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 mr1251 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
vg0217116431 sf0217110561 2 17116431 4.03E-69 1.61E-27
vg0217106167 sf0217100297 2 17106167 6.08E-69 3.65E-28
vg0900336799 sf0900335799 9 336799 2.40E-34 1.60E-11
vg0216562778 sf0216556908 2 16562778 5.88E-34 1.17E-06
vg0900337327 sf0900336327 9 337327 1.44E-33 6.84E-12
vg0720349785 sf0720348792 7 20349785 1.08E-32 NA
vg1114596727 sf1114133045 11 14596727 2.09E-32 1.15E-08
vg0213525745 sf0213525741 2 13525745 5.00E-32 5.90E-08
vg1114473442 sf1114009759 11 14473442 1.51E-31 8.58E-09
vg0812023942 sf0812022947 8 12023942 7.49E-30 4.18E-08
vg0216564970 sf0216559100 2 16564970 8.49E-27 4.46E-08
vg0217653945 sf0217648075 2 17653945 5.50E-25 1.20E-06
vg0631235279 sf0631234281 6 31235279 6.13E-25 4.51E-06
vg0217232931 sf0217227061 2 17232931 NA 1.26E-17
vg1114870126 sf1114406440 11 14870126 NA 6.35E-10
vg0217270732 sf0217264862 2 17270732 NA 1.18E-08
vg0217411940 sf0217406070 2 17411940 NA 5.23E-08
vg1112889066 sf1112425387 11 12889066 NA 1.97E-07
vg1005364262 sf1005380799 10 5364262 NA 2.48E-07
vg0404020437 sf0404016044 4 4020437 NA 2.50E-07
vg0908235271 sf0908234271 9 8235271 NA 3.77E-07
vg0216761078 sf0216755208 2 16761078 NA 4.15E-07
vg0217819624 sf0217813755 2 17819624 NA 1.82E-06
vg1122447657 sf1121981528 11 22447657 NA 2.14E-06
vg0607317396 sf0607316397 6 7317396 NA 3.63E-06
vg0216615616 sf0216609746 2 16615616 NA 4.12E-06