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 mr1748 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
vg0802944461 sf0802943464 8 2944461 1.55E-08 5.98E-09
vg0406710690 sf0406706137 4 6710690 2.44E-08 1.23E-06
vg0311297814 sf0311296532 3 11297814 5.03E-08 3.12E-06
vg0715902147 sf0715901154 7 15902147 5.79E-08 NA
vg0125316689 sf0125315645 1 25316689 6.91E-08 NA
vg1013435415 sf1013364185 10 13435415 7.44E-08 2.51E-06
vg0231688782 sf0231682913 2 31688782 1.99E-07 6.50E-08
vg0224323881 sf0224318012 2 24323881 2.65E-07 3.80E-06
vg0910315478 sf0910314477 9 10315478 3.41E-07 NA
vg0607086577 sf0607085578 6 7086577 3.91E-07 1.19E-07
vg1224449038 sf1224415491 12 24449038 8.84E-07 7.20E-07
vg0525912304 sf0525849725 5 25912304 1.12E-06 3.28E-06
vg0334854019 sf0334846889 3 34854019 1.12E-06 1.11E-07
vg1108752863 sf1108747473 11 8752863 2.11E-06 2.50E-06
vg0334849585 sf0334842455 3 34849585 3.88E-06 1.43E-07
vg0406502766 sf0406498209 4 6502766 4.41E-06 3.41E-06
vg0408384098 sf0408379372 4 8384098 5.32E-06 4.29E-07
vg0315822873 sf0315821520 3 15822873 5.45E-06 8.10E-07
vg0709475005 sf0709474011 7 9475005 6.62E-06 NA
vg0408695325 sf0408690601 4 8695325 NA 1.98E-06
vg1105944153 sf1105939905 11 5944153 NA 2.24E-06
vg1004957918 sf1004974455 10 4957918 NA 2.65E-06
vg1200344922 sf1200343922 12 344922 NA 2.77E-06
vg0200442960 sf0200442960 2 442960 NA 3.81E-06
vg0527455021 sf0527392377 5 27455021 NA 4.01E-06
vg0502032617 sf0502032599 5 2032617 NA 6.81E-06