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 mr1116 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
vg0222687210 sf0222681341 2 22687210 1.51E-39 9.74E-23
vg1110425815 sf1110420360 11 10425815 4.00E-25 1.67E-11
vg1006352888 sf1006368511 10 6352888 1.00E-23 9.51E-10
vg0526731344 sf0526668702 5 26731344 8.72E-23 5.22E-08
vg0525743914 sf0525681335 5 25743914 9.48E-22 6.25E-09
vg0505931121 sf0505931060 5 5931121 1.94E-21 1.06E-06
vg0500863267 sf0500863249 5 863267 5.54E-21 2.26E-08
vg0700238464 sf0700237464 7 238464 7.40E-21 2.37E-07
vg0825750246 sf0825747532 8 25750246 1.17E-19 2.72E-07
vg0434772415 sf0434587306 4 34772415 3.13E-19 1.55E-08
vg0335918912 sf0335911781 3 35918912 7.68E-19 3.15E-08
vg1117963441 sf1117497299 11 17963441 7.92E-19 1.27E-08
vg1108600295 sf1108594905 11 8600295 3.21E-18 2.81E-08
vg0302174053 sf0302173049 3 2174053 3.60E-18 NA
vg0434765214 sf0434580105 4 34765214 1.31E-17 4.29E-07
vg0222988287 sf0222982418 2 22988287 2.27E-17 8.32E-08
vg0434845674 sf0434660565 4 34845674 3.81E-17 3.64E-07
vg0305905054 sf0305904054 3 5905054 9.57E-17 5.17E-08
vg0222722554 sf0222716685 2 22722554 NA 1.40E-12
vg1006914384 sf1006930007 10 6914384 NA 2.38E-11
vg0626215270 sf0626214273 6 26215270 NA 1.52E-09
vg0222685452 sf0222679583 2 22685452 NA 8.32E-09
vg0419662846 sf0419490881 4 19662846 NA 3.86E-08
vg1009512226 sf1009441047 10 9512226 NA 5.26E-08
vg0222952563 sf0222946694 2 22952563 NA 7.54E-08
vg1016246436 sf1016175210 10 16246436 NA 3.35E-07
vg0321293433 sf0321291943 3 21293433 NA 3.41E-07
vg0709837237 sf0709836243 7 9837237 NA 5.35E-07
vg1005848089 sf1005864627 10 5848089 NA 6.57E-07