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 mr1619 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
vg0406393570 sf0406389010 4 6393570 1.70E-146 5.49E-28
vg0406535527 sf0406530970 4 6535527 4.73E-146 5.45E-30
vg0411344776 sf0411335479 4 11344776 7.84E-116 NA
vg0307375905 sf0307374903 3 7375905 1.70E-115 NA
vg0122842459 sf0122841415 1 22842459 1.38E-112 NA
vg1017003480 sf1016932252 10 17003480 2.88E-110 NA
vg0420244177 sf0420072223 4 20244177 1.75E-102 2.68E-06
vg0412479470 sf0412470185 4 12479470 1.10E-101 3.96E-07
vg0406521772 sf0406517215 4 6521772 NA 1.12E-13
vg0407565723 sf0407560992 4 7565723 NA 1.98E-12
vg0411637990 sf0411628696 4 11637990 NA 1.89E-09
vg0222742146 sf0222736277 2 22742146 NA 3.92E-09
vg0222719698 sf0222713829 2 22719698 NA 4.75E-09
vg0406362113 sf0406357553 4 6362113 NA 2.36E-08
vg0406532594 sf0406528037 4 6532594 NA 3.76E-08
vg1209897018 sf1209894428 12 9897018 NA 4.80E-08
vg0817328107 sf0817325393 8 17328107 NA 1.39E-07
vg1016503788 sf1016432561 10 16503788 NA 1.43E-07
vg0313739243 sf0313737960 3 13739243 NA 2.57E-07
vg0807357132 sf0807356137 8 7357132 NA 3.82E-07
vg0522637550 sf0522574993 5 22637550 NA 6.22E-07
vg1010292912 sf1010221733 10 10292912 NA 1.24E-06
vg0900608673 sf0900607673 9 608673 NA 1.55E-06
vg0819139306 sf0819136593 8 19139306 NA 2.03E-06
vg0406147466 sf0406142906 4 6147466 NA 2.09E-06
vg0313663936 sf0313662653 3 13663936 NA 2.72E-06
vg1010229159 sf1010157980 10 10229159 NA 3.05E-06
vg0613667272 sf0613666273 6 13667272 NA 4.48E-06