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 mr1255 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
vg0217047369 sf0217041499 2 17047369 7.27E-48 3.21E-28
vg0213525745 sf0213525741 2 13525745 3.11E-19 8.20E-08
vg0214316674 sf0214310804 2 14316674 2.46E-18 7.87E-08
vg0900337327 sf0900336327 9 337327 3.22E-18 3.08E-09
vg0900336799 sf0900335799 9 336799 6.47E-18 2.81E-09
vg0216372724 sf0216366854 2 16372724 6.26E-16 1.34E-10
vg0210017956 sf0210017954 2 10017956 1.49E-14 4.92E-07
vg0216278300 sf0216272430 2 16278300 2.33E-14 1.30E-06
vg0210804274 sf0210804272 2 10804274 1.25E-13 1.03E-07
vg1005364864 sf1005381401 10 5364864 3.82E-12 1.68E-07
vg0217677243 sf0217671373 2 17677243 1.72E-11 2.12E-06
vg1219227024 sf1219198494 12 19227024 3.94E-11 1.67E-06
vg0217322508 sf0217316638 2 17322508 7.39E-11 1.99E-06
vg0217737734 sf0217731864 2 17737734 7.82E-11 3.53E-07
vg0218810920 sf0218805051 2 18810920 4.37E-08 1.51E-06
vg0210480404 sf0210480402 2 10480404 4.42E-08 1.18E-06
vg0217338921 sf0217333051 2 17338921 5.46E-07 1.59E-07
vg1121625049 sf1121158926 11 21625049 1.25E-06 6.40E-07
vg1216729378 sf1216723332 12 16729378 3.29E-06 2.42E-06
vg0610125469 sf0610124470 6 10125469 8.03E-06 2.48E-06
vg0711195681 sf0711194687 7 11195681 9.97E-06 1.57E-06
vg0611109671 sf0611108672 6 11109671 NA 2.28E-06
vg0213112189 sf0213112185 2 13112189 NA 3.14E-06