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 mr1027 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
vg0133471333 sf0133470289 1 33471333 1.44E-93 4.69E-15
vg0133600221 sf0133599177 1 33600221 7.42E-93 1.63E-15
vg0133359419 sf0133358375 1 33359419 6.30E-87 3.12E-06
vg0137169061 sf0137168018 1 37169061 1.42E-86 NA
vg0434911930 sf0434726820 4 34911930 6.74E-86 2.13E-06
vg1101297328 sf1101296329 11 1297328 7.66E-86 NA
vg0129939389 sf0129938344 1 29939389 5.83E-85 NA
vg1006715758 sf1006731381 10 6715758 NA 4.30E-09
vg1006715361 sf1006730984 10 6715361 NA 5.50E-09
vg0303534207 sf0303533203 3 3534207 NA 2.84E-08
vg1011536743 sf1011465562 10 11536743 NA 3.62E-07
vg0625009550 sf0625008553 6 25009550 NA 5.84E-07
vg0420468639 sf0420296683 4 20468639 NA 7.08E-07
vg1009401525 sf1009330346 10 9401525 NA 8.09E-07
vg1009912343 sf1009841164 10 9912343 NA 1.38E-06
vg1008811441 sf1008740303 10 8811441 NA 1.61E-06
vg1013333671 sf1013262440 10 13333671 NA 1.66E-06
vg0314801437 sf0314800124 3 14801437 NA 2.06E-06
vg0820942801 sf0820940088 8 20942801 NA 2.11E-06
vg1214802925 sf1214800266 12 14802925 NA 3.29E-06
vg1006120882 sf1006137418 10 6120882 NA 3.37E-06
vg0207699992 sf0207699991 2 7699992 NA 3.61E-06
vg1008202012 sf1008130874 10 8202012 NA 3.68E-06
vg0800292859 sf0800291859 8 292859 NA 3.96E-06
vg0316245980 sf0316244628 3 16245980 NA 4.83E-06
vg0400611332 sf0400610332 4 611332 NA 8.79E-06