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 mr1144 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
vg0610567118 sf0610566119 6 10567118 1.82E-105 2.17E-37
vg0233932146 sf0233926277 2 33932146 2.95E-52 NA
vg0614491664 sf0614490665 6 14491664 2.90E-51 4.20E-06
vg0617620218 sf0617619221 6 17620218 1.60E-50 2.74E-07
vg0311731956 sf0311730674 3 11731956 5.36E-50 NA
vg0617821393 sf0617820396 6 17821393 6.64E-44 3.36E-08
vg0613854532 sf0613853533 6 13854532 5.39E-43 3.03E-07
vg0610539571 sf0610538572 6 10539571 NA 2.08E-18
vg0610763769 sf0610762770 6 10763769 NA 4.88E-13
vg0610764498 sf0610763499 6 10764498 NA 3.51E-12
vg0610685711 sf0610684712 6 10685711 NA 2.59E-10
vg0611127784 sf0611126785 6 11127784 NA 3.17E-09
vg0609930953 sf0609929954 6 9930953 NA 4.31E-09
vg0610679715 sf0610678716 6 10679715 NA 4.53E-09
vg0610443927 sf0610442928 6 10443927 NA 3.73E-08
vg0615907055 sf0615906057 6 15907055 NA 7.79E-08
vg1116906166 sf1116441045 11 16906166 NA 1.09E-07
vg0610738394 sf0610737395 6 10738394 NA 1.45E-07
vg0613063833 sf0613062834 6 13063833 NA 1.78E-07
vg0614543893 sf0614542894 6 14543893 NA 2.33E-07
vg0613339384 sf0613338385 6 13339384 NA 3.07E-07
vg0610118930 sf0610117931 6 10118930 NA 7.72E-07
vg0609926308 sf0609925309 6 9926308 NA 1.16E-06
vg0606968664 sf0606967665 6 6968664 NA 1.71E-06
vg0614829825 sf0614828826 6 14829825 NA 1.82E-06
vg0610082555 sf0610081556 6 10082555 NA 1.86E-06
vg0612236193 sf0612235194 6 12236193 NA 2.05E-06
vg0610089141 sf0610088142 6 10089141 NA 2.58E-06
vg0612071255 sf0612070256 6 12071255 NA 2.98E-06