Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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 /data/cromwell-executions/qc/ab3c6393-2513-4a10-8211-3bc3bb23b484/call-ldsc/inputs/-261021509/ieu-b-5101.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-5101/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Feb  3 12:51:41 2023
Reading summary statistics from /data/cromwell-executions/qc/ab3c6393-2513-4a10-8211-3bc3bb23b484/call-ldsc/inputs/-261021509/ieu-b-5101.vcf.gz ...
Read summary statistics for 6849546 SNPs.
Dropped 24731 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1106108 SNPs remain.
After merging with regression SNP LD, 1106108 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3712 (0.0247)
Lambda GC: 1.2021
Mean Chi^2: 1.2532
Intercept: 1.0302 (0.0081)
Ratio: 0.1192 (0.0318)
Analysis finished at Fri Feb  3 12:53:16 2023
Total time elapsed: 1.0m:34.54s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.916,
    "inflation_factor": 1.1745,
    "mean_EFFECT": 0.0006,
    "n": 30761,
    "n_snps": 6849675,
    "n_clumped_hits": 8,
    "n_p_sig": 711,
    "n_mono": 0,
    "n_ns": 0,
    "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": 69835,
    "n_est": 30113.9048,
    "ratio_se_n": 0.9894,
    "mean_diff": -0.0003,
    "ratio_diff": 6.4166,
    "sd_y_est1": 2.2019,
    "sd_y_est2": 2.1787,
    "r2_sum1": 0.0467,
    "r2_sum2": 0.0096,
    "r2_sum3": 0.0098,
    "r2_sum4": 0.0101,
    "ldsc_nsnp_merge_refpanel_ld": 1106108,
    "ldsc_nsnp_merge_regression_ld": 1106108,
    "ldsc_observed_scale_h2_beta": 0.3712,
    "ldsc_observed_scale_h2_se": 0.0247,
    "ldsc_intercept_beta": 1.0302,
    "ldsc_intercept_se": 0.0081,
    "ldsc_lambda_gc": 1.2021,
    "ldsc_mean_chisq": 1.2532,
    "ldsc_ratio": 0.1193
}

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 99 0.9999855 3 58 0 6845344 0 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
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.656872e+00 5.768023e+00 1.000000 4.000000e+00 8.000000e+00 1.300000e+01 2.20000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.877727e+07 5.660684e+07 828.000000 3.206041e+07 6.917237e+07 1.149259e+08 2.49233e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 5.684000e-04 4.820720e-02 -0.785699 -2.049850e-02 2.000000e-04 2.120320e-02 8.98795e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.732770e-02 2.839070e-02 0.016600 1.910000e-02 2.500000e-02 4.400000e-02 3.25900e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.733658e-01 2.964229e-01 0.000000 2.091000e-01 4.647999e-01 7.302995e-01 1.00000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.733651e-01 2.964245e-01 0.000000 2.090621e-01 4.647733e-01 7.303131e-01 1.00000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 2.820830e-01 2.714093e-01 0.009000 5.100000e-02 1.830000e-01 4.510000e-01 9.89600e-01 ▇▃▂▂▁
numeric AF_reference 69835 0.9898046 NA NA NA NA NA 2.699794e-01 2.467966e-01 0.000000 6.549520e-02 1.926920e-01 4.209270e-01 1.00000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 2.987321e+04 2.656566e+03 15323.000000 3.076100e+04 3.076100e+04 3.076100e+04 3.07610e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 55326 rs3107975 T C 0.0726030 0.0941 0.4403003 0.4403801 0.030 0.0459265 29674
1 91536 rs6702460 G T 0.0078003 0.0486 0.8726000 0.8724866 0.405 0.4207270 20673
1 234313 rs8179466 C T -0.1348980 0.0794 0.0891005 0.0893254 0.090 NA 20673
1 254186 rs148663102 T C -0.1129000 0.1227 0.3571001 0.3575046 0.017 0.0175719 26358
1 526736 rs28863004 C G -0.0222017 0.0935 0.8124000 0.8123067 0.032 0.1317890 29674
1 533198 rs78497331 C T 0.0513986 0.1102 0.6412996 0.6409206 0.020 0.0814696 29674
1 534192 rs6680723 C T 0.0840993 0.0604 0.1638000 0.1638096 0.208 NA 20673
1 534583 rs6683466 C G 0.0377953 0.0777 0.6270007 0.6266652 0.041 NA 29674
1 565728 rs199661867 C A -0.0040020 0.0909 0.9647000 0.9648835 0.026 0.0315495 29674
1 569004 rs9285835 T C 0.0162005 0.0895 0.8565001 0.8563588 0.034 NA 29674
