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 mr1076 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 4.79E-26 4.78E-26
vg0912061274 sf0912060273 9 12061274 5.77E-14 5.77E-14
vg0700416280 sf0700415280 7 416280 2.86E-13 2.86E-13
vg0107214556 sf0107213556 1 7214556 3.16E-13 3.16E-13
vg0907121871 sf0907120871 9 7121871 1.45E-11 1.45E-11
vg0811122650 sf0811121655 8 11122650 2.02E-11 2.02E-11
vg0408294186 sf0408289460 4 8294186 2.01E-10 2.01E-10
vg1101911438 sf1101910439 11 1911438 2.63E-10 2.63E-10
vg1020494793 sf1020423272 10 20494793 3.75E-10 3.75E-10
vg0422855440 sf0422670325 4 22855440 8.97E-10 8.97E-10
vg1217240367 sf1217234322 12 17240367 1.08E-09 1.08E-09
vg0124676100 sf0124675056 1 24676100 1.21E-09 1.21E-09
vg0200846970 sf0200846970 2 846970 1.28E-09 1.28E-09
vg0719051231 sf0719050238 7 19051231 1.43E-09 1.43E-09
vg0719135307 sf0719134314 7 19135307 2.45E-09 2.45E-09
vg0420062824 sf0419890860 4 20062824 2.77E-09 2.77E-09
vg1208212616 sf1208210021 12 8212616 5.01E-09 5.01E-09
vg0514963706 sf0514906249 5 14963706 5.42E-09 5.42E-09
vg0218519344 sf0218513475 2 18519344 6.99E-09 6.99E-09
vg0113185672 sf0113184646 1 13185672 7.21E-09 7.21E-09
vg0625385908 sf0625384911 6 25385908 7.81E-09 7.81E-09
vg0223262220 sf0223256351 2 23262220 2.47E-06 2.47E-06