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 mr1083 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
vg0717227488 sf0717226495 7 17227488 2.78E-17 4.44E-14
vg0719001862 sf0719000869 7 19001862 2.91E-16 1.58E-15
vg1214370012 sf1214367353 12 14370012 4.12E-16 2.21E-14
vg0216351953 sf0216346083 2 16351953 3.64E-15 5.09E-11
vg0217670144 sf0217664274 2 17670144 1.42E-14 1.60E-11
vg1217000030 sf1216993984 12 17000030 1.56E-14 1.48E-11
vg0613011415 sf0613010416 6 13011415 2.28E-13 2.84E-10
vg1101084213 sf1101083214 11 1084213 2.37E-12 5.98E-09
vg1210300519 sf1210297932 12 10300519 2.58E-12 7.14E-11
vg0323471529 sf0323469703 3 23471529 2.73E-12 4.82E-10
vg0315778980 sf0315777627 3 15778980 2.78E-12 3.47E-10
vg0613034657 sf0613033658 6 13034657 3.80E-12 5.35E-09
vg0428334488 sf0428149346 4 28334488 4.23E-12 7.14E-10
vg1201578984 sf1201577984 12 1578984 4.68E-12 6.13E-10
vg0623192972 sf0623191975 6 23192972 4.80E-12 1.15E-09
vg0719833084 sf0719832091 7 19833084 7.01E-12 1.15E-09
vg1201579614 sf1201578614 12 1579614 8.44E-12 3.91E-09
vg0429428460 sf0429243327 4 29428460 2.55E-11 1.94E-09
vg0305696086 sf0305695086 3 5696086 8.27E-11 1.85E-09
vg1201356688 sf1201355688 12 1356688 1.04E-10 8.82E-10
vg0610070340 sf0610069341 6 10070340 3.81E-10 7.59E-09
vg0305696088 sf0305695088 3 5696088 4.47E-10 4.57E-09
vg0719001860 sf0719000867 7 19001860 9.96E-09 3.49E-07
vg1214952447 sf1214949789 12 14952447 1.46E-06 NA