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 mr1204 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
vg0130736176 sf0130735132 1 30736176 1.00E-10 2.47E-10
vg0128530844 sf0128529799 1 28530844 5.96E-10 7.65E-06
vg0130644853 sf0130643809 1 30644853 9.48E-10 5.13E-10
vg0130623883 sf0130622839 1 30623883 5.48E-09 NA
vg1009283499 sf1009212320 10 9283499 2.01E-08 6.17E-07
vg0610452215 sf0610451216 6 10452215 3.69E-08 NA
vg1200418022 sf1200417022 12 418022 5.99E-08 1.50E-06
vg0131493846 sf0131492802 1 31493846 7.85E-08 NA
vg0112986526 sf0112985500 1 12986526 2.18E-07 4.65E-06
vg1214199203 sf1214196543 12 14199203 2.19E-07 2.02E-07
vg0322532678 sf0322531167 3 22532678 4.54E-07 NA
vg0115899007 sf0115897981 1 15899007 3.95E-06 4.13E-06
vg0405975125 sf0405970566 4 5975125 7.08E-06 9.06E-07
vg0432523363 sf0432338255 4 32523363 9.76E-06 4.61E-06
vg0916030541 sf0916029540 9 16030541 NA 3.29E-07
vg0402172542 sf0402168137 4 2172542 NA 1.98E-06
vg1214678248 sf1214675587 12 14678248 NA 2.08E-06
vg0132938965 sf0132937921 1 32938965 NA 3.68E-06
vg0427084332 sf0426899204 4 27084332 NA 4.90E-06
vg0805469573 sf0805468576 8 5469573 NA 6.47E-06
vg0433011573 sf0432826459 4 33011573 NA 7.79E-06
vg1214198276 sf1214195616 12 14198276 NA 7.86E-06