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/95ee3370-f0ac-4521-b9b7-e9abdfffbdc4/call-ldsc/inputs/562856218/ieu-b-40.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-40/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Aug 20 17:20:21 2020
Reading summary statistics from /data/cromwell-executions/qc/95ee3370-f0ac-4521-b9b7-e9abdfffbdc4/call-ldsc/inputs/562856218/ieu-b-40.vcf.gz ...
Read summary statistics for 2336255 SNPs.
Dropped 638 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1048422 SNPs remain.
After merging with regression SNP LD, 1048422 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.193 (0.0063)
Lambda GC: 2.727
Mean Chi^2: 3.9675
Intercept: 1.1825 (0.0209)
Ratio: 0.0615 (0.007)
Analysis finished at Thu Aug 20 17:22:39 2020
Total time elapsed: 2.0m:18.5s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9272,
    "inflation_factor": 2.7889,
    "mean_EFFECT": 0,
    "n": 795640,
    "n_snps": 2336260,
    "n_clumped_hits": 507,
    "n_p_sig": 41209,
    "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": 12471,
    "n_est": 806121.932,
    "ratio_se_n": 1.0066,
    "mean_diff": -2.6717e-06,
    "ratio_diff": 2.5008,
    "sd_y_est1": 1.0874,
    "sd_y_est2": 1.0945,
    "r2_sum1": 0.0524,
    "r2_sum2": 0.0443,
    "r2_sum3": 0.0437,
    "r2_sum4": 0.0463,
    "ldsc_nsnp_merge_refpanel_ld": 1048422,
    "ldsc_nsnp_merge_regression_ld": 1048422,
    "ldsc_observed_scale_h2_beta": 0.193,
    "ldsc_observed_scale_h2_se": 0.0063,
    "ldsc_intercept_beta": 1.1825,
    "ldsc_intercept_se": 0.0209,
    "ldsc_lambda_gc": 2.727,
    "ldsc_mean_chisq": 3.9675,
    "ldsc_ratio": 0.0615
}
 

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 1.000000 3 34 0 2336259 0 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
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 8.579708e+00 5.653368e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.20000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.912649e+07 5.559340e+07 1.29940e+04 3.317651e+07 7.073592e+07 1.145473e+08 2.49219e+08 ▇▇▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 1.860000e-05 4.911600e-03 -1.06000e-01 -2.700000e-03 0.000000e+00 2.700000e-03 7.80000e-02 ▁▁▇▂▁
numeric SE 0 1.000000 NA NA NA NA NA 2.613400e-03 1.252300e-03 1.60000e-03 1.800000e-03 2.100000e-03 2.900000e-03 4.34000e-02 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 3.431542e-01 3.130294e-01 0.00000e+00 4.600020e-02 2.599998e-01 5.999997e-01 1.00000e+00 ▇▃▂▂▂
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 3.430163e-01 3.131608e-01 0.00000e+00 4.550030e-02 2.637178e-01 5.992887e-01 1.00000e+00 ▇▃▂▂▂
numeric AF 0 1.000000 NA NA NA NA NA 3.588528e-01 2.716627e-01 9.82200e-03 1.249000e-01 2.912000e-01 5.610000e-01 9.90061e-01 ▇▅▃▂▂
numeric AF_reference 12471 0.994662 NA NA NA NA NA 3.619453e-01 2.559926e-01 5.99000e-04 1.473640e-01 2.977240e-01 5.471250e-01 9.99601e-01 ▇▆▃▃▂
numeric N 0 1.000000 NA NA NA NA NA 6.833649e+05 3.208988e+04 4.85648e+05 6.798850e+05 6.885660e+05 6.915470e+05 7.95640e+05 ▁▁▁▇▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 753541 rs2073813 G A -0.0040 0.0028 0.1499999 0.1531275 0.14250 0.3019170 517173
1 754192 rs3131968 A G 0.0023 0.0028 0.4100001 0.4114022 0.85630 0.6785140 551519
1 777122 rs2980319 A T 0.0019 0.0027 0.4799997 0.4816173 0.86320 0.7472040 598447
1 779322 rs4040617 A G -0.0021 0.0027 0.4500005 0.4367000 0.13530 0.2264380 587624
1 780785 rs2977612 T A 0.0019 0.0027 0.4899999 0.4816173 0.85500 0.6693290 582906
1 785989 rs2980300 T C 0.0019 0.0027 0.4700002 0.4816173 0.85270 0.6269970 585492