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A -0.0001000 0.0648 0.9994000 0.9987688 0.044 0.0473243 30761
22 51221190 rs369304721 G A -0.0473033 0.0839 0.5723003 0.5728864 0.036 NA 30761
22 51221731 rs115055839 T C -0.0187040 0.0573 0.7440995 0.7441048 0.055 0.0625000 30761
22 51221835 rs4330207 C G -0.0011993 0.1197 0.9920000 0.9920061 0.015 0.0053914 17504
22 51222100 rs114553188 G T -0.0034042 0.0549 0.9505000 0.9505570 0.048 0.0880591 30761
22 51223637 rs375798137 G A -0.0023971 0.0554 0.9651000 0.9654869 0.048 0.0788738 30761
22 51229805 rs9616985 T C -0.0230034 0.0589 0.6964998 0.6961298 0.054 0.0730831 30761
22 51232488 rs376461333 A G 0.2640960 0.2010 0.1888000 0.1888763 0.014 NA 20590
22 51234048 rs141330630 T C -0.0563047 0.0878 0.5216005 0.5213384 0.018 0.0095847 30761
22 51237063 rs3896457 T C 0.0328022 0.0276 0.2350001 0.2346422 0.306 0.2050720 30761

bcf preview

1   55326   rs3107975   T   C   .   PASS    AF=0.03 ES:SE:LP:AF:SS:SI:NC:ID 0.072603:0.0941:0.356251:0.03:29674:0.236:13457:rs3107975
1   91536   rs1251109649    G   T   .   PASS    AF=0.405    ES:SE:LP:AF:SS:SI:NC:ID 0.00780034:0.0486:0.0591848:0.405:20673:0.176:10428:rs1251109649
1   234313  rs8179466   C   T   .   PASS    AF=0.09 ES:SE:LP:AF:SS:SI:NC:ID -0.134898:0.0794:1.05012:0.09:20673:0.196:10428:rs8179466
1   254186  rs148663102 T   C   .   PASS    AF=0.017    ES:SE:LP:AF:SS:SI:NC:ID -0.1129:0.1227:0.44721:0.017:26358:0.308:12413:rs148663102
1   526736  rs28863004  C   G   .   PASS    AF=0.032    ES:SE:LP:AF:SS:SI:NC:ID -0.0222017:0.0935:0.0902301:0.032:29674:0.237:13457:rs28863004
1   533198  rs1557498752    C   T   .   PASS    AF=0.02 ES:SE:LP:AF:SS:SI:NC:ID 0.0513986:0.1102:0.192939:0.02:29674:0.276:13457:rs1557498752
1   534192  rs6680723   C   T   .   PASS    AF=0.208    ES:SE:LP:AF:SS:SI:NC:ID 0.0840993:0.0604:0.785686:0.208:20673:0.166:10428:rs6680723
1   534583  rs6683466   C   G   .   PASS    AF=0.041    ES:SE:LP:AF:SS:SI:NC:ID 0.0377953:0.0777:0.202732:0.041:29674:0.271:13457:rs6683466
1   565728  rs199661867 C   A   .   PASS    AF=0.026    ES:SE:LP:AF:SS:SI:NC:ID -0.00400198:0.0909:0.0156077:0.026:29674:0.304:13457:rs199661867
1   569004  rs9285835   T   C   .   PASS    AF=0.034    ES:SE:LP:AF:SS:SI:NC:ID 0.0162005:0.0895:0.0672726:0.034:29674:0.258:13457:rs9285835
1   592007  rs771664146 G   A   .   PASS    AF=0.02 ES:SE:LP:AF:SS:SI:NC:ID -0.177903:0.1088:0.9914:0.02:29674:0.283:13457:rs771664146
1   693731  rs12238997  A   G   .   PASS    AF=0.095    ES:SE:LP:AF:SS:SI:NC:ID -0.023404:0.0362:0.285922:0.095:30761:0.612:14004:rs12238997
1   706368  rs963699400 A   G   .   PASS    AF=0.383    ES:SE:LP:AF:SS:SI:NC:ID 0.0492953:0.0329:0.872247:0.383:27180:0.301:12981:rs963699400
1   713158  rs183634591 T   A   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0630037:0.1149:0.234108:0.014:18816:0.626:8944:rs183634591
1   713250  rs149143617 G   C   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0638987:0.1147:0.238598:0.014:18816:0.625:8944:rs149143617
1   713977  rs74512038  C   T   .   PASS    AF=0.11 ES:SE:LP:AF:SS:SI:NC:ID -0.0439977:0.0352:0.675101:0.11:29674:0.535:13457:rs74512038
1   714439  rs74707816  G   A   .   PASS    AF=0.098    ES:SE:LP:AF:SS:SI:NC:ID -0.0481042:0.0369:0.715344:0.098:29674:0.525:13457:rs74707816
1   714596  rs149887893 T   C   .   PASS    AF=0.024    ES:SE:LP:AF:SS:SI:NC:ID -0.0116024:0.0831:0.0510982:0.024:30761:0.451:14004:rs149887893
1   714622  rs117741916 G   C   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.0251024:0.1125:0.0842837:0.015:18816:0.648:8944:rs117741916
1   715140  rs142907433 G   C   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.0248974:0.1124:0.083704:0.015:18816:0.649:8944:rs142907433
1   715142  rs151120166 G   T   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.0249999:0.1124:0.0839674:0.015:18816:0.649:8944:rs151120166
1   715265  rs12184267  C   T   .   PASS    AF=0.017    ES:SE:LP:AF:SS:SI:NC:ID -0.0993022:0.1512:0.291494:0.017:20751:0.262:9627:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.018    ES:SE:LP:AF:SS:SI:NC:ID -0.0925974:0.1485:0.273517:0.018:20751:0.265:9627:rs12184277
