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 mr1380 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
vg1117079321 sf1116613173 11 17079321 3.15E-08 6.97E-07
vg0432023544 sf0431838437 4 32023544 3.20E-08 1.66E-06
vg0122379413 sf0122378368 1 22379413 5.33E-08 5.66E-06
vg0601266368 sf0601265369 6 1266368 4.75E-07 4.22E-06
vg0122431881 sf0122430836 1 22431881 5.50E-07 NA
vg0121726963 sf0121725918 1 21726963 8.31E-07 3.29E-06
vg0807447586 sf0807446591 8 7447586 2.10E-06 3.49E-06
vg1217716094 sf1217710049 12 17716094 5.71E-06 2.60E-06
vg1117300240 sf1116834092 11 17300240 NA 2.95E-06
vg0115889211 sf0115888185 1 15889211 NA 4.72E-06
vg0715115538 sf0715114545 7 15115538 NA 7.02E-06