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 mr1155 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
vg0719050935 sf0719049942 7 19050935 2.54E-15 4.11E-14
vg0719106959 sf0719105966 7 19106959 6.67E-15 4.77E-14
vg0719040523 sf0719039530 7 19040523 6.38E-14 3.09E-14
vg0719067465 sf0719066472 7 19067465 1.84E-11 8.45E-17
vg0719006525 sf0719005532 7 19006525 2.18E-11 8.47E-17
vg0815150136 sf0815147422 8 15150136 2.52E-09 1.01E-06
vg0419912063 sf0419740099 4 19912063 3.87E-09 NA
vg0715273808 sf0715272815 7 15273808 7.17E-09 6.86E-07
vg0413556513 sf0413547227 4 13556513 7.65E-09 1.75E-07
vg0828401472 sf0828398758 8 28401472 1.12E-08 2.73E-09
vg0810682226 sf0810681230 8 10682226 1.02E-07 2.01E-06
vg0519903067 sf0519840543 5 19903067 5.35E-07 2.80E-06
vg0724845026 sf0724844032 7 24845026 8.71E-07 7.53E-07
vg0721707193 sf0721706200 7 21707193 1.84E-06 1.02E-07
vg0810647541 sf0810646545 8 10647541 9.75E-06 NA
vg0700416280 sf0700415280 7 416280 NA 4.59E-08
vg0112097431 sf0112096405 1 12097431 NA 6.05E-08
vg1100694812 sf1100693815 11 694812 NA 6.52E-08
vg0124676757 sf0124675713 1 24676757 NA 2.14E-07
vg0804028565 sf0804027568 8 4028565 NA 2.37E-07
vg0125082086 sf0125081042 1 25082086 NA 5.19E-07
vg0912061274 sf0912060273 9 12061274 NA 8.66E-07
vg0125091428 sf0125090384 1 25091428 NA 1.18E-06
vg0428917438 sf0428732299 4 28917438 NA 1.41E-06
vg0709019375 sf0709018381 7 9019375 NA 1.69E-06
vg0422855440 sf0422670325 4 22855440 NA 2.04E-06
vg0719546836 sf0719545843 7 19546836 NA 3.01E-06
vg0107198487 sf0107197487 1 7198487 NA 3.22E-06
vg0223177745 sf0223171876 2 23177745 NA 8.53E-06