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/4ef9477d-b87a-4522-9af1-7aec3e1d35ae/call-ldsc/inputs/-261045349/ieu-b-4760.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4760/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Tue Aug 24 16:59:52 2021
Reading summary statistics from /data/cromwell-executions/qc/4ef9477d-b87a-4522-9af1-7aec3e1d35ae/call-ldsc/inputs/-261045349/ieu-b-4760.vcf.gz ...
Read summary statistics for 0 SNPs.
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.
Traceback (most recent call last):
  File "./ldsc/ldsc.py", line 647, in <module>
    sumstats.estimate_h2(args, log)
  File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
    args, log, args.h2)
  File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
    sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
  File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
    raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.

Analysis finished at Tue Aug 24 17:00:44 2021
Total time elapsed: 52.35s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9494,
    "inflation_factor": 1.1919,
    "mean_EFFECT": 6.1286e-06,
    "n": "-Inf",
    "n_snps": 9631490,
    "n_clumped_hits": 9,
    "n_p_sig": 939,
    "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": 142774,
    "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": 0,
    "ldsc_nsnp_merge_regression_ld": "NA",
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": "NA",
    "ldsc_intercept_se": "NA",
    "ldsc_lambda_gc": "NA",
    "ldsc_mean_chisq": "NA",
    "ldsc_ratio": "NA"
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq NA
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio NA
ldsc_intercept_beta NA
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 65 0.9999933 3 58 0 9631299 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 9631490 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 8.625340e+00 5.751054e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.884816e+07 5.629880e+07 828.0000 3.256524e+07 6.944762e+07 1.145820e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 6.100000e-06 9.644700e-03 -0.1861 -3.100000e-03 0.000000e+00 3.100000e-03 4.596000e-01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 6.621900e-03 6.571900e-03 0.0019 2.400000e-03 3.900000e-03 8.700000e-03 1.674000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.712439e-01 2.964466e-01 0.0000 2.078002e-01 4.615003e-01 7.280999e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.710952e-01 2.965843e-01 0.0000 2.079367e-01 4.604566e-01 7.279708e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.070865e-01 2.570060e-01 0.0014 1.470000e-02 8.310000e-02 3.234000e-01 9.986000e-01 ▇▂▁▁▁
numeric AF_reference 142774 0.9851763 NA NA NA NA NA NA NA 2.093574e-01 2.486414e-01 0.0000 1.277960e-02 1.036340e-01 3.254790e-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 0.0046 0.0036 0.1935998 0.2013278 0.6239 0.7821490 NA
1 54676 rs2462492 C T 0.0052 0.0035 0.1419999 0.1373547 0.4002 NA NA
1 86028 rs114608975 T C -0.0008 0.0056 0.8913999 0.8864030 0.1036 0.0277556 NA
1 91536 rs6702460 G T 0.0012 0.0035 0.7380997 0.7317059 0.4568 0.4207270 NA
1 234313 rs8179466 C T -0.0135 0.0069 0.0492006 0.0504037 0.0745 NA NA
1 534192 rs6680723 C T -0.0036 0.0040 0.3602002 0.3681203 0.2409 NA NA
1 546697 rs12025928 A G -0.0005 0.0050 0.9163000 0.9203443 0.9135 NA NA
1 693731 rs12238997 A G 0.0000 0.0033 0.9930000 1.0000000 0.1162 0.1417730 NA
1 705882 rs72631875 G A -0.0114 0.0049 0.0195799 0.0199903 0.0673 0.0315495 NA
1 706368 rs55727773 A G -0.0002 0.0025 0.9462999 0.9362373 0.5158 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A -0.0076 0.0052 0.1435000 0.1438677 0.0420 0.0473243 NA
22 51219766 rs182321900 C T -0.0113 0.0240 0.6381004 0.6377598 0.0020 NA NA
22 51220146 rs868950473 C T -0.0107 0.0238 0.6529005 0.6530134 0.0020 NA NA
22 51221190 rs369304721 G A -0.0053 0.0052 0.3021997 0.3080934 0.0498 NA NA
22 51221731 rs115055839 T C -0.0050 0.0039 0.1933998 0.1998247 0.0733 0.0625000 NA
22 51222100 rs114553188 G T 0.0007 0.0046 0.8695000 0.8790498 0.0544 0.0880591 NA
22 51223637 rs375798137 G A 0.0005 0.0046 0.9117001 0.9134439 0.0540 0.0788738 NA
22 51229805 rs9616985 T C -0.0049 0.0039 0.2025000 0.2089673 0.0731 0.0730831 NA
22 51232488 rs376461333 A G 0.0098 0.0091 0.2844003 0.2815146 0.0200 NA NA
22 51237063 rs3896457 T C 0.0022 0.0024 0.3529003 0.3593173 0.2980 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.6239   ES:SE:LP:AF:ID  0.0046:0.0036:0.713095:0.6239:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.4002   ES:SE:LP:AF:ID  0.0052:0.0035:0.847712:0.4002:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.1036   ES:SE:LP:AF:ID  -0.0008:0.0056:0.0499274:0.1036:rs114608975
1   91536   rs1251109649    G   T   .   PASS    AF=0.4568   ES:SE:LP:AF:ID  0.0012:0.0035:0.131885:0.4568:rs1251109649
