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 mr1085 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
vg0719053396 sf0719052403 7 19053396 2.95E-15 7.26E-16
vg0719006525 sf0719005532 7 19006525 4.31E-15 1.04E-15
vg0719063677 sf0719062684 7 19063677 4.59E-13 7.25E-17
vg0107214556 sf0107213556 1 7214556 1.28E-08 1.04E-07
vg0912061274 sf0912060273 9 12061274 1.98E-08 5.48E-08
vg0700416280 sf0700415280 7 416280 5.53E-08 5.22E-09
vg0419763927 sf0419591962 4 19763927 8.69E-07 1.66E-07
vg0907121871 sf0907120871 9 7121871 1.04E-06 6.94E-07
vg0408294186 sf0408289460 4 8294186 1.06E-06 7.07E-07
vg0203976342 sf0203976339 2 3976342 1.23E-06 6.63E-07
vg0702575490 sf0702574491 7 2575490 2.06E-06 3.18E-07
vg0820065663 sf0820062950 8 20065663 2.33E-06 7.22E-07
vg0230093704 sf0230087835 2 30093704 3.03E-06 2.16E-06
vg1214321077 sf1214318417 12 14321077 5.81E-06 1.93E-06
vg0422772120 sf0422587003 4 22772120 5.99E-06 1.93E-06
vg0810748562 sf0810747567 8 10748562 7.11E-06 4.62E-07
vg0200846970 sf0200846970 2 846970 7.64E-06 1.60E-06
vg0828401472 sf0828398758 8 28401472 NA 1.41E-08
vg0804028565 sf0804027568 8 4028565 NA 6.91E-07
vg0701436306 sf0701435306 7 1436306 NA 1.69E-06
vg0626936733 sf0626935736 6 26936733 NA 2.40E-06
vg0810682742 sf0810681746 8 10682742 NA 4.50E-06