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 mr1850 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
vg0611885115 sf0611884116 6 11885115 2.54E-34 6.99E-13
vg0610275164 sf0610274165 6 10275164 9.10E-30 9.51E-12
vg0616573493 sf0616572495 6 16573493 1.26E-22 1.44E-07
vg0611885798 sf0611884799 6 11885798 3.60E-22 NA
vg0621535653 sf0621534656 6 21535653 7.71E-19 NA
vg0609219049 sf0609218050 6 9219049 9.60E-18 1.11E-06
vg0624749710 sf0624748713 6 24749710 1.39E-17 4.09E-09
vg0610212566 sf0610211567 6 10212566 3.20E-15 4.98E-10
vg0106990017 sf0106989017 1 6990017 NA 3.01E-11
vg0610102626 sf0610101627 6 10102626 NA 3.82E-11
vg0624615989 sf0624614992 6 24615989 NA 1.13E-10
vg0506412276 sf0506412215 5 6412276 NA 1.72E-09
vg0208996721 sf0208996719 2 8996721 NA 2.57E-09
vg1207647527 sf1207644931 12 7647527 NA 3.84E-09
vg1122937279 sf1122471150 11 22937279 NA 3.93E-09
vg0805258928 sf0805257931 8 5258928 NA 4.64E-09
vg0624640066 sf0624639069 6 24640066 NA 4.99E-09
vg1218661069 sf1218632504 12 18661069 NA 1.32E-08
vg0605515624 sf0605514625 6 5515624 NA 1.92E-08
vg0412960919 sf0412951630 4 12960919 NA 2.13E-08
vg1215582510 sf1215579807 12 15582510 NA 2.48E-08
vg0624778270 sf0624777273 6 24778270 NA 3.31E-08
vg0403922278 sf0403917884 4 3922278 NA 4.14E-08
vg0216842048 sf0216836178 2 16842048 NA 4.66E-08
vg0504297582 sf0504297559 5 4297582 NA 4.98E-08
vg0511404761 sf0511404691 5 11404761 NA 5.23E-08
vg0233554175 sf0233548306 2 33554175 NA 5.85E-08
vg0910350606 sf0910349605 9 10350606 NA 6.84E-08
vg0712338155 sf0712337162 7 12338155 NA 1.00E-07
vg0806462678 sf0806461683 8 6462678 NA 1.62E-07
vg0412735652 sf0412726362 4 12735652 NA 7.10E-06