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 mr1118 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
vg0421387824 sf0421215877 4 21387824 1.92E-18 2.81E-14
vg0504875404 sf0504875381 5 4875404 3.35E-14 7.85E-09
vg0336193973 sf0336186899 3 36193973 5.35E-14 5.47E-10
vg0210316954 sf0210316952 2 10316954 6.15E-12 1.36E-06
vg1203128564 sf1203127567 12 3128564 8.00E-12 5.29E-06
vg0424049928 sf0423864789 4 24049928 1.18E-11 1.43E-07
vg1001348300 sf1001347277 10 1348300 1.06E-10 1.20E-06
vg0105833744 sf0105832744 1 5833744 1.58E-10 1.42E-06
vg1126461419 sf1125989832 11 26461419 2.74E-10 1.40E-06
vg0219279605 sf0219273737 2 19279605 3.62E-10 1.76E-06
vg0628759426 sf0628758428 6 28759426 7.92E-10 1.50E-06
vg0819366916 sf0819364203 8 19366916 1.42E-09 2.72E-07
vg0215890449 sf0215884579 2 15890449 2.41E-09 7.67E-07
vg0515214255 sf0515156797 5 15214255 4.38E-09 1.48E-06
vg0906313471 sf0906312471 9 6313471 9.73E-09 6.29E-07
vg1117137503 sf1116671355 11 17137503 2.40E-08 1.55E-07
vg0309964337 sf0309963273 3 9964337 4.36E-08 1.53E-06
vg0210666524 sf0210666522 2 10666524 1.24E-07 7.90E-07
vg0219292377 sf0219286509 2 19292377 6.65E-07 7.00E-07
vg1227451463 sf1227417863 12 27451463 2.15E-06 1.02E-06
vg0812003263 sf0812002268 8 12003263 NA 3.50E-07
vg1208630676 sf1208628083 12 8630676 NA 3.62E-07
vg0408484082 sf0408479355 4 8484082 NA 6.36E-07
vg0709674359 sf0709673365 7 9674359 NA 8.23E-07