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 mr1490 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
vg1215976937 sf1215974233 12 15976937 4.78E-164 1.09E-57
vg1215965939 sf1215963235 12 15965939 5.21E-164 5.17E-58
vg1215968758 sf1215966054 12 15968758 1.30E-160 5.23E-58
vg1210219854 sf1210217266 12 10219854 1.99E-80 NA
vg1210161923 sf1210159334 12 10161923 1.06E-73 9.78E-07
vg1224007541 sf1223973994 12 24007541 1.68E-69 NA
vg0217071443 sf0217065573 2 17071443 4.45E-63 NA
vg1213439429 sf1213436767 12 13439429 8.59E-60 NA
vg1212938220 sf1212935559 12 12938220 1.61E-58 1.29E-06
vg1223876846 sf1223843299 12 23876846 2.86E-52 2.72E-07
vg1215871396 sf1215868692 12 15871396 NA 9.29E-27
vg1215970855 sf1215968151 12 15970855 NA 2.56E-13
vg1215871822 sf1215869118 12 15871822 NA 6.02E-12
vg0610620315 sf0610619316 6 10620315 NA 1.25E-08
vg1216535261 sf1216532554 12 16535261 NA 2.20E-08
vg1216278472 sf1216275768 12 16278472 NA 3.54E-08
vg1216413575 sf1216410868 12 16413575 NA 6.88E-08
vg1216151894 sf1216149190 12 16151894 NA 8.06E-08
vg1215962650 sf1215959946 12 15962650 NA 1.02E-07
vg1216471161 sf1216468454 12 16471161 NA 3.74E-07
vg1215223836 sf1215221133 12 15223836 NA 6.30E-07
vg1215261373 sf1215258671 12 15261373 NA 8.98E-07
vg0432732386 sf0432547273 4 32732386 NA 1.10E-06
vg1104366840 sf1104362742 11 4366840 NA 1.16E-06
vg0401349008 sf0401344558 4 1349008 NA 1.89E-06
vg0710900579 sf0710899585 7 10900579 NA 2.00E-06
vg1018220310 sf1018148869 10 18220310 NA 2.24E-06