1 798026 rs4951864 C T -0.0089 0.0035 0.0109999 0.0109950 0.91786 0.8941690 532795
1 798801 rs12132517 G A 0.0088 0.0035 0.0120000 0.0119274 0.08045 0.0740815 528849
1 798959 rs11240777 G A 0.0014 0.0024 0.5700002 0.5596689 0.21040 0.4099440 547671
1 990380 rs3121561 C T -0.0010 0.0021 0.6400000 0.6339387 0.28680 0.3434500 605446
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51158017 rs6010065 G C 0.0039 0.0018 0.0280001 0.0302603 0.46220 0.5475240 686976
22 51162059 rs10451 G A 0.0022 0.0019 0.2599998 0.2469070 0.30670 0.3865810 637122
22 51163138 rs715586 C T 0.0028 0.0023 0.2399999 0.2234554 0.14790 0.0902556 777640
22 51165664 rs8137951 G A 0.0026 0.0018 0.1499999 0.1486140 0.30430 0.4063500 789190
22 51171497 rs2301584 G A 0.0001 0.0025 0.9800000 0.9680931 0.17810 0.2533950 604784
22 51173542 rs4824147 T C 0.0030 0.0040 0.4400003 0.4532547 0.95919 0.9812300 583357
22 51175626 rs3810648 A G -0.0040 0.0037 0.2700001 0.2796610 0.06437 0.1084270 672619
22 51178090 rs2285395 G A -0.0029 0.0037 0.4299995 0.4331670 0.05548 0.0666933 773206
22 51196164 rs8136603 A T -0.0063 0.0042 0.1299999 0.1336144 0.05589 0.1427720 649010
22 51229805 rs9616985 T C 0.0049 0.0036 0.1800002 0.1734786 0.05163 0.0730831 585003

bcf preview

1   753541  rs1388595942    G   A   .   PASS    AF=0.1425   ES:SE:LP:AF:SS:ID   -0.004:0.0028:0.823909:0.1425:517173:rs1388595942
1   754192  rs3131968   A   G   .   PASS    AF=0.8563   ES:SE:LP:AF:SS:ID   0.0023:0.0028:0.387216:0.8563:551519:rs3131968
1   777122  rs2980319   A   T   .   PASS    AF=0.8632   ES:SE:LP:AF:SS:ID   0.0019:0.0027:0.318759:0.8632:598447:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1353   ES:SE:LP:AF:SS:ID   -0.0021:0.0027:0.346787:0.1353:587624:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.855    ES:SE:LP:AF:SS:ID   0.0019:0.0027:0.309804:0.855:582906:rs2977612
1   785989  rs2980300   T   C   .   PASS    AF=0.8527   ES:SE:LP:AF:SS:ID   0.0019:0.0027:0.327902:0.8527:585492:rs2980300
1   798026  rs4951864   C   T   .   PASS    AF=0.91786  ES:SE:LP:AF:SS:ID   -0.0089:0.0035:1.95861:0.91786:532795:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.08045  ES:SE:LP:AF:SS:ID   0.0088:0.0035:1.92082:0.08045:528849:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.2104   ES:SE:LP:AF:SS:ID   0.0014:0.0024:0.244125:0.2104:547671:rs11240777
1   990380  rs3121561   C   T   .   PASS    AF=0.2868   ES:SE:LP:AF:SS:ID   -0.001:0.0021:0.19382:0.2868:605446:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.1476   ES:SE:LP:AF:SS:ID   0.0021:0.0025:0.387216:0.1476:623366:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.717    ES:SE:LP:AF:SS:ID   0.0039:0.002:1.31876:0.717:680426:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1428   ES:SE:LP:AF:SS:ID   0.0041:0.0025:1:0.1428:635407:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5608   ES:SE:LP:AF:SS:ID   0.0005:0.0018:0.09691:0.5608:668398:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5544   ES:SE:LP:AF:SS:ID   0.0007:0.0018:0.167491:0.5544:669144:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1387   ES:SE:LP:AF:SS:ID   0.0058:0.0026:1.60206:0.1387:635927:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.569    ES:SE:LP:AF:SS:ID   0.0006:0.0018:0.130768:0.569:682317:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5697   ES:SE:LP:AF:SS:ID   0.0005:0.0018:0.113509:0.5697:682866:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1486   ES:SE:LP:AF:SS:ID   0.0059:0.0026:1.65758:0.1486:630682:rs10907177
1   1021415 rs386627436 A   G   .   PASS    AF=0.7181   ES:SE:LP:AF:SS:ID   0.0043:0.002:1.55284:0.7181:670750:rs386627436
