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
vg1215869969 sf1215867265 12 15869969 2.13E-165 3.17E-54
vg1215968758 sf1215966054 12 15968758 1.03E-156 1.85E-51
vg1210219854 sf1210217266 12 10219854 1.59E-88 1.45E-07
vg1210348009 sf1210345422 12 10348009 6.89E-86 7.89E-08
vg1212938220 sf1212935559 12 12938220 3.33E-74 1.56E-08
vg1224007541 sf1223973994 12 24007541 4.59E-73 NA
vg0621221946 sf0621220949 6 21221946 8.24E-72 3.24E-06
vg1215871396 sf1215868692 12 15871396 NA 3.15E-26
vg1215970855 sf1215968151 12 15970855 NA 5.54E-14
vg1215966147 sf1215963443 12 15966147 NA 1.32E-12
vg0610620315 sf0610619316 6 10620315 NA 1.91E-11
vg1215976560 sf1215973856 12 15976560 NA 7.00E-11
vg1216075902 sf1216073198 12 16075902 NA 1.94E-10
vg1215916036 sf1215913332 12 15916036 NA 2.76E-10
vg1215886190 sf1215883486 12 15886190 NA 3.06E-09
vg1216165822 sf1216163118 12 16165822 NA 9.02E-09
vg1216492299 sf1216489592 12 16492299 NA 1.04E-08
vg1216345874 sf1216343170 12 16345874 NA 2.04E-08
vg1216156576 sf1216153872 12 16156576 NA 2.72E-08
vg1223877720 sf1223844173 12 23877720 NA 3.98E-08
vg0102116003 sf0102115003 1 2116003 NA 4.31E-08
vg0901048761 sf0901047761 9 1048761 NA 8.34E-08
vg0218132013 sf0218126144 2 18132013 NA 9.88E-08
vg1216087745 sf1216085041 12 16087745 NA 1.53E-07
vg1216020353 sf1216017649 12 16020353 NA 2.19E-07
vg1215221275 sf1215218572 12 15221275 NA 2.58E-07
vg1216273753 sf1216271049 12 16273753 NA 3.18E-07
vg1216567137 sf1216564430 12 16567137 NA 3.18E-07