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 mr1094 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
vg0610566343 sf0610565344 6 10566343 8.81E-107 2.19E-41
vg0610683043 sf0610682044 6 10683043 3.00E-76 1.50E-25
vg0233932146 sf0233926277 2 33932146 2.00E-54 NA
vg0615150907 sf0615149908 6 15150907 1.72E-53 NA
vg0719259692 sf0719258699 7 19259692 2.07E-53 NA
vg0612571543 sf0612570544 6 12571543 2.81E-53 NA
vg0423897544 sf0423712402 4 23897544 8.26E-53 NA
vg0610532672 sf0610531673 6 10532672 NA 7.46E-20
vg0610763769 sf0610762770 6 10763769 NA 2.97E-15
vg0222739831 sf0222733962 2 22739831 NA 2.50E-14
vg0610679715 sf0610678716 6 10679715 NA 1.29E-12
vg0610443193 sf0610442194 6 10443193 NA 1.88E-10
vg0610685711 sf0610684712 6 10685711 NA 3.09E-10
vg0222709519 sf0222703650 2 22709519 NA 2.74E-09
vg0609929059 sf0609928060 6 9929059 NA 3.47E-09
vg0611127784 sf0611126785 6 11127784 NA 1.04E-08
vg0222628680 sf0222622811 2 22628680 NA 4.72E-07
vg0612257699 sf0612256700 6 12257699 NA 4.84E-07
vg0610630630 sf0610629631 6 10630630 NA 5.02E-07
vg0610134394 sf0610133395 6 10134394 NA 6.94E-07
vg0610151699 sf0610150700 6 10151699 NA 6.95E-07
vg0618092647 sf0618091650 6 18092647 NA 8.33E-07
vg0206163454 sf0206163454 2 6163454 NA 1.09E-06
vg0613071268 sf0613070269 6 13071268 NA 1.21E-06
vg0421466152 sf0421294203 4 21466152 NA 1.91E-06
vg0403922278 sf0403917884 4 3922278 NA 1.98E-06
vg0619163386 sf0619162389 6 19163386 NA 2.42E-06
vg0230370414 sf0230364545 2 30370414 NA 2.65E-06
vg0609452459 sf0609451460 6 9452459 NA 2.65E-06