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 mr1491 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 1.37E-54 1.17E-25
vg1210709343 sf1210706756 12 10709343 1.09E-41 1.51E-19
vg1223872806 sf1223839259 12 23872806 1.57E-33 3.72E-09
vg1017701671 sf1017630444 10 17701671 1.06E-20 6.10E-06
vg1213439429 sf1213436767 12 13439429 9.66E-20 NA
vg1017841259 sf1017770032 10 17841259 4.13E-19 2.03E-07
vg1214626805 sf1214624145 12 14626805 7.74E-17 2.37E-09
vg0526374490 sf0526311853 5 26374490 3.52E-16 1.05E-09
vg1216192507 sf1216189803 12 16192507 4.28E-16 1.42E-14
vg0317164649 sf0317163459 3 17164649 1.96E-15 5.93E-08
vg1215956521 sf1215953817 12 15956521 1.43E-13 6.29E-07
vg0921645479 sf0921644998 9 21645479 1.28E-12 1.72E-07
vg0216865447 sf0216859577 2 16865447 3.38E-12 1.08E-06
vg1215237966 sf1215235263 12 15237966 3.29E-11 3.42E-07
vg1207824599 sf1207822005 12 7824599 3.17E-10 3.38E-08
vg1114153307 sf1113689628 11 14153307 NA 3.59E-09
vg1214847524 sf1214844865 12 14847524 NA 1.10E-07
vg1214885319 sf1214882660 12 14885319 NA 1.20E-06
vg1214620813 sf1214618153 12 14620813 NA 1.55E-06
vg1004191692 sf1004146516 10 4191692 NA 1.70E-06
vg1117783091 sf1117316947 11 17783091 NA 2.28E-06
vg1215096337 sf1215093674 12 15096337 NA 3.06E-06