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/dev/ieu-a-import/processed/ieu-a-999/ieu-a-999.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-999/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 18:49:48 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-999/ieu-a-999.vcf.gz ...
Read summary statistics for 3184205 SNPs.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1268997 SNPs remain.
After merging with regression SNP LD, 1268997 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1036 (0.0067)
Lambda GC: 1.0219
Mean Chi^2: 1.0449
Intercept: 0.9086 (0.0047)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 18:50:24 2020
Total time elapsed: 36.09s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9494,
    "inflation_factor": 1.0047,
    "mean_EFFECT": -0.002,
    "n": 100716,
    "n_snps": 3184205,
    "n_clumped_hits": 10,
    "n_p_sig": 229,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 26,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 30509,
    "n_est": 89666.1268,
    "ratio_se_n": 0.9436,
    "mean_diff": 0.002,
    "ratio_diff": 1.2917,
    "sd_y_est1": 1.3713,
    "sd_y_est2": 1.2939,
    "r2_sum1": 0.0052,
    "r2_sum2": 0.0028,
    "r2_sum3": 0.0031,
    "r2_sum4": 0.0044,
    "ldsc_nsnp_merge_refpanel_ld": 1268997,
    "ldsc_nsnp_merge_regression_ld": 1268997,
    "ldsc_observed_scale_h2_beta": 0.1036,
    "ldsc_observed_scale_h2_se": 0.0067,
    "ldsc_intercept_beta": 0.9086,
    "ldsc_intercept_se": 0.0047,
    "ldsc_lambda_gc": 1.0219,
    "ldsc_mean_chisq": 1.0449,
    "ldsc_ratio": -2.0356
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 42 0 3184205 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 2 0.9999994 NA NA NA NA NA 8.606649e+00 5.689906e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.40000e+01 ▇▆▃▃▁
numeric POS 0 1.0000000 NA NA NA NA NA 7.889217e+07 5.588516e+07 3696.0000 3.263791e+07 6.998941e+07 1.144541e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.992700e-03 2.060526e+00 -1553.1400 -6.800000e-03 0.000000e+00 6.800000e-03 9.57825e+02 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.627870e-02 2.733281e+00 0.0045 6.000000e-03 7.900000e-03 1.880000e-02 1.06531e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.990152e-01 2.895136e-01 0.0000 2.485999e-01 4.990005e-01 7.498994e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.990155e-01 2.895136e-01 0.0000 2.485632e-01 4.990049e-01 7.499161e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.328412e-01 2.749315e-01 0.0007 1.012000e-01 2.434000e-01 5.219000e-01 9.99300e-01 ▇▃▂▂▂
numeric AF_reference 30509 0.9904186 NA NA NA NA NA 3.256941e-01 2.780578e-01 0.0000 8.865810e-02 2.430110e-01 5.149760e-01 1.00000e+00 ▇▃▂▂▂
numeric N 0 1.0000000 NA NA NA NA NA 5.774869e+04 2.792082e+04 91.0000 5.277780e+04 7.313910e+04 7.606740e+04 1.00716e+05 ▂▁▁▇▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 567753 rs532073948 A G -0.0531 0.2842 0.8517999 0.8517859 0.0033 0.0005990 1073.0
1 721290 rs12565286 G C -0.0198 0.0198 0.3174001 0.3173105 0.0521 0.0371406 40531.1
1 723819 rs11804171 T A 0.0121 0.0255 0.6350998 0.6351364 0.0609 0.1345850 27584.1
1 723891 rs2977670 G C -0.0221 0.0225 0.3260003 0.3259904 0.9149 0.7799520 27808.9
1 750235 rs12138618 G A 0.0470 0.0267 0.0783592 0.0783570 0.0648 NA 25935.0
1 752566 rs3094315 G A -0.0044 0.0085 0.6047000 0.6047045 0.8170 0.7182510 57719.7
1 752721 rs3131972 A G -0.0177 0.0406 0.6629000 0.6628653 0.8031 0.6533550 2270.0
1 753405 rs3115860 C A -0.0063 0.0425 0.8822001 0.8821571 0.8587 0.7517970 2567.0
