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
vg0216659482 sf0216653612 2 16659482 1.93E-71 9.36E-33
vg0812023942 sf0812022947 8 12023942 7.62E-34 1.07E-11
vg0900336799 sf0900335799 9 336799 1.06E-33 4.51E-14
vg1114473442 sf1114009759 11 14473442 4.27E-29 2.55E-08
vg0213820023 sf0213814153 2 13820023 4.93E-29 8.68E-09
vg0610865809 sf0610864810 6 10865809 4.92E-24 1.85E-08
vg1202073188 sf1202072186 12 2073188 1.67E-23 2.00E-07
vg0115588521 sf0115587495 1 15588521 5.52E-20 5.90E-08
vg1220258870 sf1220230312 12 20258870 2.07E-19 2.29E-08
vg1114870126 sf1114406440 11 14870126 1.19E-18 1.01E-07
vg0217319248 sf0217313378 2 17319248 2.77E-17 5.98E-08
vg0217232931 sf0217227061 2 17232931 NA 8.18E-21
vg0216685337 sf0216679467 2 16685337 NA 3.21E-11
vg1005364262 sf1005380799 10 5364262 NA 3.99E-11
vg1112889066 sf1112425387 11 12889066 NA 1.39E-09
vg0217812245 sf0217806376 2 17812245 NA 2.50E-07
vg1213797573 sf1213794911 12 13797573 NA 4.84E-07
vg1208573843 sf1208571250 12 8573843 NA 5.37E-07
vg1106417917 sf1106413669 11 6417917 NA 9.38E-07
vg0217679949 sf0217674079 2 17679949 NA 1.40E-06