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}
*********************************************************************
* 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-49/ieu-a-49.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-49/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Wed Feb 5 10:58:16 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-49/ieu-a-49.vcf.gz ...
Read summary statistics for 2528446 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, 1172834 SNPs remain.
After merging with regression SNP LD, 1172834 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1395 (0.0067)
Lambda GC: 1.0421
Mean Chi^2: 1.1602
Intercept: 0.7765 (0.0069)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 10:58:49 2020
Total time elapsed: 32.5s
{
"af_correlation": 0.9177,
"inflation_factor": 1.0475,
"mean_EFFECT": -0,
"n": 213038,
"n_snps": 2528446,
"n_clumped_hits": 52,
"n_p_sig": 1097,
"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": 43647,
"n_miss_AF_reference": 22242,
"n_est": 213036.0476,
"ratio_se_n": 1,
"mean_diff": -2.0302e-06,
"ratio_diff": 0.2848,
"sd_y_est1": 1.4579,
"sd_y_est2": 1.4579,
"r2_sum1": 0.0183,
"r2_sum2": 0.0086,
"r2_sum3": 0.0086,
"r2_sum4": 0.0134,
"ldsc_nsnp_merge_refpanel_ld": 1172834,
"ldsc_nsnp_merge_regression_ld": 1172834,
"ldsc_observed_scale_h2_beta": 0.1395,
"ldsc_observed_scale_h2_se": 0.0067,
"ldsc_intercept_beta": 0.7765,
"ldsc_intercept_se": 0.0069,
"ldsc_lambda_gc": 1.0421,
"ldsc_mean_chisq": 1.1602,
"ldsc_ratio": -1.3951
}
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 | 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 |
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 SNPsn_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:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 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.
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.
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.
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.
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
> 0.5ldsc_intercept_beta
: ldsc_intercept_beta
> 1.5n_clumped_hits
: n_clumped_hits
> 1000r2_sum<*>
: r2_sum<*>
> 0.5Plots
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 | 2528446 | 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 | 8.594228e+00 | 5.663083e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.881463e+07 | 5.566811e+07 | 11523.0000 | 3.266576e+07 | 7.021157e+07 | 1.142608e+08 | 2.49219e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.600000e-05 | 9.468900e-03 | -0.2400 | -4.300000e-03 | 0.000000e+00 | 4.300000e-03 | 2.50000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.652400e-03 | 6.307700e-03 | 0.0035 | 4.700000e-03 | 5.500000e-03 | 7.800000e-03 | 1.30000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.918886e-01 | 2.930558e-01 | 0.0000 | 2.399999e-01 | 4.899999e-01 | 7.400005e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.918791e-01 | 2.930045e-01 | 0.0000 | 2.372779e-01 | 4.917677e-01 | 7.449531e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | AF | 43647 | 0.9827376 | NA | NA | NA | NA | NA | 3.553957e-01 | 2.763523e-01 | 0.0083 | 1.167000e-01 | 2.917000e-01 | 5.583000e-01 | 9.91700e-01 | ▇▅▃▂▂ |
numeric | AF_reference | 22242 | 0.9912033 | NA | NA | NA | NA | NA | 3.600852e-01 | 2.571745e-01 | 0.0000 | 1.435700e-01 | 2.973240e-01 | 5.453270e-01 | 1.00000e+00 | ▇▆▃▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.399885e+05 | 2.074221e+04 | 50001.0000 | 1.351950e+05 | 1.452680e+05 | 1.454280e+05 | 2.13038e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 721290 | rs12565286 | G | C | -0.0091 | 0.0170 | 0.5999997 | 0.5924465 | 0.06780 | 0.0371406 | 67413 |
