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 mr1270 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
vg1017087028 sf1017015800 10 17087028 7.46E-18 5.18E-06
vg0400107976 sf0400106976 4 107976 1.34E-17 NA
vg0709749034 sf0709748040 7 9749034 1.66E-17 NA
vg1008769988 sf1008698850 10 8769988 3.13E-17 NA
vg0520272415 sf0520209888 5 20272415 4.66E-17 NA
vg0711041333 sf0711040339 7 11041333 2.50E-13 1.09E-06
vg1206797869 sf1206796759 12 6797869 3.85E-13 3.01E-06
vg0820001075 sf0819998362 8 20001075 NA 1.44E-07
vg0819864501 sf0819861788 8 19864501 NA 2.88E-07
vg1017210888 sf1017139661 10 17210888 NA 1.11E-06
vg0713357787 sf0713356794 7 13357787 NA 4.28E-06
vg1218311813 sf1218283249 12 18311813 NA 4.54E-06