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 mr1120 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
vg1009664258 sf1009593079 10 9664258 2.28E-11 9.25E-09
vg1006490817 sf1006506440 10 6490817 3.08E-11 3.81E-09
vg1007420713 sf1007436336 10 7420713 1.10E-10 4.16E-09
vg1007541987 sf1007557599 10 7541987 2.61E-10 1.26E-07
vg0501791123 sf0501791106 5 1791123 3.52E-10 1.25E-07
vg0407825687 sf0407820955 4 7825687 7.23E-10 9.97E-08
vg1222385548 sf1222351987 12 22385548 1.79E-09 3.13E-08
vg1005802319 sf1005818857 10 5802319 3.32E-09 4.64E-08
vg1008947841 sf1008876702 10 8947841 3.49E-09 5.17E-07
vg1005442099 sf1005458636 10 5442099 1.35E-08 1.04E-06
vg0724693113 sf0724692119 7 24693113 2.87E-08 7.38E-07
vg0826936491 sf0826933777 8 26936491 2.93E-08 2.89E-08
vg1221072081 sf1221038631 12 21072081 4.62E-08 1.55E-06
vg0604141656 sf0604140657 6 4141656 7.54E-08 7.71E-07
vg1006277345 sf1006292968 10 6277345 1.01E-07 7.25E-06
vg0120773756 sf0120772711 1 20773756 2.11E-07 2.48E-07
vg0810610033 sf0810609037 8 10610033 2.19E-07 1.20E-06
vg1215059927 sf1215057269 12 15059927 2.96E-07 4.96E-07
vg0329248379 sf0329241431 3 29248379 6.59E-07 1.64E-06
vg0415024546 sf0415015260 4 15024546 2.65E-06 NA
vg1108727668 sf1108722278 11 8727668 3.09E-06 NA
vg0221445039 sf0221439171 2 21445039 4.21E-06 NA
vg0719728074 sf0719727081 7 19728074 4.39E-06 4.67E-07
vg0910354924 sf0910353923 9 10354924 5.55E-06 3.75E-06
vg0335613340 sf0335606209 3 35613340 5.84E-06 4.00E-06
vg0618043063 sf0618042066 6 18043063 NA 2.28E-06