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 mr1038 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
vg0728442720 sf0728441728 7 28442720 1.05E-36 8.61E-22
vg0631155509 sf0631154511 6 31155509 2.38E-25 4.57E-11
vg1222591917 sf1222558356 12 22591917 3.11E-24 5.34E-17
vg0328157393 sf0328150447 3 28157393 1.08E-22 2.53E-06
vg0330661173 sf0330654060 3 30661173 1.73E-22 4.58E-06
vg0330077379 sf0330070418 3 30077379 9.16E-21 9.37E-10
vg0728693760 sf0728692768 7 28693760 1.10E-20 4.92E-14
vg0417792314 sf0417620352 4 17792314 5.37E-20 1.53E-11
vg0219834070 sf0219828202 2 19834070 1.91E-19 1.91E-11
vg0325722534 sf0325720552 3 25722534 2.41E-19 3.98E-11
vg0319440543 sf0319439054 3 19440543 5.82E-19 3.75E-09
vg0616470948 sf0616469950 6 16470948 2.49E-17 1.84E-10
vg0622846135 sf0622845138 6 22846135 4.58E-16 1.09E-08
vg0630964914 sf0630963916 6 30964914 1.59E-14 1.50E-07
vg0521119103 sf0521056544 5 21119103 2.17E-14 2.32E-09
vg1206967731 sf1206966621 12 6967731 5.61E-14 1.14E-08
vg0806359100 sf0806358105 8 6359100 7.85E-14 6.67E-09
vg0140074301 sf0140073258 1 40074301 3.01E-13 9.20E-11
vg1219449222 sf1219420692 12 19449222 8.39E-13 8.72E-09
vg0713786254 sf0713785261 7 13786254 1.11E-10 5.06E-11
vg0304762695 sf0304761697 3 4762695 1.48E-07 1.34E-08
vg0224289143 sf0224283274 2 24289143 2.75E-07 1.23E-06
vg1222478770 sf1222445209 12 22478770 NA 2.74E-09
vg1101299110 sf1101298111 11 1299110 NA 1.33E-08
vg0401709039 sf0401704588 4 1709039 NA 1.21E-07