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 mr1305 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
vg1005695540 sf1005712078 10 5695540 4.84E-45 1.21E-12
vg1010636917 sf1010565738 10 10636917 2.05E-36 3.16E-08
vg0434705432 sf0434520321 4 34705432 2.98E-36 3.26E-07
vg1226954152 sf1226920551 12 26954152 2.31E-32 NA
vg0327159737 sf0327152790 3 27159737 6.91E-32 NA
vg0335000939 sf0334993809 3 35000939 6.21E-27 6.91E-07
vg0327425445 sf0327418498 3 27425445 NA 3.44E-16
vg0327424324 sf0327417377 3 27424324 NA 7.55E-15
vg1005967804 sf1005984342 10 5967804 NA 4.02E-12
vg0317023117 sf0317021991 3 17023117 NA 6.52E-12
vg0202735231 sf0202735229 2 2735231 NA 2.78E-11
vg0400407662 sf0400406660 4 407662 NA 7.12E-11
vg0324795678 sf0324793757 3 24795678 NA 3.77E-10
vg0222830353 sf0222824484 2 22830353 NA 3.90E-10
vg1005691507 sf1005708045 10 5691507 NA 1.87E-09
vg0227637893 sf0227632024 2 27637893 NA 2.56E-09
vg0907876621 sf0907875621 9 7876621 NA 6.15E-09
vg0628001136 sf0628000138 6 28001136 NA 6.93E-09
vg0307990876 sf0307989814 3 7990876 NA 1.02E-08
vg1004952643 sf1004969180 10 4952643 NA 1.51E-08
vg0222778846 sf0222772977 2 22778846 NA 1.87E-08
vg0220269450 sf0220263582 2 20269450 NA 1.90E-08
vg0202722002 sf0202722000 2 2722002 NA 2.26E-08
vg1006197301 sf1006212950 10 6197301 NA 3.09E-08
vg0307386965 sf0307385963 3 7386965 NA 4.54E-08
vg1110517362 sf1110511907 11 10517362 NA 4.94E-08
vg0627991714 sf0627990716 6 27991714 NA 1.05E-07
vg0406620420 sf0406615864 4 6620420 NA 3.67E-06
vg1020492622 sf1020421101 10 20492622 NA 4.75E-06