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 mr1525 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
vg0406288626 sf0406284066 4 6288626 4.83E-10 4.83E-10
vg0405535133 sf0405530574 4 5535133 1.15E-09 1.15E-09
vg0410520697 sf0410511396 4 10520697 6.55E-09 6.55E-09
vg0809622371 sf0809621375 8 9622371 3.73E-07 3.73E-07
vg1203788125 sf1203787124 12 3788125 4.90E-07 4.90E-07
vg0405898112 sf0405893553 4 5898112 5.58E-07 5.58E-07
vg0218297603 sf0218291734 2 18297603 8.44E-07 8.44E-07
vg0809548841 sf0809547845 8 9548841 8.79E-07 8.79E-07
vg0405138699 sf0405134141 4 5138699 9.64E-07 9.64E-07
vg0414877699 sf0414868413 4 14877699 1.81E-06 1.81E-06
vg0806625593 sf0806624598 8 6625593 2.61E-06 2.61E-06
vg1208558919 sf1208556326 12 8558919 2.87E-06 2.87E-06
vg1119666919 sf1119200607 11 19666919 3.75E-06 3.75E-06
vg0806189701 sf0806188706 8 6189701 3.94E-06 3.94E-06
vg1223544640 sf1223511100 12 23544640 4.11E-06 4.11E-06