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 mr1261 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
vg1009346972 sf1009275793 10 9346972 1.08E-20 2.77E-06
vg1201339873 sf1201338873 12 1339873 1.31E-20 NA
vg0425054754 sf0424869615 4 25054754 8.84E-20 NA
vg1006502091 sf1006517714 10 6502091 1.18E-19 NA
vg0611159825 sf0611158826 6 11159825 1.20E-19 9.05E-06
vg1009328992 sf1009257813 10 9328992 NA 2.46E-08
vg0920177153 sf0920176672 9 20177153 NA 4.09E-08
vg0720872445 sf0720871452 7 20872445 NA 9.68E-08
vg1005819733 sf1005836271 10 5819733 NA 1.04E-07
vg1201024139 sf1201023139 12 1024139 NA 1.61E-07
vg1128760132 sf1128236911 11 28760132 NA 7.23E-07
vg0604049107 sf0604048108 6 4049107 NA 8.34E-07
vg1128778120 sf1128254899 11 28778120 NA 9.24E-07
vg0604026563 sf0604025564 6 4026563 NA 1.19E-06
vg0401113415 sf0401108965 4 1113415 NA 1.46E-06
vg1206236337 sf1206235227 12 6236337 NA 1.76E-06
vg1001119761 sf1001118737 10 1119761 NA 2.05E-06
vg1206968626 sf1206967516 12 6968626 NA 2.06E-06
vg1006534265 sf1006549888 10 6534265 NA 2.67E-06
vg0526394533 sf0526331896 5 26394533 NA 3.08E-06
vg0604436988 sf0604435989 6 4436988 NA 3.12E-06
vg0500913831 sf0500913814 5 913831 NA 3.22E-06
vg0817661366 sf0817658653 8 17661366 NA 3.24E-06
vg0610487848 sf0610486849 6 10487848 NA 3.46E-06
vg0717909125 sf0717908132 7 17909125 NA 3.79E-06
vg0920808559 sf0920808078 9 20808559 NA 3.90E-06
vg1010661385 sf1010590206 10 10661385 NA 4.28E-06