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 mr1350 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
vg0413666850 sf0413657564 4 13666850 4.63E-31 3.10E-06
vg1209191270 sf1209188679 12 9191270 7.84E-31 5.58E-06
vg0413668647 sf0413659361 4 13668647 1.67E-30 2.27E-07
vg1209083240 sf1209080649 12 9083240 2.94E-30 1.49E-06
vg1208817900 sf1208815307 12 8817900 1.59E-28 7.46E-06
vg0217136008 sf0217130138 2 17136008 1.15E-27 5.95E-06
vg0826557361 sf0826554647 8 26557361 1.27E-27 NA
vg0321594245 sf0321592755 3 21594245 2.88E-27 NA
vg0413764976 sf0413755690 4 13764976 NA 2.33E-11
vg0911208644 sf0911207643 9 11208644 NA 6.50E-07
vg1020438368 sf1020366847 10 20438368 NA 9.83E-07
vg0807648774 sf0807647779 8 7648774 NA 1.01E-06
vg1200140958 sf1200139958 12 140958 NA 1.02E-06
vg0212281281 sf0212281277 2 12281281 NA 1.44E-06
vg0813651729 sf0813649014 8 13651729 NA 1.48E-06
vg1222927642 sf1222894101 12 22927642 NA 1.80E-06
vg0413382898 sf0413373609 4 13382898 NA 1.95E-06
vg1227323057 sf1227289457 12 27323057 NA 2.15E-06
vg0217205918 sf0217200048 2 17205918 NA 2.32E-06
vg0432816266 sf0432631152 4 32816266 NA 2.44E-06
vg0202124487 sf0202124487 2 2124487 NA 2.50E-06
vg1114037213 sf1113573534 11 14037213 NA 2.82E-06
vg1223993351 sf1223959804 12 23993351 NA 4.69E-06
vg0527153110 sf0527090466 5 27153110 NA 6.30E-06
vg0217068717 sf0217062847 2 17068717 NA 8.08E-06