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 mr1023 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 3.94E-49 1.20E-23
vg1210709343 sf1210706756 12 10709343 1.20E-39 1.93E-19
vg1223872806 sf1223839259 12 23872806 5.07E-30 1.79E-06
vg1223827289 sf1223793742 12 23827289 1.82E-28 1.05E-06
vg1213439429 sf1213436767 12 13439429 1.76E-19 9.79E-06
vg1017701671 sf1017630444 10 17701671 7.34E-19 NA
vg0217462843 sf0217456973 2 17462843 1.73E-15 7.78E-07
vg1215956521 sf1215953817 12 15956521 6.36E-14 2.78E-06
vg1216192507 sf1216189803 12 16192507 2.75E-13 5.01E-12
vg1215916353 sf1215913649 12 15916353 8.38E-13 5.67E-07
vg1216680785 sf1216674739 12 16680785 1.84E-12 1.01E-06
vg1215237966 sf1215235263 12 15237966 1.31E-11 2.90E-06
vg1207742957 sf1207740363 12 7742957 1.79E-11 8.52E-09
vg0526374490 sf0526311853 5 26374490 2.35E-11 5.73E-07
vg0216344341 sf0216338471 2 16344341 4.56E-10 4.18E-07
vg1214847524 sf1214844865 12 14847524 7.49E-09 9.09E-07
vg1217104604 sf1217098559 12 17104604 NA 1.84E-07
vg1214626036 sf1214623376 12 14626036 NA 5.86E-07
vg1216132874 sf1216130170 12 16132874 NA 7.67E-07
vg0207793784 sf0207793783 2 7793784 NA 1.36E-06
vg0404944968 sf0404940407 4 4944968 NA 1.63E-06
vg0230033957 sf0230028088 2 30033957 NA 2.78E-06
vg0403926001 sf0403921607 4 3926001 NA 2.94E-06
vg0614455471 sf0614454472 6 14455471 NA 8.99E-06