1   234313  rs8179466   C   T   .   PASS    AF=0.0745   ES:SE:LP:AF:ID  -0.0135:0.0069:1.30803:0.0745:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.2409   ES:SE:LP:AF:ID  -0.0036:0.004:0.443456:0.2409:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.9135   ES:SE:LP:AF:ID  -0.0005:0.005:0.0379623:0.9135:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.1162   ES:SE:LP:AF:ID  -0:0.0033:0.00305075:0.1162:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.0673   ES:SE:LP:AF:ID  -0.0114:0.0049:1.70819:0.0673:rs72631875
1   706368  rs963699400 A   G   .   PASS    AF=0.5158   ES:SE:LP:AF:ID  -0.0002:0.0025:0.0239712:0.5158:rs963699400
1   714596  rs149887893 T   C   .   PASS    AF=0.033    ES:SE:LP:AF:ID  0.0056:0.0062:0.437707:0.033:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.0367   ES:SE:LP:AF:ID  0.0062:0.0056:0.568958:0.0367:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.0368   ES:SE:LP:AF:ID  0.0055:0.0056:0.480829:0.0368:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.0365   ES:SE:LP:AF:ID  0.0056:0.0057:0.487182:0.0365:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.0164   ES:SE:LP:AF:ID  -0.0031:0.0087:0.142668:0.0164:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037    ES:SE:LP:AF:ID  0.006:0.0056:0.54333:0.037:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.0371   ES:SE:LP:AF:ID  0.0054:0.0056:0.4786:0.0371:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.1013   ES:SE:LP:AF:ID  -0.0014:0.0041:0.131062:0.1013:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959    ES:SE:LP:AF:ID  -0.0072:0.0054:0.748849:0.959:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.0315   ES:SE:LP:AF:ID  0.0175:0.0098:1.13042:0.0315:rs12126395
1   725060  rs1445661281    A   T   .   PASS    AF=0.0532   ES:SE:LP:AF:ID  0.0081:0.0078:0.523024:0.0532:rs1445661281
1   726794  rs28454925  C   G   .   PASS    AF=0.0366   ES:SE:LP:AF:ID  0.0055:0.0056:0.487983:0.0366:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.0369   ES:SE:LP:AF:ID  0.0049:0.0056:0.425853:0.0369:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.8433   ES:SE:LP:AF:ID  -0.0023:0.0029:0.363713:0.8433:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.0559   ES:SE:LP:AF:ID  -0.0014:0.0047:0.11685:0.0559:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.1222   ES:SE:LP:AF:ID  0.0007:0.0032:0.0781055:0.1222:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.0258   ES:SE:LP:AF:ID  0.0063:0.0078:0.378512:0.0258:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.1215   ES:SE:LP:AF:ID  0.0002:0.0032:0.0258108:0.1215:rs141242758
1   736289  rs1254887344    T   A   .   PASS    AF=0.1323   ES:SE:LP:AF:ID  0.0019:0.0031:0.268653:0.1323:rs1254887344
1   736689  rs181876450 T   C   .   PASS    AF=0.0111   ES:SE:LP:AF:ID  0.0125:0.0113:0.56671:0.0111:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.0057   ES:SE:LP:AF:ID  0.0203:0.0147:0.778064:0.0057:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0023   ES:SE:LP:AF:ID  0.0387:0.0245:0.940437:0.0023:rs112573343
1   752478  rs146277091 G   A   .   PASS    AF=0.0369   ES:SE:LP:AF:ID  0.0051:0.0055:0.449283:0.0369:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.839    ES:SE:LP:AF:ID  -0.0016:0.0028:0.2423:0.839:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.8386   ES:SE:LP:AF:ID  -0.0016:0.0028:0.253989:0.8386:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.8699   ES:SE:LP:AF:ID  -0.0007:0.003:0.0914078:0.8699:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.1298   ES:SE:LP:AF:ID  0.0002:0.003:0.0283068:0.1298:rs1388595942
1   754063  rs12184312  G   T   .   PASS    AF=0.0374   ES:SE:LP:AF:ID  0.0051:0.0054:0.460422:0.0374:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.0376   ES:SE:LP:AF:ID  0.0049:0.0054:0.443698:0.0376:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.8692   ES:SE:LP:AF:ID  -0.0008:0.003:0.101824:0.8692:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8693   ES:SE:LP:AF:ID  -0.0008:0.003:0.102428:0.8693:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.0376   ES:SE:LP:AF:ID  0.0048:0.0054:0.43086:0.0376:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.8692   ES:SE:LP:AF:ID  -0.0008:0.003:0.0991415:0.8692:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0051   ES:SE:LP:AF:ID  -0.0159:0.0153:0.523458:0.0051:rs150578204
1   754458  rs1242318281    G   T   .   PASS    AF=0.0051   ES:SE:LP:AF:ID  -0.0159:0.0154:0.523458:0.0051:rs1242318281
1   754503  rs3115859   G   A   .   PASS    AF=0.8381   ES:SE:LP:AF:ID  -0.0018:0.0028:0.280255:0.8381:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.0376   ES:SE:LP:AF:ID  0.0048:0.0054:0.431095:0.0376:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.8387   ES:SE:LP:AF:ID  -0.0019:0.0028:0.29465:0.8387:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.0137   ES:SE:LP:AF:ID  -0.0064:0.0098:0.291154:0.0137:rs181660517
1   755435  rs1557550616    T   G   .   PASS    AF=0.0055   ES:SE:LP:AF:ID  0.018:0.015:0.633577:0.0055:rs1557550616