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 mr1613 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
vg0406526555 sf0406521998 4 6526555 1.98E-119 2.46E-28
vg0406592386 sf0406587830 4 6592386 3.37E-94 4.06E-17
vg1017228554 sf1017157327 10 17228554 4.68E-90 3.93E-06
vg0411344776 sf0411335479 4 11344776 2.10E-88 NA
vg0122833397 sf0122832353 1 22833397 2.14E-87 NA
vg0307375905 sf0307374903 3 7375905 3.99E-87 NA
vg1122454208 sf1121988079 11 22454208 1.58E-84 5.73E-07
vg0614107939 sf0614106940 6 14107939 2.83E-83 2.92E-08
vg0412479470 sf0412470185 4 12479470 3.97E-78 4.25E-06
vg0122261348 sf0122260303 1 22261348 5.46E-78 4.36E-06
vg0222726027 sf0222720158 2 22726027 NA 1.26E-09
vg0222746050 sf0222740181 2 22746050 NA 5.11E-09
vg0406521772 sf0406517215 4 6521772 NA 5.37E-09
vg0406489536 sf0406484979 4 6489536 NA 1.97E-08
vg0233608236 sf0233602367 2 33608236 NA 1.36E-07
vg1209877862 sf1209875272 12 9877862 NA 4.45E-07
vg0406578851 sf0406574294 4 6578851 NA 6.07E-07
vg0406212312 sf0406207752 4 6212312 NA 1.02E-06
vg0806593377 sf0806592382 8 6593377 NA 3.75E-06
vg0801962016 sf0801961019 8 1962016 NA 4.60E-06
vg0112184246 sf0112183220 1 12184246 NA 4.73E-06