1   1021583 rs10907178  A   C   .   PASS    AF=0.1475   ES:SE:LP:AF:SS:ID   0.0059:0.0026:1.65758:0.1475:630752:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7204   ES:SE:LP:AF:SS:ID   0.0045:0.002:1.61979:0.7204:674336:rs9442398
1   1030565 rs6687776   C   T   .   PASS    AF=0.1579   ES:SE:LP:AF:SS:ID   0.0029:0.0024:0.638272:0.1579:642429:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1579   ES:SE:LP:AF:SS:ID   0.0027:0.0025:0.568636:0.1579:621351:rs6678318
1   1031540 rs776599533 A   G   .   PASS    AF=0.7256   ES:SE:LP:AF:SS:ID   0.0018:0.002:0.420216:0.7256:633563:rs776599533
1   1036959 rs1162868282    T   C   .   PASS    AF=0.1136   ES:SE:LP:AF:SS:ID   0.0024:0.0028:0.420216:0.1136:662400:rs1162868282
1   1040026 rs6671356   T   C   .   PASS    AF=0.1369   ES:SE:LP:AF:SS:ID   0.0008:0.0026:0.113509:0.1369:650822:rs6671356
1   1046164 rs386627439 C   T   .   PASS    AF=0.1393   ES:SE:LP:AF:SS:ID   0.0003:0.0026:0.0457575:0.1393:657400:rs386627439
1   1048955 rs4970405   A   G   .   PASS    AF=0.1103   ES:SE:LP:AF:SS:ID   0.0014:0.0029:0.207608:0.1103:660764:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1393   ES:SE:LP:AF:SS:ID   0.0004:0.0026:0.0655015:0.1393:657067:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1155   ES:SE:LP:AF:SS:ID   0.002:0.0028:0.327902:0.1155:656195:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.2914   ES:SE:LP:AF:SS:ID   -0.0036:0.002:1.11351:0.2914:584935:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.02228  ES:SE:LP:AF:SS:ID   -0.0082:0.0058:0.79588:0.02228:622102:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1162   ES:SE:LP:AF:SS:ID   0.0021:0.0028:0.337242:0.1162:659082:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1161   ES:SE:LP:AF:SS:ID   0.0023:0.0028:0.387216:0.1161:659382:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1161   ES:SE:LP:AF:SS:ID   0.0023:0.0028:0.387216:0.1161:654281:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4058   ES:SE:LP:AF:SS:ID   -0.0024:0.0019:0.721246:0.4058:616267:rs11807848
1   1062015 rs1557446446    C   T   .   PASS    AF=0.02239  ES:SE:LP:AF:SS:ID   -0.0071:0.0059:0.638272:0.02239:609493:rs1557446446
1   1062638 rs9442373   C   A   .   PASS    AF=0.5558   ES:SE:LP:AF:SS:ID   0.0032:0.0018:1.10237:0.5558:625335:rs9442373
1   1064979 rs2298217   C   T   .   PASS    AF=0.1515   ES:SE:LP:AF:SS:ID   -0.0013:0.0025:0.21467:0.1515:620602:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.05888  ES:SE:LP:AF:SS:ID   0.0005:0.004:0.0409586:0.05888:508645:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.5941   ES:SE:LP:AF:SS:ID   0.0023:0.0019:0.677781:0.5941:603771:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.5997   ES:SE:LP:AF:SS:ID   0.002:0.0019:0.552842:0.5997:607558:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.92008  ES:SE:LP:AF:SS:ID   -0.0038:0.0033:0.585027:0.92008:655679:rs4970357
1   1079198 rs1310655014    T   C   .   PASS    AF=0.2335   ES:SE:LP:AF:SS:ID   -0.0049:0.0022:1.56864:0.2335:531090:rs1310655014
1   1087683 rs9442380   T   C   .   PASS    AF=0.93095  ES:SE:LP:AF:SS:ID   -0.0001:0.0035:0.0132283:0.93095:668827:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.97001  ES:SE:LP:AF:SS:ID   0.0003:0.005:0.0222764:0.97001:668339:rs4970358
1   1094738 rs4970362   A   G   .   PASS    AF=0.6901   ES:SE:LP:AF:SS:ID   0.005:0.0019:2.07058:0.6901:572533:rs4970362
1   1099342 rs9660710   A   C   .   PASS    AF=0.93259  ES:SE:LP:AF:SS:ID   -0.0006:0.0034:0.0655015:0.93259:687168:rs9660710
1   1100217 rs1202203592    C   T   .   PASS    AF=0.9444   ES:SE:LP:AF:SS:ID   -0.002:0.0039:0.207608:0.9444:685120:rs1202203592