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 mr1111 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 3.10E-102 4.52E-35
vg0610566084 sf0610565085 6 10566084 7.02E-102 1.94E-35
vg0233932146 sf0233926277 2 33932146 2.47E-57 NA
vg0428554389 sf0428369241 4 28554389 4.26E-56 NA
vg0304965334 sf0304964336 3 4965334 8.28E-54 NA
vg0717186329 sf0717185336 7 17186329 1.47E-53 NA
vg0610548087 sf0610547088 6 10548087 NA 7.72E-19
vg0610764498 sf0610763499 6 10764498 NA 5.68E-13
vg0610788671 sf0610787672 6 10788671 NA 1.75E-12
vg0609920649 sf0609919650 6 9920649 NA 9.07E-11
vg0610676484 sf0610675485 6 10676484 NA 8.29E-10
vg0610740899 sf0610739900 6 10740899 NA 9.92E-10
vg0610722873 sf0610721874 6 10722873 NA 1.08E-09
vg0615907055 sf0615906057 6 15907055 NA 2.55E-08
vg0610700215 sf0610699216 6 10700215 NA 3.15E-08
vg0617821393 sf0617820396 6 17821393 NA 4.10E-07
vg0612236193 sf0612235194 6 12236193 NA 4.49E-07
vg0613339384 sf0613338385 6 13339384 NA 6.29E-07
vg0613069322 sf0613068323 6 13069322 NA 8.24E-07
vg0402826180 sf0402821785 4 2826180 NA 1.57E-06
vg1214622240 sf1214619580 12 14622240 NA 2.58E-06
vg1219437084 sf1219408554 12 19437084 NA 3.15E-06
vg1124164458 sf1123698328 11 24164458 NA 3.65E-06
vg0518253546 sf0518193032 5 18253546 NA 7.71E-06