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 mr1659 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
vg0623294372 sf0623293375 6 23294372 3.11E-16 7.46E-08
vg0623300554 sf0623299557 6 23300554 3.24E-16 6.51E-08
vg0809149905 sf0809148909 8 9149905 9.72E-12 1.57E-06
vg0104731000 sf0104730000 1 4731000 4.67E-11 NA
vg1123001258 sf1122535129 11 23001258 5.20E-11 NA
vg0131842159 sf0131841115 1 31842159 6.56E-11 NA
vg1217897105 sf1217868539 12 17897105 7.93E-11 2.12E-06
vg1019539225 sf1019467749 10 19539225 4.90E-09 2.72E-06
vg0213593475 sf0213593471 2 13593475 2.05E-08 6.95E-06
vg0825503497 sf0825500783 8 25503497 1.06E-07 NA
vg0623300018 sf0623299021 6 23300018 NA 1.49E-08
vg0623329456 sf0623328459 6 23329456 NA 1.51E-08
vg0321406609 sf0321405119 3 21406609 NA 9.54E-07
vg1215556442 sf1215553739 12 15556442 NA 2.08E-06