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 mr1019 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
vg1215976963 sf1215974259 12 15976963 7.47E-120 4.85E-41
vg1215968758 sf1215966054 12 15968758 9.30E-120 1.92E-41
vg0630850632 sf0630849634 6 30850632 2.69E-86 2.36E-08
vg0630847922 sf0630846924 6 30847922 3.50E-86 2.12E-08
vg0800016045 sf0800015045 8 16045 9.23E-86 NA
vg0621221946 sf0621220949 6 21221946 2.62E-84 5.30E-06
vg0129561423 sf0129560378 1 29561423 7.64E-83 NA
vg1018571610 sf1018500167 10 18571610 9.29E-83 1.46E-08
vg0311689340 sf0311688058 3 11689340 4.60E-76 9.20E-08
vg1006096361 sf1006112897 10 6096361 1.60E-72 6.57E-08
vg0133470700 sf0133469656 1 33470700 1.43E-69 1.70E-08
vg0133604521 sf0133603477 1 33604521 3.04E-69 3.64E-08
vg1215871396 sf1215868692 12 15871396 NA 8.94E-24
vg1215969757 sf1215967053 12 15969757 NA 2.65E-19
vg1116068177 sf1115603049 11 16068177 NA 3.86E-11
vg1215871822 sf1215869118 12 15871822 NA 1.94E-10
vg1109319597 sf1109314174 11 9319597 NA 5.11E-10
vg1215271479 sf1215268777 12 15271479 NA 7.69E-10
vg1216346285 sf1216343581 12 16346285 NA 1.65E-09
vg0222393095 sf0222387226 2 22393095 NA 3.32E-09
vg1215438933 sf1215436231 12 15438933 NA 6.10E-09
vg1216413575 sf1216410868 12 16413575 NA 6.52E-09
vg0920348485 sf0920348004 9 20348485 NA 1.05E-08
vg1216151894 sf1216149190 12 16151894 NA 1.22E-08
vg1202865605 sf1202864607 12 2865605 NA 1.63E-08
vg0607958971 sf0607957972 6 7958971 NA 1.77E-08
vg0521485463 sf0521422904 5 21485463 NA 1.78E-08
vg0701738802 sf0701737803 7 1738802 NA 1.79E-08
vg1215673648 sf1215670945 12 15673648 NA 1.86E-08
vg0303633068 sf0303632064 3 3633068 NA 3.79E-08
vg0912172576 sf0912171575 9 12172576 NA 4.37E-08
vg1215337843 sf1215335141 12 15337843 NA 4.60E-08
vg1215909724 sf1215907020 12 15909724 NA 7.13E-08
vg1215261373 sf1215258671 12 15261373 NA 7.41E-08
vg1104978159 sf1104973970 11 4978159 NA 1.45E-07
vg0900589112 sf0900588112 9 589112 NA 7.10E-07