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 mr1197 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
vg0222578508 sf0222572639 2 22578508 1.91E-11 9.86E-10
vg0114130447 sf0114129421 1 14130447 1.12E-09 1.51E-08
vg0113920566 sf0113919540 1 13920566 2.91E-09 9.60E-08
vg0800337100 sf0800336100 8 337100 3.20E-09 2.48E-07
vg1000903085 sf1000902061 10 903085 3.76E-09 3.92E-07
vg0618926527 sf0618925530 6 18926527 9.71E-09 2.36E-06
vg1001994364 sf1001993341 10 1994364 1.01E-08 2.80E-07
vg0826034114 sf0826031400 8 26034114 3.29E-08 4.08E-06
vg0130684898 sf0130683854 1 30684898 8.06E-08 2.87E-06
vg0504438746 sf0504438723 5 4438746 1.06E-07 3.40E-06
vg0611538489 sf0611537490 6 11538489 1.14E-07 4.39E-06
vg0114130098 sf0114129072 1 14130098 1.23E-07 4.58E-06
vg0234816959 sf0234811090 2 34816959 2.01E-07 1.32E-06
vg0726748322 sf0726747328 7 26748322 2.48E-07 3.25E-06
vg0221233160 sf0221227292 2 21233160 6.10E-07 1.54E-06
vg0819413174 sf0819410461 8 19413174 7.78E-07 4.38E-06
vg0813415272 sf0813412825 8 13415272 NA 3.16E-07
vg0221185352 sf0221179484 2 21185352 NA 1.39E-06
vg0619700082 sf0619699085 6 19700082 NA 1.58E-06
vg0136919523 sf0136918480 1 36919523 NA 3.17E-06