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 mr1145 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
vg0719006525 sf0719005532 7 19006525 1.67E-16 1.66E-16
vg0719135307 sf0719134314 7 19135307 8.93E-11 8.92E-11
vg0719199004 sf0719198011 7 19199004 6.27E-10 6.26E-10
vg0107214556 sf0107213556 1 7214556 4.93E-09 4.93E-09
vg0700416280 sf0700415280 7 416280 1.32E-08 1.32E-08
vg0912061274 sf0912060273 9 12061274 2.28E-08 2.28E-08
vg0408294706 sf0408289980 4 8294706 1.23E-07 1.23E-07
vg0124225721 sf0124224677 1 24225721 1.85E-07 1.85E-07
vg0230093704 sf0230087835 2 30093704 3.42E-07 3.42E-07
vg0309326904 sf0309325840 3 9326904 4.16E-07 4.16E-07
vg0419905339 sf0419733375 4 19905339 4.71E-07 4.71E-07
vg0419763927 sf0419591962 4 19763927 4.91E-07 4.91E-07
vg0419912063 sf0419740099 4 19912063 1.10E-06 1.10E-06
vg0702575490 sf0702574491 7 2575490 1.49E-06 1.49E-06
vg0517737761 sf0517677402 5 17737761 2.28E-06 2.28E-06
vg0200846970 sf0200846970 2 846970 2.63E-06 2.63E-06
vg0815150136 sf0815147422 8 15150136 2.71E-06 2.71E-06
vg0105785581 sf0105784581 1 5785581 2.81E-06 2.81E-06
vg0517797635 sf0517737121 5 17797635 3.69E-06 3.69E-06
vg0907121871 sf0907120871 9 7121871 3.72E-06 3.72E-06
vg0233083685 sf0233077816 2 33083685 3.84E-06 3.84E-06
vg0810682742 sf0810681746 8 10682742 8.77E-06 8.77E-06