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 5.08E-202 1.75E-52
vg0406417983 sf0406413423 4 6417983 4.31E-184 2.24E-33
vg0406577150 sf0406572593 4 6577150 4.71E-160 5.11E-28
vg0411344776 sf0411335479 4 11344776 1.55E-147 NA
vg0307375905 sf0307374903 3 7375905 2.43E-143 NA
vg0122842459 sf0122841415 1 22842459 1.39E-141 NA
vg1017440840 sf1017369613 10 17440840 1.74E-140 NA
vg0406575363 sf0406570806 4 6575363 8.21E-139 5.23E-09
vg0406521772 sf0406517215 4 6521772 NA 3.35E-18
vg0407565723 sf0407560992 4 7565723 NA 2.51E-15
vg0406362113 sf0406357553 4 6362113 NA 4.08E-12
vg0406532594 sf0406528037 4 6532594 NA 5.94E-12
vg0406489536 sf0406484979 4 6489536 NA 2.85E-11
vg0411637990 sf0411628696 4 11637990 NA 1.35E-10
vg0406463663 sf0406459106 4 6463663 NA 2.70E-10
vg1216555105 sf1216552398 12 16555105 NA 6.03E-10
vg0506806644 sf0506806586 5 6806644 NA 3.67E-09
vg0817327521 sf0817324807 8 17327521 NA 4.09E-09
vg0506784564 sf0506784506 5 6784564 NA 6.70E-09
vg0125080782 sf0125079738 1 25080782 NA 2.83E-08
vg0222719698 sf0222713829 2 22719698 NA 3.17E-08
vg0715843159 sf0715842166 7 15843159 NA 5.66E-08
vg1105865316 sf1105861068 11 5865316 NA 1.16E-07
vg1216568179 sf1216565472 12 16568179 NA 1.38E-07
vg0400744237 sf0400743236 4 744237 NA 1.40E-07
vg0313206866 sf0313205584 3 13206866 NA 1.82E-07
vg0223162978 sf0223157109 2 23162978 NA 2.09E-07
vg1216532158 sf1216529451 12 16532158 NA 2.25E-07
vg0412144864 sf0412135575 4 12144864 NA 2.25E-07
vg1112804853 sf1112341174 11 12804853 NA 2.59E-07
vg1216524512 sf1216521805 12 16524512 NA 5.05E-07