1 | 723819 | rs11804171 | T | A | 0.0063 | 0.0210 | 0.7600007 | 0.7641772 | 0.03704 | 0.1345850 | 52583 |
1 | 752566 | rs3094315 | G | A | 0.0035 | 0.0079 | 0.6600001 | 0.6577383 | 0.84480 | 0.7182510 | 78741 |
1 | 754192 | rs3131968 | A | G | -0.0028 | 0.0110 | 0.8000000 | 0.7990742 | 0.87500 | 0.6785140 | 57928 |
1 | 768448 | rs12562034 | G | A | 0.0005 | 0.0130 | 0.9699999 | 0.9693197 | 0.09167 | 0.1918930 | 55895 |
1 | 775659 | rs2905035 | A | G | 0.0050 | 0.0086 | 0.5600000 | 0.5609740 | 0.87500 | 0.7450080 | 90221 |
1 | 777122 | rs2980319 | A | T | 0.0048 | 0.0086 | 0.5800000 | 0.5767491 | 0.87500 | 0.7472040 | 90223 |
1 | 779322 | rs4040617 | A | G | -0.0028 | 0.0095 | 0.7700005 | 0.7681949 | 0.12500 | 0.2264380 | 76695 |
1 | 780785 | rs2977612 | T | A | 0.0032 | 0.0094 | 0.7300002 | 0.7335361 | 0.86610 | 0.6693290 | 78483 |
1 | 785050 | rs2905062 | G | A | -0.0040 | 0.0069 | 0.5600000 | 0.5621101 | NA | 0.6269970 | 122587 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51217134 | rs117417021 | A | G | 0.0025 | 0.0079 | 0.7499995 | 0.7516566 | 0.441700 | 0.2671730 | 87440 |
22 | 51222100 | rs114553188 | G | T | -0.0083 | 0.0130 | 0.5099998 | 0.5231733 | 0.066700 | 0.0880591 | 113616 |
22 | 51223637 | rs375798137 | G | A | -0.0083 | 0.0130 | 0.5099998 | 0.5231733 | 0.066700 | 0.0788738 | 113615 |
22 | 51229805 | rs9616985 | T | C | -0.0054 | 0.0160 | 0.7300002 | 0.7357400 | 0.091700 | 0.0730831 | 84852 |
23 | 35921591 | rs2204667 | C | G | -0.0025 | 0.0061 | 0.6800001 | 0.6819262 | 0.166700 | NA | 145385 |
23 | 51666786 | rs14115 | A | G | 0.0140 | 0.0100 | 0.1700000 | 0.1615133 | 0.025000 | NA | 133485 |
23 | 70163799 | rs1626496 | A | C | -0.0062 | 0.0088 | 0.4799997 | 0.4810932 | 0.075000 | NA | 145269 |
23 | 74963352 | rs1053838 | T | G | 0.0360 | 0.0650 | 0.5800000 | 0.5796841 | 0.991379 | NA | 52190 |
23 | 91415872 | rs6562597 | G | A | 0.0110 | 0.0170 | 0.5099998 | 0.5175939 | 0.008300 | 0.0021192 | 126806 |
23 | 118495837 | rs12882977 | G | A | -0.0029 | 0.0044 | 0.5099998 | 0.5098374 | 0.516700 | 0.2307280 | 145434 |
1 721290 rs12565286 G C . PASS AF=0.0678 ES:SE:LP:AF:SS:ID -0.0091:0.017:0.221849:0.0678:67413:rs12565286
1 723819 rs11804171 T A . PASS AF=0.03704 ES:SE:LP:AF:SS:ID 0.0063:0.021:0.119186:0.03704:52583:rs11804171
1 752566 rs3094315 G A . PASS AF=0.8448 ES:SE:LP:AF:SS:ID 0.0035:0.0079:0.180456:0.8448:78741:rs3094315
1 754192 rs3131968 A G . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.0028:0.011:0.09691:0.875:57928:rs3131968
1 768448 rs12562034 G A . PASS AF=0.09167 ES:SE:LP:AF:SS:ID 0.0005:0.013:0.0132283:0.09167:55895:rs12562034
1 775659 rs2905035 A G . PASS AF=0.875 ES:SE:LP:AF:SS:ID 0.005:0.0086:0.251812:0.875:90221:rs2905035
1 777122 rs2980319 A T . PASS AF=0.875 ES:SE:LP:AF:SS:ID 0.0048:0.0086:0.236572:0.875:90223:rs2980319
1 779322 rs4040617 A G . PASS AF=0.125 ES:SE:LP:AF:SS:ID -0.0028:0.0095:0.113509:0.125:76695:rs4040617
1 780785 rs2977612 T A . PASS AF=0.8661 ES:SE:LP:AF:SS:ID 0.0032:0.0094:0.136677:0.8661:78483:rs2977612
1 785050 rs2905062 G A . PASS . ES:SE:LP:SS:ID -0.004:0.0069:0.251812:122587:rs2905062
1 785989 rs2980300 T C . PASS AF=0.8729 ES:SE:LP:AF:SS:ID 0.0025:0.0094:0.102373:0.8729:78338:rs2980300
1 798959 rs11240777 G A . PASS AF=0.1667 ES:SE:LP:AF:SS:ID -0.0031:0.0093:0.130768:0.1667:74127:rs11240777
1 962210 rs3128126 A G . PASS AF=0.425 ES:SE:LP:AF:SS:ID -0.001:0.0094:0.0362122:0.425:59247:rs3128126
1 990380 rs3121561 C T . PASS AF=0.2667 ES:SE:LP:AF:SS:ID 0.0006:0.0078:0.0268721:0.2667:104342:rs3121561
