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 mr1240 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
vg0625443240 sf0625442243 6 25443240 1.41E-13 2.17E-10
vg0136191693 sf0136190650 1 36191693 1.41E-11 1.61E-09
vg0421387824 sf0421215877 4 21387824 3.45E-11 2.04E-08
vg0142062769 sf0142061726 1 42062769 5.27E-11 1.54E-08
vg0336193973 sf0336186899 3 36193973 1.08E-10 1.17E-07
vg1115861799 sf1115397090 11 15861799 3.11E-10 9.94E-07
vg0222717674 sf0222711805 2 22717674 6.14E-10 1.25E-07
vg0432666751 sf0432481640 4 32666751 8.02E-10 2.62E-07
vg0708623561 sf0708622566 7 8623561 1.11E-09 1.88E-07
vg0628741924 sf0628740926 6 28741924 1.71E-09 4.62E-07
vg1001052700 sf1001051676 10 1052700 2.43E-09 1.80E-08
vg1216515188 sf1216512481 12 16515188 3.05E-09 3.93E-07
vg0709675216 sf0709674222 7 9675216 1.35E-08 3.09E-07
vg0107057661 sf0107056661 1 7057661 1.48E-08 1.10E-07
vg0405832898 sf0405828337 4 5832898 2.59E-08 1.58E-07
vg0627929341 sf0627928343 6 27929341 7.38E-08 1.07E-06
vg0714435734 sf0714434741 7 14435734 1.05E-07 2.41E-08
vg1018035120 sf1017963891 10 18035120 1.88E-07 4.82E-07
vg0432749163 sf0432564049 4 32749163 2.87E-07 4.87E-07
vg0224215161 sf0224209292 2 24215161 3.32E-06 8.67E-07