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 mr1147 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
vg0718800612 sf0718799619 7 18800612 1.16E-21 9.05E-06
vg0315225332 sf0315223979 3 15225332 2.45E-21 NA
vg0305033997 sf0305032999 3 5033997 2.06E-20 NA
vg0129976316 sf0129975271 1 29976316 4.52E-20 NA
vg0611473568 sf0611472569 6 11473568 4.65E-20 NA
vg0132918542 sf0132917498 1 32918542 NA 6.01E-07
vg0714251798 sf0714250805 7 14251798 NA 7.19E-07
vg1009691370 sf1009620191 10 9691370 NA 8.16E-07
vg1013275525 sf1013204295 10 13275525 NA 8.76E-07
vg1009403825 sf1009332646 10 9403825 NA 1.03E-06
vg0714251445 sf0714250452 7 14251445 NA 1.04E-06
vg0132932503 sf0132931459 1 32932503 NA 1.21E-06
vg0719000915 sf0718999922 7 19000915 NA 1.51E-06
vg0819119130 sf0819116417 8 19119130 NA 1.89E-06
vg0118115278 sf0118114232 1 18115278 NA 2.24E-06
vg0203485364 sf0203485362 2 3485364 NA 2.40E-06
vg1009558279 sf1009487100 10 9558279 NA 2.67E-06
vg1006547989 sf1006563612 10 6547989 NA 4.70E-06
vg0230101347 sf0230095478 2 30101347 NA 4.86E-06