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 mr1188 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
vg1108660993 sf1108655603 11 8660993 1.03E-16 6.89E-08
vg0235365192 sf0235359323 2 35365192 7.16E-16 4.07E-09
vg1108146599 sf1108142344 11 8146599 7.97E-16 8.54E-10
vg0203671161 sf0203671158 2 3671161 7.09E-15 5.17E-06
vg0815897027 sf0815894313 8 15897027 1.20E-13 1.90E-08
vg0319091202 sf0319089962 3 19091202 1.45E-13 2.41E-06
vg0622020773 sf0622019776 6 22020773 1.15E-12 1.53E-07
vg0630551197 sf0630550199 6 30551197 1.98E-12 9.14E-07
vg0815897030 sf0815894316 8 15897030 2.59E-12 4.55E-08
vg0617228589 sf0617227592 6 17228589 6.19E-12 1.09E-06
vg0918661273 sf0918660272 9 18661273 6.59E-12 3.35E-08
vg1100538307 sf1100537310 11 538307 3.11E-11 1.54E-06
vg0523609640 sf0523547061 5 23609640 5.45E-11 4.40E-07
vg1007891011 sf1007906621 10 7891011 1.67E-10 1.35E-08
vg0319058704 sf0319057464 3 19058704 4.42E-10 7.69E-07
vg1004252046 sf1004268584 10 4252046 8.60E-10 2.24E-07
vg0823397143 sf0823394430 8 23397143 1.37E-09 1.82E-06
vg1104321369 sf1104317271 11 4321369 1.14E-06 1.26E-06
vg0433760044 sf0433574924 4 33760044 NA 1.36E-08
vg0523780082 sf0523717503 5 23780082 NA 1.29E-07
vg1214643661 sf1214641001 12 14643661 NA 2.94E-07
vg1114456299 sf1113992616 11 14456299 NA 3.92E-07
vg0901691244 sf0901690244 9 1691244 NA 8.93E-07
vg0804318898 sf0804317901 8 4318898 NA 9.28E-07
vg0117098473 sf0117097427 1 17098473 NA 1.36E-06