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 mr1526 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
vg0610608095 sf0610607096 6 10608095 5.09E-72 1.55E-18
vg0610642844 sf0610641845 6 10642844 3.67E-71 1.65E-19
vg0610458025 sf0610457026 6 10458025 2.97E-67 1.30E-18
vg0627249569 sf0627248572 6 27249569 5.20E-51 NA
vg0715903913 sf0715902920 7 15903913 3.95E-50 NA
vg0708450740 sf0708449745 7 8450740 2.71E-49 NA
vg0616950705 sf0616949708 6 16950705 3.54E-49 NA
vg0617631923 sf0617630926 6 17631923 1.29E-43 3.06E-07
vg0610422329 sf0610421330 6 10422329 NA 7.91E-10
vg0610763769 sf0610762770 6 10763769 NA 2.77E-09
vg0610014317 sf0610013318 6 10014317 NA 8.09E-09
vg0617636590 sf0617635593 6 17636590 NA 3.10E-07
vg0804123286 sf0804122289 8 4123286 NA 5.52E-07
vg1209943592 sf1209941002 12 9943592 NA 5.76E-07
vg0609903615 sf0609902616 6 9903615 NA 1.22E-06
vg0610476027 sf0610475028 6 10476027 NA 1.37E-06
vg1017706073 sf1017634846 10 17706073 NA 1.84E-06
vg1122530345 sf1122064216 11 22530345 NA 2.14E-06
vg0407237964 sf0407233234 4 7237964 NA 4.16E-06
vg0526989730 sf0526927086 5 26989730 NA 4.24E-06
vg0610137789 sf0610136790 6 10137789 NA 4.55E-06
vg0410045473 sf0410036170 4 10045473 NA 5.45E-06