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 mr1983 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
vg0817041494 sf0817038780 8 17041494 5.29E-08 5.29E-08
vg0305129097 sf0305128099 3 5129097 2.06E-07 2.06E-07
vg0142427760 sf0142426716 1 42427760 4.44E-07 4.44E-07
vg1222365340 sf1222331779 12 22365340 9.61E-07 9.60E-07
vg1122231601 sf1121765472 11 22231601 1.14E-06 1.15E-06
vg0414201574 sf0414192290 4 14201574 1.58E-06 1.58E-06
vg0134321681 sf0134320638 1 34321681 1.93E-06 1.93E-06
vg1125658815 sf1125192654 11 25658815 2.06E-06 2.05E-06
vg0626068609 sf0626067612 6 26068609 2.43E-06 2.43E-06
vg0717522436 sf0717521443 7 17522436 2.45E-06 2.44E-06
vg0902887171 sf0902886171 9 2887171 2.82E-06 2.82E-06
vg0105521069 sf0105520069 1 5521069 3.11E-06 3.11E-06
vg0413435802 sf0413426516 4 13435802 3.27E-06 3.27E-06
vg1222257972 sf1222224519 12 22257972 3.80E-06 3.80E-06
vg0417863778 sf0417691820 4 17863778 3.89E-06 3.89E-06
vg1209941601 sf1209939011 12 9941601 4.06E-06 4.07E-06
vg1222419954 sf1222386393 12 22419954 4.35E-06 4.34E-06
vg1126487074 sf1126015488 11 26487074 5.95E-06 5.94E-06