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 mr1900 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
vg1124468452 sf1124002292 11 24468452 3.83E-15 1.15E-11
vg1124965681 sf1124499521 11 24965681 2.90E-13 1.49E-12
vg1124952413 sf1124486253 11 24952413 9.93E-12 7.41E-12
vg1125121217 sf1124655057 11 25121217 4.30E-11 1.72E-10
vg0813872533 sf0813869819 8 13872533 1.16E-09 1.95E-06
vg1206990413 sf1206989303 12 6990413 1.70E-09 3.06E-07
vg0713133553 sf0713132560 7 13133553 3.50E-09 3.57E-06
vg0812016101 sf0812015106 8 12016101 4.32E-09 4.50E-07
vg0815712004 sf0815709290 8 15712004 1.01E-08 3.07E-06
vg0502683697 sf0502683673 5 2683697 1.53E-08 7.95E-06
vg1127802594 sf1127330980 11 27802594 2.33E-08 3.74E-09
vg0127069672 sf0127068628 1 27069672 8.07E-08 1.94E-06
vg0503762591 sf0503762568 5 3762591 3.25E-07 4.41E-06
vg1123203627 sf1122737498 11 23203627 1.23E-06 1.46E-07
vg1128168473 sf1127645252 11 28168473 2.64E-06 5.31E-07
vg0919896432 sf0919895951 9 19896432 NA 2.46E-06