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-11618/UKB-b-11618_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11618/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:41:01 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11618/UKB-b-11618_data.vcf.gz ...
Read summary statistics for 2689379 SNPs.
Dropped 326 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, 676297 SNPs remain.
After merging with regression SNP LD, 676297 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0014 (0.0013)
Lambda GC: 0.9918
Mean Chi^2: 0.9947
Intercept: 1.0101 (0.0099)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Thu Oct 17 14:41:40 2019
Total time elapsed: 38.7s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7894,
    "inflation_factor": 1,
    "mean_EFFECT": -4.9425e-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": 21324,
    "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": 676297,
    "ldsc_nsnp_merge_regression_ld": 676297,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0101,
    "ldsc_intercept_se": 0.0099,
    "ldsc_lambda_gc": 0.9918,
    "ldsc_mean_chisq": 0.9947,
    "ldsc_ratio": -1.9057
}
 

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 1.000000 4 58 0 2689056 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 2689379 0.000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA NA NA 8.661185e+00 5.767950e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.000000 NA NA NA NA NA NA NA 7.855649e+07 5.663250e+07 5687.0000000 3.173045e+07 6.895619e+07 1.147381e+08 2.492013e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA NA NA -5.000000e-07 1.313000e-04 -0.0006187 -8.880000e-05 -9.000000e-07 8.740000e-05 7.961000e-04 ▁▅▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA NA NA 1.314000e-04 8.100000e-06 0.0001181 1.244000e-04 1.290000e-04 1.371000e-04 2.656000e-04 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA NA NA 5.016123e-01 2.884651e-01 0.0000026 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA NA NA 5.016097e-01 2.884350e-01 0.0000026 2.521439e-01 5.016227e-01 7.513258e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA NA NA 4.464040e-01 1.608109e-01 0.2164510 3.050330e-01 4.208610e-01 5.743110e-01 7.835490e-01 ▇▆▅▃▃
numeric AF_reference 21324 0.992071 NA NA NA NA NA NA NA 4.288017e-01 1.823398e-01 0.0001997 2.837460e-01 4.105430e-01 5.625000e-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 0.0000410 0.0002174 0.8499999 0.8504555 0.623765 0.7821490 NA
1 54676 rs2462492 C T -0.0005342 0.0002154 0.0129999 0.0131427 0.400401 NA NA
1 91536 rs6702460 G T -0.0001143 0.0002121 0.5900000 0.5898422 0.456846 0.4207270 NA
1 534192 rs6680723 C T -0.0000503 0.0002423 0.8400000 0.8354754 0.240959 NA NA
1 706368 rs55727773 A G 0.0000646 0.0001504 0.6700003 0.6676693 0.515645 0.2751600 NA
1 763394 rs369924889 G A -0.0002696 0.0001763 0.1299999 0.1262749 0.706753 0.6176120 NA
1 768253 rs2977608 A C -0.0001128 0.0001439 0.4299995 0.4329700 0.761297 0.4894170 NA
1 776546 rs12124819 A G -0.0001952 0.0001608 0.2200002 0.2245762 0.265385 0.0756789 NA
1 808631 rs11240779 G A -0.0000852 0.0001461 0.5600000 0.5600014 0.772619 0.4534740 NA
1 808928 rs11240780 C T -0.0000881 0.0001464 0.5500004 0.5472360 0.772847 0.4522760 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51180501 rs5770999 T C 0.0000417 0.0001415 0.7700005 0.7684606 0.713656 0.6369810 NA
