPs remain.
After merging with regression SNP LD, 820956 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0035 (0.0014)
Lambda GC: 1.0352
Mean Chi^2: 1.0353
Intercept: 0.9984 (0.0092)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:40:54 2019
Total time elapsed: 36.56s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8415,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -8.4094e-08,
    "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": 26768,
    "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": 820956,
    "ldsc_nsnp_merge_regression_ld": 820956,
    "ldsc_observed_scale_h2_beta": 0.0035,
    "ldsc_observed_scale_h2_se": 0.0014,
    "ldsc_intercept_beta": 0.9984,
    "ldsc_intercept_se": 0.0092,
    "ldsc_lambda_gc": 1.0352,
    "ldsc_mean_chisq": 1.0353,
    "ldsc_ratio": -0.0453
}
 

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 3338701 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 3339191 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 8.662769e+00 5.772860e+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 7.854916e+07 5.672254e+07 828.0000000 3.157906e+07 6.893605e+07 1.147786e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.000000e-07 1.608000e-04 -0.0008885 -1.072000e-04 -2.000000e-07 1.070000e-04 8.325000e-04 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.572000e-04 1.480000e-05 0.0001361 1.443000e-04 1.526000e-04 1.677000e-04 3.365000e-04 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.946772e-01 2.904521e-01 0.0000014 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 4.946766e-01 2.904253e-01 0.0000014 2.417902e-01 4.930049e-01 7.466972e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.218026e-01 1.893585e-01 0.1634760 2.557765e-01 3.857200e-01 5.673490e-01 8.365230e-01 ▇▆▅▃▂
numeric AF_reference 26768 0.9919837 NA NA NA NA NA NA NA 4.073865e-01 2.008909e-01 0.0000000 2.442090e-01 3.783950e-01 5.545130e-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 0.0000236 0.0002505 0.9299999 0.9250222 0.623763 0.7821490 NA
1 54676 rs2462492 C T -0.0000474 0.0002481 0.8499999 0.8485977 0.400401 NA NA
1 91536 rs6702460 G T 0.0000316 0.0002443 0.9000000 0.8971822 0.456851 0.4207270 NA
1 534192 rs6680723 C T -0.0003147 0.0002791 0.2599998 0.2594286 0.240960 NA NA
1 706368 rs55727773 A G 0.0001707 0.0001732 0.3200000 0.3243929 0.515650 0.2751600 NA
1 763394 rs369924889 G A 0.0001505 0.0002031 0.4600002 0.4587653 0.706753 0.6176120 NA
1 768253 rs2977608 A C 0.0001402 0.0001658 0.4000000 0.3975513 0.761304 0.4894170 NA
1 776546 rs12124819 A G 0.0001407 0.0001852 0.4500005 0.4474706 0.265390 0.0756789 NA
1 798400 rs10900604 A G -0.0000448 0.0001768 0.8000000 0.8000628 0.206580 0.4105430 NA
1 798959 rs11240777 G A -0.0000427 0.0001769 0.8100000 0.8091068 0.206409 0.4099440 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51182485 rs6009961 A G 0.0000358 0.0001636 0.8300000 0.8267224 0.715505 0.6383790 NA
22 51186143 rs2879914 T C 0.0000068 0.0001517 0.9599999 0.9640558 0.381826 0.2733630 NA
22 51186228 rs3865766 C T -0.0000715 0.0001478 0.6300007 0.6284284 0.451063 0.4532750 NA
22 51192586 rs5771006 G A 0.0001232 0.0001992 0.5400003 0.5362569 0.167620 0.0848642 NA
22 51193227 rs34608236 T G 0.0001583 0.0002036 0.4400003 0.4367119 0.168489 0.0692891 NA
22 51197266 rs61290853 A G 0.0000484 0.0001526 0.7499995 0.7513842 0.386333 0.4229230 NA
22 51198027 rs34939255 A G 0.0001705 0.0001728 0.3200000 0.3237222 0.254557 0.0984425 NA
22 51211106 rs9628250 T C 0.0001749 0.0001713 0.3100002 0.3070914 0.271547 0.1671330 NA
22 51212875 rs2238837 A C 0.0000871 0.0001628 0.5900000 0.5925936 0.331455 0.3724040 NA
22 51237063 rs3896457 T C 0.0000954 0.0001666 0.5700002 0.5669447 0.297971 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623763 ES:SE:LP:AF:ID  2.357e-05:0.000250453:0.0315171:0.623763:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -4.73681e-05:0.00024812:0.0705811:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  3.15699e-05:0.000244308:0.0457575:0.456851:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.24096  ES:SE:LP:AF:ID  -0.000314709:0.000279061:0.585027:0.24096:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.51565  ES:SE:LP:AF:ID  0.00017072:0.000173237:0.49485:0.51565:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  0.000150476:0.000203104:0.337242:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761304 ES:SE:LP:AF:ID  0.000140241:0.000165769:0.39794:0.761304:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.26539  ES:SE:LP:AF:ID  0.00014066:0.000185167:0.346787:0.26539:rs12124819
