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 mr1203 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 7.17E-183 1.83E-45
vg0411344776 sf0411335479 4 11344776 4.64E-138 5.34E-06
vg1017228554 sf1017157327 10 17228554 2.66E-134 7.49E-07
vg0307375905 sf0307374903 3 7375905 2.34E-132 9.78E-06
vg0122867992 sf0122866948 1 22867992 3.90E-131 1.00E-08
vg0822652220 sf0822649507 8 22652220 2.94E-113 2.26E-08
vg0807746257 sf0807745261 8 7746257 1.06E-112 1.48E-06
vg0406521772 sf0406517215 4 6521772 NA 2.23E-18
vg0407565317 sf0407560586 4 7565317 NA 4.49E-13
vg0411637990 sf0411628696 4 11637990 NA 2.87E-12
vg0406532594 sf0406528037 4 6532594 NA 7.40E-12
vg0406289584 sf0406285024 4 6289584 NA 8.06E-12
vg0817329442 sf0817326728 8 17329442 NA 1.08E-10
vg0406526167 sf0406521610 4 6526167 NA 3.44E-09
vg0806743013 sf0806742018 8 6743013 NA 6.80E-09
vg0233648100 sf0233642231 2 33648100 NA 7.31E-09
vg0406449684 sf0406445127 4 6449684 NA 7.91E-09
vg1012004873 sf1011933688 10 12004873 NA 1.39E-08
vg0912877788 sf0912876787 9 12877788 NA 1.83E-08
vg1209878209 sf1209875619 12 9878209 NA 2.17E-08
vg0812764718 sf0812762543 8 12764718 NA 3.23E-08
vg0233663084 sf0233657215 2 33663084 NA 3.35E-08
vg0406527348 sf0406522791 4 6527348 NA 6.01E-08
vg1216582806 sf1216580099 12 16582806 NA 7.80E-08
vg1216535929 sf1216533222 12 16535929 NA 7.91E-08
vg0420171320 sf0419999358 4 20171320 NA 8.90E-07
vg1000756369 sf1000755345 10 756369 NA 2.25E-06