22 51181919 rs9616825 G C 0.0000680 0.0001408 0.6300007 0.6289430 0.695470 0.6194090 NA
22 51182485 rs6009961 A G 0.0000366 0.0001420 0.8000000 0.7968541 0.715502 0.6383790 NA
22 51186143 rs2879914 T C 0.0001267 0.0001317 0.3400001 0.3358273 0.381825 0.2733630 NA
22 51186228 rs3865766 C T 0.0001791 0.0001283 0.1600000 0.1627199 0.451061 0.4532750 NA
22 51197266 rs61290853 A G 0.0002106 0.0001325 0.1100001 0.1119112 0.386333 0.4229230 NA
22 51198027 rs34939255 A G -0.0001887 0.0001500 0.2099999 0.2083625 0.254562 0.0984425 NA
22 51211106 rs9628250 T C -0.0001879 0.0001487 0.2099999 0.2062785 0.271547 0.1671330 NA
22 51212875 rs2238837 A C 0.0001362 0.0001413 0.3400001 0.3351502 0.331457 0.3724040 NA
22 51237063 rs3896457 T C 0.0001989 0.0001446 0.1700000 0.1691245 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  4.09944e-05:0.000217434:0.0705811:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -0.000534191:0.00021541:1.88606:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  -0.000114334:0.000212097:0.229148:0.456846:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -5.03159e-05:0.000242271:0.0757207:0.240959:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  6.45728e-05:0.000150397:0.173925:0.515645:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  -0.000269595:0.000176326:0.886057:0.706753:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  -0.000112845:0.000143913:0.366532:0.761297:rs2977608
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  -0.00019523:0.000160756:0.657577:0.265385:rs12124819
1   808631  rs11240779  G   A   .   PASS    AF=0.772619 ES:SE:LP:AF:ID  -8.51575e-05:0.000146108:0.251812:0.772619:rs11240779
1   808928  rs11240780  C   T   .   PASS    AF=0.772847 ES:SE:LP:AF:ID  -8.80915e-05:0.000146354:0.259637:0.772847:rs11240780
1   814495  rs74461805  C   A   .   PASS    AF=0.340396 ES:SE:LP:AF:ID  -4.16756e-05:0.00020622:0.0757207:0.340396:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697255 ES:SE:LP:AF:ID  6.20608e-05:0.000137972:0.187087:0.697255:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705397 ES:SE:LP:AF:ID  0.000120834:0.000135475:0.431798:0.705397:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705442 ES:SE:LP:AF:ID  0.000122846:0.000135471:0.443698:0.705442:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705627 ES:SE:LP:AF:ID  0.000119832:0.000135477:0.420216:0.705627:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705655 ES:SE:LP:AF:ID  0.000120289:0.000135491:0.431798:0.705655:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730129 ES:SE:LP:AF:ID  0.00018707:0.000139183:0.744727:0.730129:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294377 ES:SE:LP:AF:ID  -0.000120914:0.000135485:0.431798:0.294377:rs28765502
1   833223  rs13303211  C   T   .   PASS    AF=0.236703 ES:SE:LP:AF:ID  -0.000185665:0.000144245:0.69897:0.236703:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.236691 ES:SE:LP:AF:ID  -0.000191371:0.000144246:0.744727:0.236691:rs28752186
1   833641  rs28594623  T   C   .   PASS    AF=0.23975  ES:SE:LP:AF:ID  -0.000185915:0.000143784:0.69897:0.23975:rs28594623
1   833824  rs28484835  T   C   .   PASS    AF=0.236693 ES:SE:LP:AF:ID  -0.000191488:0.000144245:0.744727:0.236693:rs28484835
1   834832  rs4411087   G   C   .   PASS    AF=0.237178 ES:SE:LP:AF:ID  -0.000195988:0.000144134:0.769551:0.237178:rs4411087
