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 mr1486 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
vg1001438303 sf1001437280 10 1438303 7.32E-77 3.23E-35
vg1001432912 sf1001431889 10 1432912 3.41E-54 6.90E-13
vg0305127472 sf0305126474 3 5127472 1.30E-52 NA
vg1225029132 sf1224995585 12 25029132 3.39E-52 NA
vg1001242224 sf1001241201 10 1242224 8.58E-52 3.45E-10
vg0917940762 sf0917939761 9 17940762 7.14E-51 NA
vg0304643446 sf0304642448 3 4643446 6.95E-48 NA
vg1011329331 sf1011258151 10 11329331 1.80E-44 2.84E-07
vg1001244211 sf1001243188 10 1244211 NA 3.06E-19
vg1001245650 sf1001244627 10 1245650 NA 2.04E-18
vg1001363789 sf1001362766 10 1363789 NA 2.12E-16
vg1001406501 sf1001405478 10 1406501 NA 6.87E-15
vg1001457313 sf1001456290 10 1457313 NA 3.21E-13
vg1001393945 sf1001392922 10 1393945 NA 3.80E-11
vg1001405062 sf1001404039 10 1405062 NA 7.52E-11
vg1001213195 sf1001212172 10 1213195 NA 1.37E-10
vg1000297002 sf1000296002 10 297002 NA 9.02E-09
vg1219872223 sf1219843693 12 19872223 NA 1.07E-08
vg1002108639 sf1002107616 10 2108639 NA 1.40E-08
vg0314649425 sf0314648112 3 14649425 NA 5.98E-08
vg1001831505 sf1001830482 10 1831505 NA 9.03E-08
vg1002138376 sf1002137353 10 2138376 NA 1.19E-07
vg1002253792 sf1002252769 10 2253792 NA 1.22E-07
vg1011639148 sf1011567963 10 11639148 NA 1.59E-07
vg0420245925 sf0420073971 4 20245925 NA 2.13E-07
vg0707361067 sf0707360072 7 7361067 NA 7.09E-07
vg0324205406 sf0324203485 3 24205406 NA 7.71E-07
vg1219937863 sf1219909333 12 19937863 NA 9.65E-07
vg0909037704 sf0909036703 9 9037704 NA 1.12E-06
vg0505457754 sf0505457732 5 5457754 NA 1.22E-06
vg0812970658 sf0812968483 8 12970658 NA 1.32E-06