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 mr1549 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
vg0705453437 sf0705452438 7 5453437 5.82E-74 6.29E-29
vg0705417443 sf0705416444 7 5417443 9.85E-74 5.15E-29
vg0719701370 sf0719700377 7 19701370 8.62E-48 1.29E-06
vg0717004102 sf0717003109 7 17004102 3.14E-47 1.56E-08
vg0728359154 sf0728358162 7 28359154 4.08E-46 NA
vg0701513997 sf0701512997 7 1513997 6.30E-46 NA
vg0716595668 sf0716594675 7 16595668 6.72E-46 1.04E-08
vg0622627045 sf0622626048 6 22627045 4.51E-44 1.15E-07
vg1226720029 sf1226686427 12 26720029 3.25E-42 2.15E-07
vg0101086387 sf0101085387 1 1086387 1.94E-41 2.68E-07
vg0413012466 sf0413003176 4 13012466 1.27E-39 8.82E-08
vg0137992319 sf0137991276 1 37992319 3.03E-37 1.43E-07
vg0823591909 sf0823589195 8 23591909 8.90E-35 2.51E-07
vg0819139396 sf0819136683 8 19139396 3.62E-33 1.50E-06
vg0705438489 sf0705437490 7 5438489 NA 3.02E-21
vg0412966608 sf0412957319 4 12966608 NA 9.20E-10
vg0826601883 sf0826599169 8 26601883 NA 2.83E-09
vg0401701969 sf0401697518 4 1701969 NA 8.58E-09
vg0401291884 sf0401287434 4 1291884 NA 1.79E-08
vg0909595977 sf0909594976 9 9595977 NA 2.19E-08
vg0909586409 sf0909585408 9 9586409 NA 2.46E-08
vg1206397770 sf1206396660 12 6397770 NA 3.72E-08
vg1020568417 sf1020496896 10 20568417 NA 4.29E-08
vg0210667883 sf0210667881 2 10667883 NA 5.81E-08
vg0404517518 sf0404513121 4 4517518 NA 1.03E-07
vg1000766238 sf1000765214 10 766238 NA 1.43E-07
vg0429645134 sf0429460002 4 29645134 NA 1.52E-07
vg0705295921 sf0705294922 7 5295921 NA 1.61E-07
vg0808191687 sf0808190691 8 8191687 NA 1.89E-07
vg0601368496 sf0601367497 6 1368496 NA 1.98E-07
vg0401701856 sf0401697405 4 1701856 NA 2.16E-07
vg0500777407 sf0500777389 5 777407 NA 2.73E-07
vg0138594460 sf0138593417 1 38594460 NA 3.77E-07
vg1206398354 sf1206397244 12 6398354 NA 8.01E-07
vg0502914537 sf0502914513 5 2914537 NA 1.94E-06
vg0427825849 sf0427640709 4 27825849 NA 6.52E-06