1   835499  rs4422948   A   G   .   PASS    AF=0.241162 ES:SE:LP:AF:ID  -0.000128231:0.000143128:0.431798:0.241162:rs4422948
1   836896  rs28705752  T   C   .   PASS    AF=0.269511 ES:SE:LP:AF:ID  -0.000112566:0.000138108:0.376751:0.269511:rs28705752
1   838555  rs4970383   C   A   .   PASS    AF=0.246204 ES:SE:LP:AF:ID  -0.000154311:0.000142144:0.552842:0.246204:rs4970383
1   839103  rs28562941  A   G   .   PASS    AF=0.270019 ES:SE:LP:AF:ID  -0.000111208:0.000138205:0.376751:0.270019:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400124 ES:SE:LP:AF:ID  4.29064e-05:0.000124964:0.136677:0.400124:rs4970382
1   841085  rs1574243   C   G   .   PASS    AF=0.237102 ES:SE:LP:AF:ID  -0.000147896:0.000145151:0.508638:0.237102:rs1574243
1   842362  rs28540380  C   T   .   PASS    AF=0.235323 ES:SE:LP:AF:ID  -0.000350746:0.000147325:1.76955:0.235323:rs28540380
1   843405  rs11516185  A   G   .   PASS    AF=0.362606 ES:SE:LP:AF:ID  5.76879e-05:0.000155125:0.148742:0.362606:rs11516185
1   850218  rs6664536   T   A   .   PASS    AF=0.590331 ES:SE:LP:AF:ID  -0.000169896:0.0001246:0.769551:0.590331:rs6664536
1   850371  rs6679046   G   T   .   PASS    AF=0.603723 ES:SE:LP:AF:ID  -0.000162114:0.000125299:0.69897:0.603723:rs6679046
1   850780  rs6657440   C   T   .   PASS    AF=0.603942 ES:SE:LP:AF:ID  -0.000161552:0.000125282:0.69897:0.603942:rs6657440
1   851204  rs28552953  G   C   .   PASS    AF=0.224621 ES:SE:LP:AF:ID  -5.2806e-05:0.000148219:0.142668:0.224621:rs28552953
1   852037  rs4970463   G   A   .   PASS    AF=0.589686 ES:SE:LP:AF:ID  -0.000188029:0.000124802:0.886057:0.589686:rs4970463
1   852063  rs28436996  G   A   .   PASS    AF=0.589665 ES:SE:LP:AF:ID  -0.000186012:0.000124746:0.853872:0.589665:rs28436996
1   852875  rs13303369  C   T   .   PASS    AF=0.607671 ES:SE:LP:AF:ID  -0.000155704:0.000125561:0.677781:0.607671:rs13303369
1   853954  rs1806509   C   A   .   PASS    AF=0.607829 ES:SE:LP:AF:ID  -0.000157952:0.000125578:0.677781:0.607829:rs1806509
1   854777  rs13303019  A   G   .   PASS    AF=0.610316 ES:SE:LP:AF:ID  -0.000136174:0.000125702:0.552842:0.610316:rs13303019
1   854978  rs13303057  A   C   .   PASS    AF=0.603283 ES:SE:LP:AF:ID  -0.00015665:0.00012533:0.677781:0.603283:rs13303057
1   855075  rs6673914   C   G   .   PASS    AF=0.610337 ES:SE:LP:AF:ID  -0.000134375:0.000125704:0.537602:0.610337:rs6673914
1   856099  rs28534711  T   G   .   PASS    AF=0.389936 ES:SE:LP:AF:ID  0.000147782:0.000125728:0.619789:0.389936:rs28534711
1   856108  rs28742275  A   G   .   PASS    AF=0.38992  ES:SE:LP:AF:ID  0.000147754:0.000125735:0.619789:0.38992:rs28742275
1   856476  rs4040605   A   G   .   PASS    AF=0.350356 ES:SE:LP:AF:ID  0.000114782:0.000129165:0.431798:0.350356:rs4040605
1   858040  rs4970460   C   A   .   PASS    AF=0.217965 ES:SE:LP:AF:ID  -0.000148594:0.00014863:0.49485:0.217965:rs4970460
1   858051  rs4970459   C   T   .   PASS    AF=0.219021 ES:SE:LP:AF:ID  -0.000129528:0.000148111:0.420216:0.219021:rs4970459
1   858801  rs7418179   A   G   .   PASS    AF=0.765846 ES:SE:LP:AF:ID  2.28504e-05:0.000144992:0.0604807:0.765846:rs7418179
1   860416  rs61464428  G   A   .   PASS    AF=0.766638 ES:SE:LP:AF:ID  -1.34231e-05:0.000145064:0.0315171:0.766638:rs61464428
1   860688  rs60837925  G   A   .   PASS    AF=0.766104 ES:SE:LP:AF:ID  -1.54533e-05:0.000144964:0.0362122:0.766104:rs60837925