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 mr1255 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
vg0217071444 sf0217065574 2 17071444 2.07E-35 3.65E-24
vg0217023273 sf0217017403 2 17023273 2.82E-35 1.75E-24
vg0900336799 sf0900335799 9 336799 9.75E-17 9.95E-12
vg0812023942 sf0812022947 8 12023942 4.35E-16 1.07E-08
vg0216104235 sf0216098365 2 16104235 1.70E-13 2.92E-09
vg1005364262 sf1005380799 10 5364262 1.98E-13 6.30E-11
vg0213820023 sf0213814153 2 13820023 2.41E-13 5.92E-07
vg0610865809 sf0610864810 6 10865809 2.74E-11 1.29E-07
vg0217737368 sf0217731498 2 17737368 4.68E-11 1.11E-07
vg1202073188 sf1202072186 12 2073188 2.62E-10 1.67E-06
vg0217377961 sf0217372091 2 17377961 8.50E-10 4.42E-06
vg0115588521 sf0115587495 1 15588521 1.26E-09 7.28E-07
vg0217953313 sf0217947444 2 17953313 1.52E-09 4.62E-06
vg0216661646 sf0216655776 2 16661646 1.53E-09 9.71E-08
vg0217130932 sf0217125062 2 17130932 1.65E-09 1.80E-06
vg1114870126 sf1114406440 11 14870126 5.92E-09 3.67E-06
vg0217366855 sf0217360985 2 17366855 1.02E-08 3.99E-08
vg1112889066 sf1112425387 11 12889066 1.72E-08 8.66E-08
vg1208573843 sf1208571250 12 8573843 6.92E-08 1.82E-06
vg0217679949 sf0217674079 2 17679949 9.88E-08 9.90E-07