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 mr1252 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
vg0401719938 sf0401715487 4 1719938 1.89E-13 3.34E-08
vg0130736176 sf0130735132 1 30736176 4.29E-13 1.14E-08
vg0400132403 sf0400131403 4 132403 9.60E-13 3.36E-09
vg0428761895 sf0428576746 4 28761895 5.97E-11 NA
vg0431611553 sf0431426448 4 31611553 6.73E-11 NA
vg0112986526 sf0112985500 1 12986526 7.51E-11 NA
vg0723551233 sf0723550240 7 23551233 7.94E-11 4.46E-06
vg0424149847 sf0423964708 4 24149847 1.79E-10 3.45E-06
vg0402290555 sf0402286150 4 2290555 2.38E-09 2.78E-06
vg0432523363 sf0432338255 4 32523363 1.54E-08 4.15E-06
vg0335947825 sf0335940694 3 35947825 2.10E-08 8.58E-06
vg0614838575 sf0614837576 6 14838575 2.75E-08 2.38E-06
vg0800207863 sf0800206863 8 207863 4.65E-08 4.18E-06
vg0132744722 sf0132743678 1 32744722 4.87E-08 4.40E-06
vg0918876795 sf0918875795 9 18876795 4.91E-08 9.48E-07
vg0223422615 sf0223416746 2 23422615 9.83E-08 3.41E-06
vg0317321849 sf0317320659 3 17321849 1.31E-07 8.42E-06
vg0916030541 sf0916029540 9 16030541 NA 4.75E-07
vg0601365150 sf0601364151 6 1365150 NA 7.07E-07
vg0601409744 sf0601408745 6 1409744 NA 8.69E-07
vg0520296343 sf0520233816 5 20296343 NA 1.17E-06
vg0225142897 sf0225137028 2 25142897 NA 1.32E-06
vg0726684254 sf0726683260 7 26684254 NA 1.41E-06
vg1206196271 sf1206195162 12 6196271 NA 2.56E-06
vg0317442397 sf0317441179 3 17442397 NA 3.22E-06