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 mr1498 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
vg0106730666 sf0106729666 1 6730666 7.83E-49 5.55E-36
vg0106693749 sf0106692749 1 6693749 1.13E-47 1.49E-37
vg0105607941 sf0105606941 1 5607941 3.88E-23 3.22E-14
vg0106703618 sf0106702618 1 6703618 2.48E-22 2.84E-09
vg0107100004 sf0107099004 1 7100004 2.17E-20 2.81E-12
vg0106470262 sf0106469262 1 6470262 2.83E-18 1.20E-13
vg0105637070 sf0105636070 1 5637070 7.26E-18 1.94E-12
vg0105363790 sf0105362790 1 5363790 6.68E-16 2.83E-08
vg0105394768 sf0105393768 1 5394768 1.88E-15 1.86E-09
vg0108087881 sf0108086881 1 8087881 7.27E-15 1.48E-06
vg1222445672 sf1222412111 12 22445672 1.25E-12 NA
vg0106686529 sf0106685529 1 6686529 7.14E-12 3.21E-17
vg0106582661 sf0106581661 1 6582661 1.31E-09 2.36E-07
vg0105214835 sf0105213835 1 5214835 4.19E-09 4.96E-09
vg0106669651 sf0106668651 1 6669651 6.07E-09 2.32E-18
vg0106874407 sf0106873407 1 6874407 1.02E-08 6.22E-16
vg1000501724 sf1000500700 10 501724 2.59E-08 4.18E-09
vg1000475572 sf1000474548 10 475572 5.39E-08 1.82E-08
vg1125103431 sf1124637271 11 25103431 1.55E-07 2.19E-08
vg0106731234 sf0106730234 1 6731234 2.30E-07 5.98E-09
vg0105709551 sf0105708551 1 5709551 3.50E-07 3.02E-07
vg1125082946 sf1124616786 11 25082946 3.79E-07 2.05E-08
vg1125118463 sf1124652303 11 25118463 NA 3.12E-10
vg0107059016 sf0107058016 1 7059016 NA 2.66E-09
vg0106686584 sf0106685584 1 6686584 NA 4.13E-08
vg1125014870 sf1124548710 11 25014870 NA 5.39E-07
vg0419458305 sf0419286342 4 19458305 NA 6.13E-07
vg0804931252 sf0804930255 8 4931252 NA 8.85E-06