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 mr1458 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
vg1218526277 sf1218497713 12 18526277 2.66E-92 6.04E-22
vg1218908610 sf1218880045 12 18908610 4.88E-91 6.64E-18
vg1218514358 sf1218485794 12 18514358 1.28E-87 5.73E-23
vg0141073686 sf0141072643 1 41073686 8.69E-64 NA
vg1204491827 sf1204490815 12 4491827 6.30E-61 NA
vg0627836229 sf0627835231 6 27836229 3.67E-57 NA
vg0205732616 sf0205732616 2 5732616 8.96E-57 NA
vg0520296343 sf0520233816 5 20296343 3.71E-52 NA
vg1218591659 sf1218563095 12 18591659 NA 3.58E-11
vg1218883751 sf1218855186 12 18883751 NA 1.18E-10
vg1218493508 sf1218464944 12 18493508 NA 1.04E-09
vg1218849677 sf1218821112 12 18849677 NA 4.96E-09
vg1218594158 sf1218565594 12 18594158 NA 3.51E-08
vg0406750129 sf0406745575 4 6750129 NA 5.14E-08
vg1218267405 sf1218238841 12 18267405 NA 1.65E-07
vg1218067516 sf1218038952 12 18067516 NA 4.82E-07
vg0200448299 sf0200448299 2 448299 NA 7.16E-07
vg1218022476 sf1217993912 12 18022476 NA 7.60E-07
vg1218107426 sf1218078862 12 18107426 NA 9.28E-07
vg1216543392 sf1216540685 12 16543392 NA 9.66E-07
vg1219397480 sf1219368950 12 19397480 NA 1.28E-06
vg1218056766 sf1218028202 12 18056766 NA 1.41E-06
vg1216964213 sf1216958167 12 16964213 NA 2.25E-06
vg0141367464 sf0141366421 1 41367464 NA 2.37E-06
vg1218710263 sf1218681698 12 18710263 NA 2.67E-06
vg1217982066 sf1217953502 12 17982066 NA 2.81E-06
vg1011721445 sf1011650260 10 11721445 NA 3.12E-06
vg1217370443 sf1217364398 12 17370443 NA 3.16E-06
vg0305244603 sf0305243603 3 5244603 NA 3.18E-06
vg1217798352 sf1217769786 12 17798352 NA 3.39E-06
vg0623262186 sf0623261189 6 23262186 NA 6.59E-06