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 mr1968 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
vg0808040055 sf0808039059 8 8040055 1.56E-28 1.05E-07
vg0823242788 sf0823240075 8 23242788 1.13E-27 3.22E-06
vg0808042725 sf0808041729 8 8042725 2.14E-27 1.32E-08
vg0205314016 sf0205314015 2 5314016 1.05E-26 NA
vg0628585588 sf0628584590 6 28585588 7.16E-26 NA
vg0726326130 sf0726325136 7 26326130 8.16E-26 NA
vg0142478677 sf0142477633 1 42478677 8.38E-26 1.68E-07
vg0205284721 sf0205284719 2 5284721 7.15E-24 4.97E-06
vg0235431697 sf0235425828 2 35431697 1.44E-21 5.19E-07
vg0707041646 sf0707040651 7 7041646 NA 2.14E-08
vg0428862203 sf0428677059 4 28862203 NA 6.52E-08
vg0234416765 sf0234410896 2 34416765 NA 8.50E-08
vg0507073939 sf0507073881 5 7073939 NA 1.49E-07
vg0502322336 sf0502322311 5 2322336 NA 4.86E-07
vg0805068918 sf0805067921 8 5068918 NA 6.54E-07
vg0718144985 sf0718143992 7 18144985 NA 7.40E-07
vg0805064264 sf0805063267 8 5064264 NA 8.02E-07
vg0605538242 sf0605537243 6 5538242 NA 1.22E-06
vg0719741206 sf0719740213 7 19741206 NA 1.50E-06
vg0417379902 sf0417207945 4 17379902 NA 1.65E-06
vg0101236707 sf0101235707 1 1236707 NA 2.66E-06
vg0100716547 sf0100715547 1 716547 NA 3.04E-06
vg0501457111 sf0501457095 5 1457111 NA 3.05E-06