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 mr1238 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
vg1124335549 sf1123869393 11 24335549 1.64E-23 2.86E-20
vg1015982479 sf1015911251 10 15982479 2.24E-15 1.62E-14
vg1124965681 sf1124499521 11 24965681 1.20E-14 5.81E-16
vg1125256797 sf1124790637 11 25256797 8.71E-14 1.51E-12
vg1125256577 sf1124790417 11 25256577 8.92E-14 8.05E-13
vg0521578860 sf0521511524 5 21578860 1.28E-13 3.22E-11
vg0812970437 sf0812968262 8 12970437 1.33E-13 1.44E-10
vg1124348003 sf1123881847 11 24348003 8.06E-12 1.18E-10
vg0520747897 sf0520685338 5 20747897 3.24E-11 8.97E-11
vg0815665575 sf0815662861 8 15665575 5.80E-11 2.01E-08
vg1126054242 sf1125582656 11 26054242 1.06E-10 8.92E-10
vg1127793570 sf1127321956 11 27793570 1.60E-10 1.68E-09
vg1206990413 sf1206989303 12 6990413 1.98E-10 4.31E-08
vg0715539794 sf0715538801 7 15539794 2.42E-10 4.12E-11
vg0526207590 sf0526144954 5 26207590 2.87E-10 1.98E-08
vg1125116622 sf1124650462 11 25116622 6.22E-10 7.18E-09
vg1123203627 sf1122737498 11 23203627 1.02E-09 3.80E-10
vg1124340538 sf1123874382 11 24340538 1.36E-09 1.70E-10
vg1124950335 sf1124484175 11 24950335 3.13E-09 4.05E-09
vg1211902154 sf1211899489 12 11902154 1.45E-06 1.76E-06
vg1123971097 sf1123504967 11 23971097 NA 3.17E-09
vg1125184358 sf1124718198 11 25184358 NA 1.89E-08