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 mr1623 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
vg1003025941 sf1003024918 10 3025941 5.56E-14 NA
vg1023134936 sf1023063408 10 23134936 1.25E-13 NA
vg0900837068 sf0900836068 9 837068 1.27E-13 NA
vg0303775288 sf0303774284 3 3775288 1.65E-13 NA
vg0907755322 sf0907754322 9 7755322 1.86E-13 NA
vg0103961186 sf0103960186 1 3961186 2.28E-12 8.32E-06
vg0202159140 sf0202159140 2 2159140 5.82E-12 3.46E-06
vg0920511311 sf0920510830 9 20511311 2.19E-11 NA
vg1218153803 sf1218125239 12 18153803 3.09E-11 5.00E-07
vg1101470341 sf1101469342 11 1470341 NA 3.58E-07
vg1101470344 sf1101469345 11 1470344 NA 1.27E-06
vg1112898481 sf1112434802 11 12898481 NA 3.03E-06
vg0521737035 sf0521674477 5 21737035 NA 3.86E-06
vg0115332952 sf0115331926 1 15332952 NA 3.90E-06
vg0208608994 sf0208608993 2 8608994 NA 5.32E-06