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
vg0719067465 sf0719066472 7 19067465 7.39E-20 5.18E-18
vg0719006525 sf0719005532 7 19006525 7.56E-20 4.72E-18
vg0406192421 sf0406187861 4 6192421 5.76E-12 6.77E-09
vg0228933475 sf0228927606 2 28933475 1.15E-11 1.80E-07
vg0719049384 sf0719048391 7 19049384 3.46E-11 8.40E-15
vg0719040385 sf0719039392 7 19040385 8.53E-11 8.63E-16
vg1100694812 sf1100693815 11 694812 8.59E-11 7.06E-09
vg1101911438 sf1101910439 11 1911438 8.98E-11 5.22E-10
vg0228803071 sf0228797202 2 28803071 1.11E-10 1.55E-07
vg0707738691 sf0707737696 7 7738691 1.82E-10 6.14E-09
vg0417642687 sf0417470728 4 17642687 3.31E-10 2.95E-07
vg0809442889 sf0809441893 8 9442889 1.51E-09 1.95E-07
vg1213429246 sf1213426584 12 13429246 1.55E-09 3.17E-07
vg1107392564 sf1107388309 11 7392564 2.57E-09 3.44E-07
vg0218608139 sf0218602270 2 18608139 2.59E-09 2.77E-07
vg0428739520 sf0428554372 4 28739520 9.01E-09 1.86E-07
vg1017997693 sf1017926465 10 17997693 5.55E-08 1.48E-08
vg0610494475 sf0610493476 6 10494475 6.36E-08 3.58E-06
vg1002266462 sf1002265439 10 2266462 1.16E-07 NA
vg0700550440 sf0700549440 7 550440 2.22E-07 1.20E-07
vg0124647921 sf0124646877 1 24647921 5.69E-07 4.18E-08
vg0708709394 sf0708708399 7 8709394 8.56E-07 6.49E-08
vg0126364837 sf0126363793 1 26364837 1.14E-06 3.50E-07
vg0329561125 sf0329554165 3 29561125 NA 2.02E-08
vg0312684585 sf0312683303 3 12684585 NA 1.55E-07
vg0207355509 sf0207355509 2 7355509 NA 2.99E-07