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 mr1504 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
vg0138132963 sf0138131920 1 38132963 1.25E-130 8.59E-26
vg1119351587 sf1118885275 11 19351587 2.02E-100 NA
vg0922680808 sf0922680327 9 22680808 2.10E-97 NA
vg0107563270 sf0107562270 1 7563270 2.26E-97 NA
vg0313856584 sf0313855301 3 13856584 2.52E-97 NA
vg0313856271 sf0313854988 3 13856271 1.29E-96 4.53E-06
vg0917797570 sf0917796569 9 17797570 1.30E-96 2.04E-06
vg1119875423 sf1119409346 11 19875423 4.98E-95 1.70E-06
vg1017577102 sf1017505875 10 17577102 2.14E-94 1.98E-06
vg1227310775 sf1227277175 12 27310775 3.03E-91 2.33E-06
vg1112875793 sf1112412114 11 12875793 8.84E-91 4.15E-06
vg1116629534 sf1116164412 11 16629534 3.11E-88 3.29E-06
vg0138160627 sf0138159584 1 38160627 NA 2.98E-09
vg0138161332 sf0138160289 1 38161332 NA 3.16E-09
vg0108147243 sf0108146243 1 8147243 NA 7.55E-08
vg0630161553 sf0630160555 6 30161553 NA 8.17E-08
vg0819129757 sf0819127044 8 19129757 NA 1.11E-07
vg0810945945 sf0810944950 8 10945945 NA 2.91E-07
vg0310332396 sf0310331312 3 10332396 NA 9.97E-07
vg0138183041 sf0138181998 1 38183041 NA 1.24E-06
vg0206309823 sf0206309823 2 6309823 NA 1.37E-06
vg0101266799 sf0101265799 1 1266799 NA 2.15E-06
vg0814102960 sf0814100246 8 14102960 NA 2.29E-06
vg0111820619 sf0111819593 1 11820619 NA 2.29E-06
vg0140812330 sf0140811287 1 40812330 NA 2.38E-06
vg0821073577 sf0821070864 8 21073577 NA 3.37E-06
vg0811513583 sf0811512588 8 11513583 NA 4.44E-06
vg0406209150 sf0406204590 4 6209150 NA 6.72E-06
vg0118657073 sf0118656027 1 18657073 NA 7.62E-06