1 754192 rs3131968 A G -0.0006 0.0102 0.9531001 0.9530927 0.8262 0.6785140 45588.9
1 761732 rs2286139 C T -0.0263 0.0217 0.2255002 0.2255194 0.8497 0.6257990 8666.0
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 51666786 rs14115 A G -0.0019 0.0115 0.8688000 0.8687729 0.0689 NA 71280.8
23 57663373 rs28962478 A G 0.1546 0.1419 0.2759002 0.2759336 0.0838 NA 4966.0
23 70163799 rs1626496 A C -0.0014 0.0105 0.8938999 0.8939298 0.0831 NA 72008.5
23 74963352 rs1053838 T G -0.0427 0.0729 0.5581000 0.5580544 0.9924 NA 30659.0
23 91415872 rs6562597 G A -0.0031 0.0210 0.8826000 0.8826434 0.0258 0.0021192 58575.8
23 118495837 rs12882977 G A -0.0009 0.0055 0.8700001 0.8700174 0.4724 0.2307280 75474.4
23 147220746 rs2944613 T A -0.1776 0.2563 0.4883003 0.4883485 0.0273 NA 416.0
24 3631296 rs2176440 T C 0.0384 0.1332 0.7731006 0.7731261 0.0440 NA 961.0
NA 3696 rs17052208 C T 0.0375 0.2261 0.8683000 0.8682704 0.0369 NA 4966.0
NA 4223 rs9629043 C T -0.0704 0.1087 0.5172006 0.5172087 0.0286 NA 2013.0

bcf preview

1   567753  rs11510103  A   G   .   PASS    AF=0.0033   ES:SE:LP:AF:SS:ID   -0.0531:0.2842:0.0696624:0.0033:1073:rs11510103
1   721290  rs12565286  G   C   .   PASS    AF=0.0521   ES:SE:LP:AF:SS:ID   -0.0198:0.0198:0.498393:0.0521:40531.1:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.0609   ES:SE:LP:AF:SS:ID   0.0121:0.0255:0.197158:0.0609:27584.1:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.9149   ES:SE:LP:AF:SS:ID   -0.0221:0.0225:0.486782:0.9149:27808.9:rs2977670
1   750235  rs12138618  G   A   .   PASS    AF=0.0648   ES:SE:LP:AF:SS:ID   0.047:0.0267:1.10591:0.0648:25935:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.817    ES:SE:LP:AF:SS:ID   -0.0044:0.0085:0.21846:0.817:57719.7:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.8031   ES:SE:LP:AF:SS:ID   -0.0177:0.0406:0.178552:0.8031:2270:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.8587   ES:SE:LP:AF:SS:ID   -0.0063:0.0425:0.0544329:0.8587:2567:rs3115860
1   754192  rs3131968   A   G   .   PASS    AF=0.8262   ES:SE:LP:AF:SS:ID   -0.0006:0.0102:0.0208615:0.8262:45588.9:rs3131968
1   761732  rs2286139   C   T   .   PASS    AF=0.8497   ES:SE:LP:AF:SS:ID   -0.0263:0.0217:0.646853:0.8497:8666:rs2286139
1   768448  rs12562034  G   A   .   PASS    AF=0.1563   ES:SE:LP:AF:SS:ID   0.0201:0.0123:0.990549:0.1563:34124:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.8556   ES:SE:LP:AF:SS:ID   -0.0089:0.0103:0.411728:0.8556:46474.1:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.2379   ES:SE:LP:AF:SS:ID   -0.0151:0.014:0.551603:0.2379:17584:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.8514   ES:SE:LP:AF:SS:ID   -0.0059:0.0095:0.271971:0.8514:57825:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.1472   ES:SE:LP:AF:SS:ID   0.0028:0.01:0.108184:0.1472:53604.5:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8548   ES:SE:LP:AF:SS:ID   -0.0065:0.0107:0.2648:0.8548:43451.4:rs2977612
1   785050  rs2905062   G   A   .   PASS    AF=0.8221   ES:SE:LP:AF:SS:ID   -0.0044:0.0077:0.24657:0.8221:73488.4:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8242   ES:SE:LP:AF:SS:ID   0.0012:0.0093:0.0470623:0.8242:54943.8:rs2980300
1   791853  rs6684487   G   A   .   PASS    AF=0.0871   ES:SE:LP:AF:SS:ID   -0.0519:0.0918:0.242756:0.0871:961:rs6684487
1   798026  rs4951864   C   T   .   PASS    AF=0.8973   ES:SE:LP:AF:SS:ID   -0.017:0.0184:0.44916:0.8973:30054:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1115   ES:SE:LP:AF:SS:ID   0.0213:0.0198:0.549751:0.1115:22149:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.2377   ES:SE:LP:AF:SS:ID   -0.0002:0.0103:0.00678428:0.2377:42489.3:rs11240777
