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
vg0610564701 sf0610563702 6 10564701 5.53E-42 3.07E-21
vg0610459123 sf0610458124 6 10459123 2.62E-38 1.62E-24
vg0610459095 sf0610458096 6 10459095 2.75E-38 1.56E-24
vg0610584301 sf0610583302 6 10584301 7.37E-28 4.09E-15
vg0610606146 sf0610605147 6 10606146 3.01E-26 1.41E-18
vg0610412338 sf0610411339 6 10412338 4.63E-26 9.67E-14
vg0610646456 sf0610645457 6 10646456 1.15E-22 3.46E-14
vg0610683007 sf0610682008 6 10683007 1.04E-21 1.19E-17
vg0617319066 sf0617318069 6 17319066 3.69E-18 NA
vg0617383481 sf0617382484 6 17383481 2.62E-17 3.43E-06
vg0614652165 sf0614651166 6 14652165 1.92E-16 NA
vg0609930953 sf0609929954 6 9930953 2.66E-14 1.32E-10
vg0610061410 sf0610060411 6 10061410 4.96E-14 1.81E-06
vg0610799620 sf0610798621 6 10799620 9.97E-13 3.90E-08
vg0403566658 sf0403562260 4 3566658 1.30E-12 1.39E-06
vg1009646441 sf1009575262 10 9646441 8.25E-11 3.39E-06
vg0610642043 sf0610641044 6 10642043 2.26E-10 2.58E-09
vg0613063818 sf0613062819 6 13063818 3.06E-10 5.01E-07
vg0611471474 sf0611470475 6 11471474 3.41E-10 3.21E-07
vg1007459711 sf1007475334 10 7459711 2.31E-09 NA
vg0617641436 sf0617640439 6 17641436 NA 2.86E-07
vg0611649853 sf0611648854 6 11649853 NA 3.78E-07
vg0611125937 sf0611124938 6 11125937 NA 1.51E-06
vg0610611540 sf0610610541 6 10611540 NA 2.26E-06
vg0142683571 sf0142682527 1 42683571 NA 2.78E-06
vg0226057933 sf0226052064 2 26057933 NA 2.99E-06
vg0410126465 sf0410117162 4 10126465 NA 3.32E-06
vg0909731506 sf0909730505 9 9731506 NA 3.78E-06