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 mr1128 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
vg0135794714 sf0135793671 1 35794714 3.85E-17 5.59E-06
vg0133081413 sf0133080369 1 33081413 1.13E-14 NA
vg0229918346 sf0229912477 2 29918346 1.54E-14 NA
vg1203606348 sf1203605347 12 3606348 2.01E-14 NA
vg0211536788 sf0211536784 2 11536788 3.85E-14 NA
vg0910217057 sf0910216056 9 10217057 1.25E-13 3.62E-06
vg0130669509 sf0130668465 1 30669509 2.09E-11 NA
vg1009316722 sf1009245543 10 9316722 2.56E-11 3.11E-08
vg1009466924 sf1009395745 10 9466924 3.05E-10 1.27E-06
vg0907140771 sf0907139771 9 7140771 4.00E-10 1.14E-07
vg0130732040 sf0130730996 1 30732040 NA 5.68E-12
vg1009411390 sf1009340211 10 9411390 NA 7.27E-09
vg1007617621 sf1007633230 10 7617621 NA 2.84E-08
vg0311434951 sf0311433669 3 11434951 NA 5.68E-07
vg0714251118 sf0714250125 7 14251118 NA 7.08E-07
vg0123297322 sf0123296278 1 23297322 NA 1.29E-06
vg1011062873 sf1010991693 10 11062873 NA 2.08E-06
vg1008324314 sf1008253176 10 8324314 NA 2.36E-06
vg0823525833 sf0823523119 8 23525833 NA 4.10E-06
vg0203965193 sf0203965190 2 3965193 NA 4.13E-06
vg1121617585 sf1121151462 11 21617585 NA 4.37E-06
vg0426777183 sf0426592060 4 26777183 NA 4.84E-06
vg0107395608 sf0107394608 1 7395608 NA 5.83E-06
vg0314708663 sf0314707350 3 14708663 NA 6.56E-06
vg1006596224 sf1006611847 10 6596224 NA 6.85E-06