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 mr1236 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
vg0217246451 sf0217240581 2 17246451 5.29E-19 4.26E-11
vg0216752739 sf0216746869 2 16752739 5.23E-18 2.72E-12
vg0216971299 sf0216965429 2 16971299 1.14E-17 2.83E-12
vg0216980968 sf0216975098 2 16980968 1.25E-16 2.00E-10
vg0106675404 sf0106674404 1 6675404 7.34E-15 4.32E-08
vg1114596727 sf1114133045 11 14596727 5.43E-14 9.14E-07
vg0216884223 sf0216878353 2 16884223 2.60E-13 1.32E-07
vg0900336793 sf0900335793 9 336793 3.59E-13 1.22E-06
vg0900337342 sf0900336342 9 337342 5.16E-13 2.91E-07
vg0217527253 sf0217521383 2 17527253 1.54E-12 1.57E-10
vg1207456492 sf1207453898 12 7456492 4.34E-11 9.03E-08
vg0106680441 sf0106679441 1 6680441 1.20E-09 4.21E-08
vg1214134657 sf1214131997 12 14134657 2.83E-09 4.30E-06
vg0721065888 sf0721064895 7 21065888 8.40E-09 NA
vg0106715630 sf0106714630 1 6715630 2.01E-07 2.78E-09
vg0826412433 sf0826409719 8 26412433 1.45E-06 1.37E-06
vg0215664387 sf0215658517 2 15664387 2.13E-06 3.60E-06
vg0217292905 sf0217287035 2 17292905 7.97E-06 2.96E-06
vg0518984986 sf0518922470 5 18984986 NA 2.11E-08
vg0400674565 sf0400673564 4 674565 NA 2.03E-06
vg1125578856 sf1125112695 11 25578856 NA 2.13E-06
vg1214794309 sf1214791650 12 14794309 NA 4.15E-06
vg1001344040 sf1001343017 10 1344040 NA 7.36E-06