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 mr1108 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
vg0610752378 sf0610751379 6 10752378 1.21E-09 1.21E-09
vg0817249650 sf0817246936 8 17249650 5.79E-07 5.79E-07
vg0807758172 sf0807757176 8 7758172 6.81E-07 6.81E-07
vg1215018131 sf1215015473 12 15018131 8.14E-07 8.14E-07
vg1215507555 sf1215504852 12 15507555 1.14E-06 1.14E-06
vg0419529348 sf0419357386 4 19529348 1.15E-06 1.15E-06
vg0715209847 sf0715208854 7 15209847 1.73E-06 1.73E-06
vg0626895745 sf0626894748 6 26895745 2.03E-06 2.04E-06
vg0619275607 sf0619274610 6 19275607 2.54E-06 2.54E-06
vg0811475238 sf0811474243 8 11475238 2.55E-06 2.55E-06
vg0709480436 sf0709479442 7 9480436 2.74E-06 2.74E-06
vg0817334525 sf0817331811 8 17334525 2.80E-06 2.80E-06
vg0400503363 sf0400502361 4 503363 3.76E-06 3.76E-06
vg0611683955 sf0611682956 6 11683955 3.92E-06 3.92E-06
vg0809578434 sf0809577438 8 9578434 4.40E-06 4.40E-06
vg0610460953 sf0610459954 6 10460953 4.40E-06 4.41E-06
vg0728808531 sf0728807539 7 28808531 4.47E-06 4.47E-06
vg0421388213 sf0421216266 4 21388213 4.74E-06 4.74E-06