1   715517  rs138194918 G   C   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.025605:0.1122:0.086451:0.015:18816:0.649:8944:rs138194918
1   715767  rs1302749095    T   C   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.0255024:0.1121:0.0861861:0.015:18816:0.649:8944:rs1302749095
1   715977  rs1413986825    T   C   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.025605:0.1121:0.086451:0.015:18816:0.65:8944:rs1413986825
1   717485  rs12184279  C   A   .   PASS    AF=0.017    ES:SE:LP:AF:SS:SI:NC:ID -0.104603:0.1512:0.310514:0.017:20751:0.263:9627:rs12184279
1   719511  rs181042612 A   G   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.025605:0.1117:0.0869283:0.015:18816:0.652:8944:rs181042612
1   720223  rs149231255 G   A   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.025605:0.1117:0.0867691:0.015:18816:0.652:8944:rs149231255
1   720381  rs116801199 G   T   .   PASS    AF=0.026    ES:SE:LP:AF:SS:SI:NC:ID -0.0194987:0.0791:0.094312:0.026:30761:0.471:14004:rs116801199
1   721054  rs79249784  T   C   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.025605:0.1116:0.0868752:0.015:18816:0.653:8944:rs79249784
1   721290  rs12565286  G   C   .   PASS    AF=0.026    ES:SE:LP:AF:SS:SI:NC:ID -0.0202045:0.0788:0.098106:0.026:30761:0.476:14004:rs12565286
1   723183  rs371791859 G   A   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0451961:0.1143:0.159643:0.014:18816:0.643:8944:rs371791859
1   723891  rs2977670   G   C   .   PASS    AF=0.866    ES:SE:LP:AF:SS:SI:NC:ID 0.0478991:0.0326:0.8471:0.866:30761:0.514:14004:rs2977670
1   724475  rs1192343231    T   A   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0252973:0.109:0.0880438:0.014:20622:0.639:9801:rs1192343231
1   724588  rs368213959 A   T   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.0353992:0.112:0.123782:0.015:18816:0.654:8944:rs368213959
1   724849  rs12126395  C   A   .   PASS    AF=0.028    ES:SE:LP:AF:SS:SI:NC:ID 0.188899:0.1491:0.687611:0.028:19494:0.178:9741:rs12126395
1   725245  rs373605788 T   C   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.025205:0.1089:0.0877779:0.014:20622:0.639:9801:rs373605788
1   726449  rs1410278091    T   C   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0243952:0.1088:0.0849169:0.014:20622:0.64:9801:rs1410278091
1   726794  rs28454925  C   G   .   PASS    AF=0.017    ES:SE:LP:AF:SS:SI:NC:ID -0.072702:0.1529:0.197637:0.017:20751:0.269:9627:rs28454925
1   727244  rs373212657 T   C   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.055703:0.1148:0.202248:0.014:18816:0.65:8944:rs373212657
1   727655  rs12565110  C   T   .   PASS    AF=0.097    ES:SE:LP:AF:SS:SI:NC:ID -0.0513963:0.0368:0.788346:0.097:29674:0.53:13457:rs12565110
1   728647  rs369904269 C   T   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.055703:0.1148:0.202386:0.014:18816:0.651:8944:rs369904269
1   729452  rs560378878 C   T   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0249999:0.1087:0.0869813:0.014:20622:0.641:9801:rs560378878
1   729632  rs116720794 C   T   .   PASS    AF=0.017    ES:SE:LP:AF:SS:SI:NC:ID -0.0689009:0.1549:0.182699:0.017:20751:0.268:9627:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.775    ES:SE:LP:AF:SS:SI:NC:ID 0.0331949:0.0244:0.759451:0.775:30761:0.663:14004:rs4951859
1   729957  rs116982056 T   C   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0248051:0.1087:0.0863451:0.014:20622:0.641:9801:rs116982056
1   730087  rs148120343 T   C   .   PASS    AF=0.024    ES:SE:LP:AF:SS:SI:NC:ID 0.0197028:0.1023:0.0719628:0.024:30761:0.291:14004:rs148120343
1   730323  rs142513910 A   G   .   PASS    AF=0.015    ES:SE:LP:AF:SS:SI:NC:ID 0.0152964:0.1079:0.0520274:0.015:20622:0.642:9801:rs142513910
1   731062  rs372561974 C   T   .   PASS    AF=0.014    ES:SE:LP:AF:SS:SI:NC:ID 0.0259026:0.1086:0.0908185:0.014:20622:0.649:9801:rs372561974