Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1247 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0222679274 sf0222673405 2 22679274 2.00E-40 1.57E-15
vg0222673217 sf0222667348 2 22673217 8.67E-39 1.42E-15
vg1110107976 sf1110102553 11 10107976 7.75E-32 8.14E-08
vg1110591251 sf1110585796 11 10591251 4.31E-31 7.15E-08
vg0529002068 sf0528939423 5 29002068 4.66E-31 2.68E-06
vg0702584931 sf0702583932 7 2584931 7.04E-30 2.78E-06
vg0624499979 sf0624498982 6 24499979 1.41E-29 1.75E-08
vg0818212763 sf0818210050 8 18212763 1.77E-28 7.97E-07
vg1204557439 sf1204556427 12 4557439 5.84E-25 6.35E-08
vg0222730246 sf0222724377 2 22730246 6.25E-23 1.79E-08
vg0222952563 sf0222946694 2 22952563 NA 9.46E-10
vg1204507349 sf1204506337 12 4507349 NA 7.55E-09
vg0222716046 sf0222710177 2 22716046 NA 1.94E-08
vg0628791328 sf0628790330 6 28791328 NA 4.81E-08
vg0222722554 sf0222716685 2 22722554 NA 7.47E-08
vg1006914384 sf1006930007 10 6914384 NA 1.26E-07
vg1110039605 sf1110034182 11 10039605 NA 1.77E-07
vg0219344371 sf0219338503 2 19344371 NA 3.97E-07
vg0626215270 sf0626214273 6 26215270 NA 4.75E-07
vg0709749074 sf0709748080 7 9749074 NA 6.49E-07
vg0917445593 sf0917444592 9 17445593 NA 7.06E-07
vg0226543196 sf0226537327 2 26543196 NA 7.78E-07
vg0224246969 sf0224241100 2 24246969 NA 8.78E-07
vg0432750231 sf0432565117 4 32750231 NA 1.21E-06
vg0420192125 sf0420020165 4 20192125 NA 1.28E-06
vg0434845674 sf0434660565 4 34845674 NA 1.60E-06
vg1218455068 sf1218426504 12 18455068 NA 1.81E-06
vg0432159315 sf0431974208 4 32159315 NA 2.02E-06
vg1016363154 sf1016291930 10 16363154 NA 2.13E-06
vg1109959621 sf1109954198 11 9959621 NA 2.47E-06
vg0626309167 sf0626308170 6 26309167 NA 4.26E-06
vg1204509767 sf1204508755 12 4509767 NA 7.10E-06
vg0709435736 sf0709434742 7 9435736 NA 7.14E-06