1   799463  rs4245756   T   C   .   PASS    AF=0.9266   ES:SE:LP:AF:SS:ID   0.0217:0.1505:0.0528605:0.9266:416:rs4245756
1   838555  rs4970383   C   A   .   PASS    AF=0.2622   ES:SE:LP:AF:SS:ID   -0.0152:0.0351:0.177178:0.2622:2270:rs4970383
1   846808  rs4475691   C   T   .   PASS    AF=0.1891   ES:SE:LP:AF:SS:ID   0.0428:0.0265:0.973467:0.1891:4861:rs4475691
1   846864  rs950122    G   C   .   PASS    AF=0.1745   ES:SE:LP:AF:SS:ID   -0.0035:0.0249:0.0514892:0.1745:16007:rs950122
1   854250  rs7537756   A   G   .   PASS    AF=0.194    ES:SE:LP:AF:SS:ID   0.0234:0.0394:0.257589:0.194:2270:rs7537756
1   861808  rs13302982  A   G   .   PASS    AF=0.9595   ES:SE:LP:AF:SS:ID   0.0357:0.0828:0.176265:0.9595:2270:rs13302982
1   873558  rs1110052   G   T   .   PASS    AF=0.6858   ES:SE:LP:AF:SS:ID   -0.0363:0.0346:0.531505:0.6858:2270:rs1110052
1   879317  rs7523549   C   T   .   PASS    AF=0.0201   ES:SE:LP:AF:SS:ID   -0.0862:0.2012:0.175029:0.0201:961:rs7523549
1   882033  rs2272756   G   A   .   PASS    AF=0.2473   ES:SE:LP:AF:SS:ID   -0.007:0.014:0.209644:0.2473:16417:rs2272756
1   888659  rs3748597   T   C   .   PASS    AF=0.9098   ES:SE:LP:AF:SS:ID   0.0139:0.0277:0.21056:0.9098:7795:rs3748597
1   891945  rs13303106  A   G   .   PASS    AF=0.634    ES:SE:LP:AF:SS:ID   0.0105:0.0328:0.125576:0.634:2270:rs13303106
1   894573  rs13303010  G   A   .   PASS    AF=0.9062   ES:SE:LP:AF:SS:ID   0.1111:0.062:1.13585:0.9062:1787:rs13303010
1   900505  rs28705211  G   C   .   PASS    AF=0.4168   ES:SE:LP:AF:SS:ID   0.024:0.0311:0.356251:0.4168:2586:rs28705211
1   900730  rs3935066   G   A   .   PASS    AF=0.9279   ES:SE:LP:AF:SS:ID   0.1535:0.097:0.945004:0.9279:961:rs3935066
1   903104  rs6696281   C   T   .   PASS    AF=0.0372   ES:SE:LP:AF:SS:ID   -0.1072:0.1009:0.540608:0.0372:1787:rs6696281
1   910935  rs2340592   G   A   .   PASS    AF=0.1922   ES:SE:LP:AF:SS:ID   0.1105:0.0457:1.8066:0.1922:1787:rs2340592
1   915227  rs13303355  A   G   .   PASS    AF=0.9806   ES:SE:LP:AF:SS:ID   0.0957:0.1983:0.201073:0.9806:961:rs13303355
1   918384  rs13303118  G   T   .   PASS    AF=0.5743   ES:SE:LP:AF:SS:ID   0.006:0.0171:0.139243:0.5743:8186.92:rs13303118
1   918573  rs2341354   A   G   .   PASS    AF=0.5776   ES:SE:LP:AF:SS:ID   0.0137:0.019:0.327071:0.5776:7894:rs2341354
1   922009  rs6693747   G   A   .   PASS    AF=0.2146   ES:SE:LP:AF:SS:ID   -0.0161:0.0602:0.102868:0.2146:961:rs6693747
1   924898  rs6665000   C   A   .   PASS    AF=0.9687   ES:SE:LP:AF:SS:ID   0.057:0.0808:0.318307:0.9687:2896:rs6665000
1   926431  rs4970403   A   T   .   PASS    AF=0.9629   ES:SE:LP:AF:SS:ID   0.0409:0.0554:0.336865:0.9629:4821:rs4970403
1   927309  rs2341362   T   C   .   PASS    AF=0.9687   ES:SE:LP:AF:SS:ID   0.0595:0.08:0.340084:0.9687:2895.99:rs2341362
1   928836  rs9777703   C   T   .   PASS    AF=0.9693   ES:SE:LP:AF:SS:ID   -0.0201:0.0586:0.135726:0.9693:5487:rs9777703
1   932457  rs1891910   G   A   .   PASS    AF=0.2317   ES:SE:LP:AF:SS:ID   -0.007:0.0368:0.0710412:0.2317:2270:rs1891910
1   940203  rs35940137  G   A   .   PASS    AF=0.0619   ES:SE:LP:AF:SS:ID   0.0102:0.0721:0.0518316:0.0619:2270:rs35940137
1   943468  rs3121567   T   C   .   PASS    AF=0.9715   ES:SE:LP:AF:SS:ID   -0.1209:0.0788:0.90309:0.9715:3219.99:rs3121567
1   944564  rs3128117   T   C   .   PASS    AF=0.4193   ES:SE:LP:AF:SS:ID   0.0299:0.0282:0.539102:0.4193:2895.98:rs3128117