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 mr1310 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
vg1000576410 sf1000575386 10 576410 1.42E-35 9.92E-24
vg0528039299 sf0527976654 5 28039299 1.03E-15 2.11E-08
vg1128844615 sf1128321394 11 28844615 1.32E-13 3.31E-06
vg1128846586 sf1128323365 11 28846586 1.32E-13 3.89E-07
vg1008205459 sf1008134321 10 8205459 2.85E-13 7.72E-06
vg1008206965 sf1008135827 10 8206965 5.42E-13 4.97E-06
vg1010974418 sf1010903238 10 10974418 1.18E-11 NA
vg0328403714 sf0328396767 3 28403714 1.62E-08 1.37E-06
vg1000770027 sf1000769003 10 770027 9.91E-08 3.68E-06
vg1125046291 sf1124580131 11 25046291 NA 4.57E-11
vg1000736288 sf1000735264 10 736288 NA 2.02E-10
vg1125103445 sf1124637285 11 25103445 NA 1.81E-08
vg0301337606 sf0301336604 3 1337606 NA 9.40E-08
vg1125118463 sf1124652303 11 25118463 NA 1.08E-07
vg0327915031 sf0327908085 3 27915031 NA 2.13E-07
vg1125085942 sf1124619782 11 25085942 NA 2.94E-07
vg0611078070 sf0611077071 6 11078070 NA 2.25E-06
vg0826744653 sf0826741939 8 26744653 NA 2.40E-06
vg1000973578 sf1000972554 10 973578 NA 3.59E-06
vg1006275829 sf1006291452 10 6275829 NA 4.27E-06