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 mr1502 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
vg1117992760 sf1117526618 11 17992760 5.08E-14 1.89E-06
vg0142015207 sf0142014164 1 42015207 1.40E-13 NA
vg1117996370 sf1117530228 11 17996370 1.42E-13 1.24E-06
vg0232210538 sf0232204669 2 32210538 6.42E-13 NA
vg0912633839 sf0912632838 9 12633839 2.59E-12 NA
vg0102142891 sf0102141891 1 2142891 2.81E-12 NA
vg0221812870 sf0221807001 2 21812870 3.05E-12 8.07E-08
vg0315238169 sf0315236816 3 15238169 4.06E-11 4.19E-06
vg0430557936 sf0430372811 4 30557936 4.47E-11 2.81E-07
vg1003548056 sf1003547033 10 3548056 5.46E-11 3.47E-06
vg0124341089 sf0124340045 1 24341089 4.24E-09 NA
vg0221919301 sf0221913432 2 21919301 4.64E-08 1.09E-07
vg1014028348 sf1013957114 10 14028348 NA 1.99E-06
vg0400611332 sf0400610332 4 611332 NA 2.81E-06
vg0221866544 sf0221860675 2 21866544 NA 2.94E-06
vg0234396020 sf0234390151 2 34396020 NA 3.89E-06
vg0234397521 sf0234391652 2 34397521 NA 5.60E-06
vg0103530099 sf0103529099 1 3530099 NA 7.45E-06
vg0311006870 sf0311005588 3 11006870 NA 8.92E-06