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 mr1745 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
vg0430597974 sf0430412849 4 30597974 1.53E-59 1.70E-34
vg0430613365 sf0430428240 4 30613365 3.36E-59 7.60E-35
vg0128937112 sf0128936067 1 28937112 3.17E-41 NA
vg0430645227 sf0430460102 4 30645227 1.22E-39 8.85E-10
vg0921373579 sf0921373098 9 21373579 2.07E-39 NA
vg0310172690 sf0310171606 3 10172690 1.57E-37 NA
vg0430617159 sf0430432034 4 30617159 NA 3.98E-15
vg1125263510 sf1124797350 11 25263510 NA 7.87E-14
vg0430479763 sf0430294641 4 30479763 NA 1.60E-13
vg0429938561 sf0429753428 4 29938561 NA 4.92E-13
vg1125403382 sf1124937221 11 25403382 NA 2.65E-11
vg1125263117 sf1124796957 11 25263117 NA 2.17E-10
vg0430855895 sf0430670775 4 30855895 NA 4.13E-10
vg0430538279 sf0430353154 4 30538279 NA 1.44E-09
vg1015945404 sf1015874175 10 15945404 NA 2.29E-09
vg0225876283 sf0225870414 2 25876283 NA 3.60E-09
vg0919877661 sf0919877180 9 19877661 NA 5.07E-09
vg0331916551 sf0331909428 3 31916551 NA 1.04E-08
vg1125601372 sf1125135211 11 25601372 NA 1.24E-08
vg0307337230 sf0307336228 3 7337230 NA 1.26E-08
vg0204236567 sf0204236564 2 4236567 NA 1.36E-08
vg0325243401 sf0325241482 3 25243401 NA 1.49E-08
vg1015868542 sf1015797312 10 15868542 NA 1.82E-08
vg1128170551 sf1127647330 11 28170551 NA 2.85E-08
vg0432702205 sf0432517094 4 32702205 NA 5.81E-08
vg0324085319 sf0324083398 3 24085319 NA 9.81E-08
vg0433305431 sf0433120321 4 33305431 NA 1.27E-07
vg0518913277 sf0518850761 5 18913277 NA 1.36E-07