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 mr1083 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
vg0719140447 sf0719139454 7 19140447 4.57E-23 9.64E-15
vg0719209499 sf0719208506 7 19209499 NA 1.12E-09
vg1202102394 sf1202101392 12 2102394 NA 8.79E-09
vg1201735910 sf1201734908 12 1735910 NA 5.91E-08
vg1202102385 sf1202101383 12 2102385 NA 8.73E-08
vg0315225430 sf0315224077 3 15225430 NA 1.13E-07
vg0304916753 sf0304915755 3 4916753 NA 1.74E-07
vg1201385569 sf1201384569 12 1385569 NA 2.30E-07
vg0719007683 sf0719006690 7 19007683 NA 3.09E-07
vg0718985745 sf0718984752 7 18985745 NA 8.38E-07
vg0706750728 sf0706749733 7 6750728 NA 1.30E-06
vg1201512648 sf1201511648 12 1512648 NA 1.31E-06
vg0503840950 sf0503840927 5 3840950 NA 1.50E-06
vg1201852439 sf1201851436 12 1852439 NA 1.52E-06
vg0315179985 sf0315178632 3 15179985 NA 1.56E-06
vg0719799826 sf0719798833 7 19799826 NA 1.80E-06
vg0613011483 sf0613010484 6 13011483 NA 2.12E-06
vg0705479079 sf0705478080 7 5479079 NA 3.00E-06
vg1105944153 sf1105939905 11 5944153 NA 3.01E-06
vg0706547098 sf0706546103 7 6547098 NA 3.16E-06
vg0910207948 sf0910206947 9 10207948 NA 3.19E-06
vg0720408008 sf0720407015 7 20408008 NA 3.24E-06
vg0304835233 sf0304834235 3 4835233 NA 3.44E-06
vg0707794523 sf0707793528 7 7794523 NA 9.54E-06