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
vg0719051105 sf0719050112 7 19051105 9.72E-83 2.03E-47
vg0304934067 sf0304933069 3 4934067 2.87E-45 NA
vg0703336791 sf0703335792 7 3336791 3.51E-45 4.35E-06
vg0715953641 sf0715952648 7 15953641 4.05E-45 2.00E-07
vg0626833038 sf0626832041 6 26833038 4.90E-44 2.10E-07
vg0719303206 sf0719302213 7 19303206 7.38E-44 1.01E-14
vg0719067465 sf0719066472 7 19067465 NA 6.39E-53
vg0719188413 sf0719187420 7 19188413 NA 1.58E-23
vg0719055344 sf0719054351 7 19055344 NA 3.17E-17
vg0828401472 sf0828398758 8 28401472 NA 4.25E-12
vg0719436399 sf0719435406 7 19436399 NA 1.20E-10
vg0718985954 sf0718984961 7 18985954 NA 6.79E-10
vg0719088893 sf0719087900 7 19088893 NA 8.51E-10
vg0719012268 sf0719011275 7 19012268 NA 3.15E-09
vg0125087111 sf0125086067 1 25087111 NA 2.25E-08
vg0434575713 sf0434390605 4 34575713 NA 5.11E-08
vg0125091428 sf0125090384 1 25091428 NA 6.29E-08
vg0722044007 sf0722043014 7 22044007 NA 1.22E-07
vg0719040975 sf0719039982 7 19040975 NA 1.97E-07
vg0718886094 sf0718885101 7 18886094 NA 2.55E-07
vg0408294758 sf0408290032 4 8294758 NA 3.32E-07
vg0127955944 sf0127954900 1 27955944 NA 4.21E-07
vg0517841440 sf0517780926 5 17841440 NA 5.40E-07
vg0718885846 sf0718884853 7 18885846 NA 7.99E-07
vg1217302382 sf1217296337 12 17302382 NA 9.66E-07
vg0707738691 sf0707737696 7 7738691 NA 1.04E-06
vg0909789099 sf0909788098 9 9789099 NA 1.07E-06
vg0514963938 sf0514906481 5 14963938 NA 1.50E-06
vg0704858080 sf0704857081 7 4858080 NA 1.52E-06