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 mr1672 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
vg1221632752 sf1221599299 12 21632752 2.91E-10 5.62E-08
vg1223453865 sf1223420325 12 23453865 6.62E-10 5.01E-09
vg1002436870 sf1002435847 10 2436870 1.45E-09 2.24E-06
vg0802773819 sf0802772822 8 2773819 2.68E-09 9.81E-07
vg0425841655 sf0425656521 4 25841655 4.69E-09 5.65E-06
vg1011167641 sf1011096461 10 11167641 3.70E-08 4.63E-06
vg0802774172 sf0802773175 8 2774172 5.09E-08 4.71E-07
vg0802171535 sf0802170538 8 2171535 5.15E-08 4.78E-06
vg0138349324 sf0138348281 1 38349324 5.76E-08 3.30E-06
vg0815150136 sf0815147422 8 15150136 6.38E-08 4.42E-07
vg0626942370 sf0626941373 6 26942370 3.02E-07 1.39E-06
vg1225842925 sf1225809319 12 25842925 3.58E-07 4.46E-07
vg0114587154 sf0114586128 1 14587154 6.52E-07 4.32E-06
vg0401637937 sf0401633486 4 1637937 1.14E-06 3.06E-06
vg1108744582 sf1108739192 11 8744582 2.16E-06 NA
vg1213485809 sf1213483147 12 13485809 2.49E-06 7.42E-07
vg1209753482 sf1209750892 12 9753482 2.49E-06 3.40E-06
vg0628044583 sf0628043585 6 28044583 2.67E-06 2.68E-06
vg0137487606 sf0137486563 1 37487606 3.45E-06 3.01E-06
vg0320153246 sf0320151757 3 20153246 NA 3.50E-06
vg1121797475 sf1121331352 11 21797475 NA 4.17E-06
vg0112570788 sf0112569762 1 12570788 NA 4.67E-06