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 mr1765 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
vg0127641541 sf0127640497 1 27641541 8.19E-24 NA
vg1005436815 sf1005453352 10 5436815 2.45E-23 NA
vg1010636917 sf1010565738 10 10636917 2.90E-23 NA
vg0821671221 sf0821668508 8 21671221 3.22E-22 NA
vg0628677175 sf0628676177 6 28677175 7.09E-22 NA
vg0334986236 sf0334979106 3 34986236 4.63E-18 1.27E-06
vg0801766010 sf0801765013 8 1766010 1.49E-17 NA
vg0327437336 sf0327430389 3 27437336 3.33E-16 4.00E-11
vg0327424324 sf0327417377 3 27424324 NA 2.51E-12
vg0324795678 sf0324793757 3 24795678 NA 1.98E-09
vg0907849208 sf0907848208 9 7849208 NA 1.21E-08
vg0323665466 sf0323663640 3 23665466 NA 3.25E-08
vg1006212604 sf1006228307 10 6212604 NA 4.42E-08
vg0317023117 sf0317021991 3 17023117 NA 1.24E-07
vg0104968508 sf0104967508 1 4968508 NA 1.46E-07
vg0628001136 sf0628000138 6 28001136 NA 2.52E-07
vg0423007797 sf0422822689 4 23007797 NA 3.39E-07
vg0325688031 sf0325686049 3 25688031 NA 4.48E-07
vg0629222122 sf0629221124 6 29222122 NA 4.65E-07
vg1000877655 sf1000876631 10 877655 NA 4.92E-07
vg0305008708 sf0305007710 3 5008708 NA 5.37E-07
vg0321057005 sf0321055515 3 21057005 NA 6.05E-07
vg0105008879 sf0105007879 1 5008879 NA 7.53E-07
vg0900419284 sf0900418284 9 419284 NA 8.89E-07
vg0231643768 sf0231637899 2 31643768 NA 1.04E-06
vg0605885969 sf0605884970 6 5885969 NA 1.08E-06
vg1021216544 sf1021145022 10 21216544 NA 1.25E-06
vg0222830353 sf0222824484 2 22830353 NA 1.26E-06