1   798400  rs10900604  A   G   .   PASS    AF=0.20658  ES:SE:LP:AF:ID  -4.47888e-05:0.000176845:0.09691:0.20658:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.206409 ES:SE:LP:AF:ID  -4.27403e-05:0.000176921:0.091515:0.206409:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.772626 ES:SE:LP:AF:ID  7.14799e-05:0.000168299:0.173925:0.772626:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772854 ES:SE:LP:AF:ID  7.29845e-05:0.000168582:0.173925:0.772854:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340397 ES:SE:LP:AF:ID  7.73412e-05:0.000237542:0.130768:0.340397:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697259 ES:SE:LP:AF:ID  0.000141437:0.000158923:0.431798:0.697259:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705403 ES:SE:LP:AF:ID  9.98986e-06:0.000156048:0.0222764:0.705403:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705448 ES:SE:LP:AF:ID  1.61919e-05:0.000156042:0.0362122:0.705448:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705634 ES:SE:LP:AF:ID  1.40944e-05:0.00015605:0.0315171:0.705634:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705662 ES:SE:LP:AF:ID  1.30987e-05:0.000156066:0.0315171:0.705662:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730134 ES:SE:LP:AF:ID  4.94391e-05:0.000160319:0.119186:0.730134:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294371 ES:SE:LP:AF:ID  -1.42956e-05:0.000156059:0.0315171:0.294371:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236696 ES:SE:LP:AF:ID  -2.39388e-05:0.000166149:0.05061:0.236696:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236684 ES:SE:LP:AF:ID  -2.3563e-05:0.000166151:0.05061:0.236684:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.239743 ES:SE:LP:AF:ID  -3.92837e-05:0.000165618:0.091515:0.239743:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236686 ES:SE:LP:AF:ID  -2.3697e-05:0.00016615:0.05061:0.236686:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.212416 ES:SE:LP:AF:ID  -6.40056e-05:0.00017269:0.148742:0.212416:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.212311 ES:SE:LP:AF:ID  -6.03776e-05:0.00017272:0.136677:0.212311:rs28385272
1   834832  rs4411087   G   C   .   PASS    AF=0.237171 ES:SE:LP:AF:ID  -3.01113e-05:0.000166022:0.0655015:0.237171:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.212956 ES:SE:LP:AF:ID  -7.55055e-05:0.000172475:0.180456:0.212956:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.212918 ES:SE:LP:AF:ID  -7.35562e-05:0.00017251:0.173925:0.212918:rs28570054
1   835499  rs4422948   A   G   .   PASS    AF=0.241155 ES:SE:LP:AF:ID  -6.21212e-05:0.000164864:0.148742:0.241155:rs4422948
1   836529  rs28731045  C   G   .   PASS    AF=0.213538 ES:SE:LP:AF:ID  -8.20722e-05:0.000172256:0.200659:0.213538:rs28731045
1   836896  rs28705752  T   C   .   PASS    AF=0.269503 ES:SE:LP:AF:ID  -2.99978e-05:0.000159081:0.0705811:0.269503:rs28705752
1   836924  rs72890788  G   A   .   PASS    AF=0.213508 ES:SE:LP:AF:ID  -8.18222e-05:0.000172277:0.200659:0.213508:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.214583 ES:SE:LP:AF:ID  -8.06674e-05:0.000171945:0.19382:0.214583:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.246197 ES:SE:LP:AF:ID  -4.86859e-05:0.00016373:0.113509:0.246197:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.27001  ES:SE:LP:AF:ID  -2.22069e-05:0.000159193:0.05061:0.27001:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400106 ES:SE:LP:AF:ID  1.76421e-05:0.000143941:0.0457575:0.400106:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237094 ES:SE:LP:AF:ID  -0.000112013:0.000167194:0.30103:0.237094:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.215384 ES:SE:LP:AF:ID  -9.10428e-05:0.00017206:0.221849:0.215384:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.235321 ES:SE:LP:AF:ID  -6.90664e-05:0.000169695:0.167491:0.235321:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362599 ES:SE:LP:AF:ID  -9.53751e-05:0.000178687:0.229148:0.362599:rs11516185
1   844300  rs61769713  C   G   .   PASS    AF=0.818815 ES:SE:LP:AF:ID  1.398e-05:0.00018364:0.0268721:0.818815:rs61769713
1   845283  rs7366404   G   T   .   PASS    AF=0.814502 ES:SE:LP:AF:ID  3.62812e-05:0.000182023:0.0757207:0.814502:rs7366404
1   845635  rs117086422 C   T   .   PASS    AF=0.20543  ES:SE:LP:AF:ID  -0.000115707:0.000174986:0.29243:0.20543:rs117086422
1   845938  rs57760052  G   A   .   PASS    AF=0.210865 ES:SE:LP:AF:ID  -0.000102015:0.000173302:0.251812:0.210865:rs57760052
1   846078  rs28612348  C   T   .   PASS    AF=0.196786 ES:SE:LP:AF:ID  -9.96204e-05:0.000177667:0.244125:0.196786:rs28612348
1   846338  rs4970334   A   G   .   PASS    AF=0.813832 ES:SE:LP:AF:ID  3.86955e-05:0.000181868:0.0809219:0.813832:rs4970334
1   846398  rs58781670  G   A   .   PASS    AF=0.204448 ES:SE:LP:AF:ID  -6.97498e-05:0.000175584:0.161151:0.204448:rs58781670
1   846489  rs4970333   T   C   .   PASS    AF=0.813925 ES:SE:LP:AF:ID  3.77243e-05:0.000181994:0.0757207:0.813925:rs4970333
1   846808  rs4475691   C   T   .   PASS    AF=0.198378 ES:SE:LP:AF:ID  -0.000104198:0.000177163:0.251812:0.198378:rs4475691