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 mr1769 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
vg0106691928 sf0106690928 1 6691928 7.44E-92 4.20E-55
vg0106688727 sf0106687727 1 6688727 1.92E-91 8.07E-55
vg0105752606 sf0105751606 1 5752606 8.11E-25 7.04E-11
vg0106683798 sf0106682798 1 6683798 6.36E-22 2.67E-21
vg0107074175 sf0107073175 1 7074175 2.95E-21 5.44E-07
vg0106156707 sf0106155707 1 6156707 1.54E-19 1.82E-08
vg0106184160 sf0106183160 1 6184160 3.17E-18 3.98E-09
vg0106671423 sf0106670423 1 6671423 5.26E-16 2.65E-21
vg0106777731 sf0106776731 1 6777731 4.05E-15 1.54E-17
vg0106961531 sf0106960531 1 6961531 7.70E-15 2.67E-08
vg0106632043 sf0106631043 1 6632043 3.13E-13 2.77E-06
vg0801594585 sf0801593587 8 1594585 3.47E-13 5.09E-07
vg0215720831 sf0215714961 2 15720831 4.11E-13 1.75E-06
vg0823004291 sf0823001578 8 23004291 6.86E-13 2.98E-07
vg0102410486 sf0102409486 1 2410486 1.05E-12 1.04E-07
vg0106669651 sf0106668651 1 6669651 1.88E-12 3.70E-16
vg0423365056 sf0423179911 4 23365056 1.67E-11 2.80E-06
vg0719884010 sf0719883017 7 19884010 7.42E-11 2.07E-06
vg0106442775 sf0106441775 1 6442775 NA 4.78E-12
vg0106670061 sf0106669061 1 6670061 NA 1.70E-11
vg0106686584 sf0106685584 1 6686584 NA 2.12E-10
vg0105587028 sf0105586028 1 5587028 NA 6.83E-09
vg0106772114 sf0106771114 1 6772114 NA 7.10E-08
vg1216564174 sf1216561467 12 16564174 NA 8.19E-07
vg0106626230 sf0106625230 1 6626230 NA 2.03E-06