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 mr1364 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
vg1216063848 sf1216061144 12 16063848 6.19E-12 2.39E-06
vg1216176111 sf1216173407 12 16176111 1.01E-11 2.28E-06
vg0630760388 sf0630759390 6 30760388 1.27E-10 NA
vg0826497314 sf0826494600 8 26497314 3.11E-10 NA
vg1119604110 sf1119137798 11 19604110 3.71E-10 NA
vg0722383200 sf0722382207 7 22383200 3.96E-10 NA
vg1216258965 sf1216256261 12 16258965 4.27E-09 3.79E-06
vg1216059532 sf1216056828 12 16059532 9.28E-09 1.44E-07
vg1119775301 sf1119308989 11 19775301 2.02E-07 NA
vg1218117927 sf1218089363 12 18117927 NA 3.58E-07
vg0212843658 sf0212843654 2 12843658 NA 6.06E-07
vg0821334599 sf0821331886 8 21334599 NA 1.05E-06
vg0107372570 sf0107371570 1 7372570 NA 1.75E-06
vg1016706016 sf1016634789 10 16706016 NA 2.14E-06
vg1209691208 sf1209688617 12 9691208 NA 2.61E-06