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 mr1904 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
vg1102103328 sf1102099186 11 2103328 1.42E-13 1.48E-06
vg1102103286 sf1102099144 11 2103286 1.98E-13 1.05E-06
vg0200488786 sf0200488786 2 488786 6.67E-12 NA
vg0404424556 sf0404420160 4 4424556 2.66E-11 NA
vg0230403360 sf0230397491 2 30403360 3.15E-11 NA
vg0232096479 sf0232090610 2 32096479 8.07E-11 NA
vg0225146033 sf0225140164 2 25146033 1.08E-10 2.94E-07
vg0400966446 sf0400961998 4 966446 3.50E-09 2.64E-06
vg0142903531 sf0142902487 1 42903531 8.70E-09 3.69E-06
vg1006601193 sf1006616816 10 6601193 8.80E-09 NA
vg1114485144 sf1114021461 11 14485144 2.62E-08 1.79E-06
vg0905248850 sf0905247850 9 5248850 1.02E-07 NA
vg0403131494 sf0403127097 4 3131494 3.65E-07 NA
vg0231688782 sf0231682913 2 31688782 NA 2.22E-06