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 mr1908 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
vg0123673583 sf0123672539 1 23673583 4.30E-13 1.29E-06
vg0307000761 sf0306999759 3 7000761 7.05E-11 NA
vg1126520434 sf1126048849 11 26520434 1.79E-10 NA
vg0222369167 sf0222363298 2 22369167 2.64E-10 1.38E-06
vg1126542743 sf1126071158 11 26542743 3.15E-10 4.74E-09
vg1127031755 sf1126560142 11 27031755 3.53E-10 2.19E-06
vg0516005213 sf0515947721 5 16005213 4.84E-09 NA
vg0333491106 sf0333483976 3 33491106 6.13E-09 4.05E-06
vg0222557366 sf0222551497 2 22557366 6.59E-09 4.75E-07
vg1101145297 sf1101144298 11 1145297 8.39E-08 1.16E-06
vg0711375094 sf0711374100 7 11375094 1.68E-07 2.44E-06
vg0122413949 sf0122412904 1 22413949 2.10E-07 5.26E-06
vg0141059442 sf0141058399 1 41059442 2.88E-07 NA
vg1126403204 sf1125931617 11 26403204 9.67E-07 2.21E-06