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 mr1437 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
vg0719007567 sf0719006574 7 19007567 1.77E-24 2.38E-18
vg0719011406 sf0719010413 7 19011406 1.62E-23 1.74E-18
vg0719140489 sf0719139496 7 19140489 1.88E-15 8.24E-09
vg0717227488 sf0717226495 7 17227488 1.95E-13 8.27E-09
vg1201625779 sf1201624779 12 1625779 2.09E-12 7.56E-06
vg1201545939 sf1201544939 12 1545939 2.75E-12 6.06E-08
vg0323471529 sf0323469703 3 23471529 5.44E-12 1.66E-06
vg0707706006 sf0707705011 7 7706006 5.58E-11 1.41E-06
vg0719003833 sf0719002840 7 19003833 1.12E-10 1.79E-06
vg1210300519 sf1210297932 12 10300519 2.54E-09 1.64E-06
vg0305260839 sf0305259839 3 5260839 3.63E-09 4.09E-06
vg0606529256 sf0606528257 6 6529256 2.60E-07 1.64E-06
vg1210504224 sf1210501637 12 10504224 1.16E-06 NA
vg0431597089 sf0431411984 4 31597089 1.42E-06 1.35E-06
vg1009396029 sf1009324850 10 9396029 1.95E-06 3.34E-06
vg1009450763 sf1009379584 10 9450763 2.18E-06 3.64E-07
vg1010596386 sf1010525207 10 10596386 2.41E-06 4.80E-06
vg1206187052 sf1206185943 12 6187052 2.72E-06 1.20E-06
vg0501722287 sf0501722271 5 1722287 4.01E-06 NA
vg1007460883 sf1007476506 10 7460883 4.71E-06 1.06E-06
vg0429231335 sf0429046192 4 29231335 4.74E-06 NA
vg0717285819 sf0717284826 7 17285819 4.82E-06 2.62E-06
vg0718985745 sf0718984752 7 18985745 5.14E-06 1.58E-09
vg0920282336 sf0920281855 9 20282336 7.00E-06 3.13E-06
vg1214119394 sf1214116734 12 14119394 7.74E-06 1.09E-06
vg0109413217 sf0109412193 1 9413217 NA 4.73E-06