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 mr1142 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
vg1215968758 sf1215966054 12 15968758 1.28E-54 1.29E-26
vg1210709343 sf1210706756 12 10709343 1.85E-42 5.17E-20
vg1223872806 sf1223839259 12 23872806 5.35E-33 2.74E-08
vg1223827289 sf1223793742 12 23827289 3.26E-31 2.18E-08
vg1017701671 sf1017630444 10 17701671 3.03E-21 3.58E-06
vg1213439429 sf1213436767 12 13439429 2.16E-20 NA
vg1017841259 sf1017770032 10 17841259 2.06E-19 9.42E-07
vg0526374490 sf0526311853 5 26374490 2.69E-17 3.24E-11
vg0217462843 sf0217456973 2 17462843 9.99E-17 5.62E-07
vg0317164649 sf0317163459 3 17164649 5.34E-15 2.50E-07
vg1216192507 sf1216189803 12 16192507 4.01E-14 5.42E-13
vg1215916353 sf1215913649 12 15916353 3.38E-13 6.65E-07
vg0921645479 sf0921644998 9 21645479 1.15E-12 6.24E-07
vg1215237966 sf1215235263 12 15237966 6.16E-12 9.13E-07
vg1210225671 sf1210223083 12 10225671 1.52E-11 1.04E-06
vg1207742957 sf1207740363 12 7742957 5.66E-11 1.39E-07
vg1214847524 sf1214844865 12 14847524 NA 8.01E-09
vg1217104604 sf1217098559 12 17104604 NA 1.11E-07
vg0413329049 sf0413319760 4 13329049 NA 1.88E-07
vg0216344351 sf0216338481 2 16344351 NA 4.29E-07
vg1216542145 sf1216539438 12 16542145 NA 8.04E-07
vg1114153307 sf1113689628 11 14153307 NA 9.39E-07
vg1215976836 sf1215974132 12 15976836 NA 1.31E-06