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 mr1135 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
vg0137929846 sf0137928803 1 37929846 1.34E-117 5.45E-28
vg0137930974 sf0137929931 1 37930974 8.24E-117 4.42E-28
vg1119431785 sf1118965473 11 19431785 7.70E-91 2.64E-07
vg1119344402 sf1118878090 11 19344402 4.27E-89 1.98E-07
vg0107563270 sf0107562270 1 7563270 4.19E-86 NA
vg1111472931 sf1111467248 11 11472931 4.57E-85 NA
vg1017577102 sf1017505875 10 17577102 7.71E-85 5.67E-07
vg1219118839 sf1219090275 12 19118839 4.06E-84 1.53E-07
vg1017579556 sf1017508329 10 17579556 5.29E-84 3.58E-07
vg1227310775 sf1227277175 12 27310775 6.53E-81 1.74E-06
vg1116636322 sf1116171200 11 16636322 1.83E-80 1.28E-07
vg1225983988 sf1225950382 12 25983988 4.22E-76 NA
vg0108147243 sf0108146243 1 8147243 NA 6.99E-09
vg0803630208 sf0803629211 8 3630208 NA 1.97E-07
vg0630161553 sf0630160555 6 30161553 NA 4.89E-07
vg0138161332 sf0138160289 1 38161332 NA 5.52E-07
vg0812088715 sf0812087720 8 12088715 NA 1.61E-06
vg0138183041 sf0138181998 1 38183041 NA 1.62E-06
vg0812112372 sf0812111377 8 12112372 NA 2.67E-06
vg1117420010 sf1116953864 11 17420010 NA 4.24E-06
vg1212214384 sf1212211722 12 12214384 NA 4.74E-06