1 998501 rs3813193 G C . PASS AF=0.15 ES:SE:LP:AF:SS:ID 0.0049:0.008:0.267606:0.15:96700:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.7373 ES:SE:LP:AF:SS:ID 0.005:0.0057:0.420216:0.7373:138449:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.1167 ES:SE:LP:AF:SS:ID 0.0054:0.0074:0.327902:0.1167:108625:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.0032:0.0053:0.259637:0.5667:139907:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.5763 ES:SE:LP:AF:SS:ID 0.0036:0.0051:0.318759:0.5763:140569:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.09649 ES:SE:LP:AF:SS:ID 0.0066:0.0075:0.420216:0.09649:108457:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.5917 ES:SE:LP:AF:SS:ID 0.0026:0.0049:0.221849:0.5917:140650:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.6017 ES:SE:LP:AF:SS:ID 0.0026:0.0049:0.221849:0.6017:140633:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.1271 ES:SE:LP:AF:SS:ID 0.0064:0.0076:0.39794:0.1271:108321:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.7167 ES:SE:LP:AF:SS:ID 0.006:0.0053:0.585027:0.7167:141242:rs3737728
1 1021583 rs10907178 A C . PASS . ES:SE:LP:SS:ID 0.0068:0.0077:0.420216:106208:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID 0.0057:0.0055:0.522879:0.725:140916:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.0021:0.0054:0.154902:0.5667:131265:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.6 ES:SE:LP:AF:SS:ID -0.0048:0.0059:0.376751:0.6:106446:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.08333 ES:SE:LP:AF:SS:ID 0.0051:0.007:0.327902:0.08333:109800:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.08621 ES:SE:LP:AF:SS:ID 0.0031:0.0078:0.161151:0.08621:96976:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.6583 ES:SE:LP:AF:SS:ID -0.0015:0.006:0.09691:0.6583:106393:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0094:0.0083:0.585027:0.05:124005:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.075 ES:SE:LP:AF:SS:ID 0.0049:0.0076:0.283997:0.075:114093:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.06667 ES:SE:LP:AF:SS:ID 0.0055:0.0078:0.318759:0.06667:120356:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.05172 ES:SE:LP:AF:SS:ID 0.009:0.0083:0.552842:0.05172:123915:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.06667 ES:SE:LP:AF:SS:ID 0.0038:0.0077:0.207608:0.06667:120269:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0097:0.0087:0.585027:0.05:121757:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.3981 ES:SE:LP:AF:SS:ID -0.0013:0.0074:0.0655015:0.3981:81343:rs7548798
1 1060235 rs7540009 G A . PASS AF=0.01667 ES:SE:LP:AF:SS:ID -0.015:0.016:0.455932:0.01667:99969:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.05833 ES:SE:LP:AF:SS:ID 0.009:0.0087:0.522879:0.05833:123865:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.05455 ES:SE:LP:AF:SS:ID 0.0093:0.0087:0.537602:0.05455:123878:rs17160826
1 1061152 rs12748370 T C . PASS . ES:SE:LP:SS:ID 0.01:0.009:0.60206:121675:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.4123 ES:SE:LP:AF:SS:ID 0.003:0.006:0.207608:0.4123:104778:rs11807848
1 1062015 rs9659914 C T . PASS AF=0.01667 ES:SE:LP:AF:SS:ID -0.014:0.018:0.366532:0.01667:88225:rs9659914
1 1062638 rs9442373 C A . PASS AF=0.5517 ES:SE:LP:AF:SS:ID 0.0011:0.0059:0.0705811:0.5517:103981:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.7542 ES:SE:LP:AF:SS:ID -0.0073:0.0088:0.387216:0.7542:79999:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.08333 ES:SE:LP:AF:SS:ID -0.0011:0.0078:0.05061:0.08333:98056:rs2298217
1 1066403 rs10907182 T C . PASS AF=0.675 ES:SE:LP:AF:SS:ID 0.0005:0.0062:0.0268721:0.675:101346:rs10907182
1 1071118 rs10907183 G C . PASS AF=0.6833 ES:SE:LP:AF:SS:ID -0.0006:0.0067:0.0315171:0.6833:98593:rs10907183
1 1077064 rs4970357 C A . PASS AF=0.92373 ES:SE:LP:AF:SS:ID 0.0005:0.01:0.0177288:0.92373:122910:rs4970357