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 mr1099 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
vg0222743508 sf0222737639 2 22743508 2.78E-71 1.15E-41
vg0222724011 sf0222718142 2 22724011 5.00E-71 1.51E-42
vg0906971590 sf0906970590 9 6971590 6.93E-37 NA
vg0222679274 sf0222673405 2 22679274 4.70E-36 1.33E-11
vg1201581391 sf1201580391 12 1581391 3.58E-32 NA
vg0700414199 sf0700413199 7 414199 4.07E-32 NA
vg0524971409 sf0524908824 5 24971409 5.21E-31 1.92E-06
vg0500664660 sf0500664660 5 664660 9.77E-31 2.72E-06
vg0222725003 sf0222719134 2 22725003 7.21E-28 1.20E-16
vg1202206444 sf1202205443 12 2206444 1.27E-27 NA
vg1202275914 sf1202274914 12 2275914 6.93E-25 3.16E-06
vg0907026290 sf0907025290 9 7026290 1.13E-24 3.96E-06
vg0224552398 sf0224546529 2 24552398 NA 5.02E-11
vg0224832469 sf0224826600 2 24832469 NA 1.08E-10
vg0524972451 sf0524909866 5 24972451 NA 5.26E-08
vg0224791280 sf0224785411 2 24791280 NA 9.90E-08
vg0223663745 sf0223657876 2 23663745 NA 1.25E-07
vg0222623248 sf0222617379 2 22623248 NA 1.26E-07
vg0224003504 sf0223997635 2 24003504 NA 6.77E-07
vg0222681985 sf0222676116 2 22681985 NA 1.05E-06
vg0222735022 sf0222729153 2 22735022 NA 1.54E-06
vg0222558409 sf0222552540 2 22558409 NA 2.19E-06
vg0224775878 sf0224770009 2 24775878 NA 2.35E-06
vg0223736835 sf0223730966 2 23736835 NA 2.38E-06
vg0224246969 sf0224241100 2 24246969 NA 2.73E-06
vg0225102455 sf0225096586 2 25102455 NA 3.36E-06
vg0224878279 sf0224872410 2 24878279 NA 3.43E-06
vg0220758243 sf0220752375 2 20758243 NA 4.00E-06
vg0224242820 sf0224236951 2 24242820 NA 4.77E-06