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 mr1120 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 3.17E-39 2.81E-16
vg0222687210 sf0222681341 2 22687210 3.01E-37 3.53E-17
vg1110591251 sf1110585796 11 10591251 2.04E-31 1.39E-09
vg0500664660 sf0500664660 5 664660 2.65E-31 1.60E-08
vg0526059096 sf0525996516 5 26059096 9.07E-30 3.26E-06
vg0328992933 sf0328985985 3 28992933 1.87E-29 NA
vg0529035169 sf0528972524 5 29035169 1.03E-28 2.08E-06
vg0624499979 sf0624498982 6 24499979 1.13E-27 8.06E-07
vg0335918912 sf0335911781 3 35918912 2.43E-27 2.22E-09
vg0607367426 sf0607366427 6 7367426 1.43E-26 2.59E-08
vg1117963441 sf1117497299 11 17963441 1.51E-26 2.01E-08
vg0819074999 sf0819072286 8 19074999 1.52E-23 2.20E-06
vg0224798029 sf0224792160 2 24798029 NA 2.42E-07
vg1200551570 sf1200550570 12 551570 NA 4.98E-07
vg1006506208 sf1006521831 10 6506208 NA 5.99E-07
vg1110012268 sf1110006845 11 10012268 NA 6.36E-07
vg1009664258 sf1009593079 10 9664258 NA 7.46E-07
vg1019183106 sf1019111662 10 19183106 NA 7.91E-07
vg0222952563 sf0222946694 2 22952563 NA 9.43E-07
vg1006524349 sf1006539972 10 6524349 NA 1.29E-06
vg0505968516 sf0505968455 5 5968516 NA 1.29E-06
vg0420266563 sf0420094608 4 20266563 NA 1.45E-06
vg0822600807 sf0822598094 8 22600807 NA 1.53E-06
vg0232357290 sf0232351421 2 32357290 NA 1.68E-06
vg0120773756 sf0120772711 1 20773756 NA 3.23E-06
vg1221072081 sf1221038631 12 21072081 NA 7.77E-06