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 mr1617 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
vg0604305910 sf0604304911 6 4305910 2.98E-46 2.32E-19
vg0604336777 sf0604335778 6 4336777 5.25E-46 1.99E-20
vg1000904661 sf1000903637 10 904661 3.90E-34 4.09E-06
vg0906750195 sf0906749195 9 6750195 6.42E-33 3.20E-06
vg0909260803 sf0909259802 9 9260803 1.77E-32 NA
vg0206136220 sf0206136220 2 6136220 2.67E-32 NA
vg0909268786 sf0909267785 9 9268786 2.68E-32 7.50E-07
vg0508706913 sf0508706841 5 8706913 2.52E-30 5.07E-09
vg0728824513 sf0728823521 7 28824513 6.85E-30 1.52E-07
vg0913424446 sf0913423445 9 13424446 1.28E-29 3.51E-07
vg0601470319 sf0601469320 6 1470319 3.49E-29 1.15E-07
vg0207150816 sf0207150816 2 7150816 4.50E-29 6.14E-07
vg0518676551 sf0518614034 5 18676551 5.63E-29 1.08E-06
vg0311662859 sf0311661577 3 11662859 1.17E-28 4.27E-07
vg0232755756 sf0232749887 2 32755756 2.30E-28 NA
vg0223422615 sf0223416746 2 23422615 4.38E-28 1.25E-06
vg0609221063 sf0609220064 6 9221063 7.28E-27 9.85E-08
vg1009864134 sf1009792955 10 9864134 1.14E-26 4.59E-07
vg0604425979 sf0604424980 6 4425979 NA 2.11E-09
vg0604439758 sf0604438759 6 4439758 NA 4.26E-08
vg0417267842 sf0417095883 4 17267842 NA 6.66E-08
vg1001508358 sf1001507335 10 1508358 NA 7.90E-08
vg0723537431 sf0723536438 7 23537431 NA 8.02E-08
vg1011204337 sf1011133157 10 11204337 NA 8.06E-08
vg1117445573 sf1116979428 11 17445573 NA 1.43E-07
vg0601502296 sf0601501297 6 1502296 NA 1.74E-07
vg0604303918 sf0604302919 6 4303918 NA 1.75E-07
vg0514667369 sf0514609912 5 14667369 NA 2.74E-07
vg0701256216 sf0701255216 7 1256216 NA 3.01E-07
vg0417591285 sf0417419326 4 17591285 NA 6.37E-07
vg0702957519 sf0702956520 7 2957519 NA 1.08E-06
vg0608454378 sf0608453379 6 8454378 NA 1.14E-06