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 mr1489 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 5.40E-28 6.35E-17
vg1210709343 sf1210706756 12 10709343 3.87E-24 1.61E-14
vg1209245522 sf1209242931 12 9245522 7.73E-24 8.06E-15
vg1223872806 sf1223839259 12 23872806 1.02E-16 7.23E-06
vg1212938220 sf1212935559 12 12938220 9.97E-16 7.76E-09
vg1017701671 sf1017630444 10 17701671 1.75E-13 NA
vg1223876846 sf1223843299 12 23876846 3.01E-13 9.96E-08
vg0526374490 sf0526311853 5 26374490 3.78E-13 7.40E-10
vg0317164649 sf0317163459 3 17164649 9.11E-12 7.77E-08
vg0315495240 sf0315493887 3 15495240 1.33E-11 1.46E-07
vg0921645479 sf0921644998 9 21645479 3.31E-11 9.13E-08
vg1215956521 sf1215953817 12 15956521 7.00E-11 5.75E-07
vg1216192507 sf1216189803 12 16192507 1.34E-10 7.80E-10
vg0706671410 sf0706670415 7 6671410 6.89E-08 2.69E-07
vg1207570300 sf1207567705 12 7570300 2.49E-07 7.72E-07
vg1220251034 sf1220222476 12 20251034 3.39E-07 3.61E-07
vg1217652673 sf1217646628 12 17652673 6.70E-07 1.18E-06
vg1004191480 sf1004146728 10 4191480 9.40E-07 7.18E-07
vg1114153307 sf1113689628 11 14153307 NA 7.53E-08
vg1218760084 sf1218731519 12 18760084 NA 1.12E-07
vg1108497933 sf1108492543 11 8497933 NA 4.95E-07
vg1214647200 sf1214644540 12 14647200 NA 5.31E-07
vg0230033957 sf0230028088 2 30033957 NA 7.24E-07
vg1200191651 sf1200190651 12 191651 NA 6.75E-06