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 mr1070 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 7.31E-26 1.57E-18
vg0719011406 sf0719010413 7 19011406 3.61E-24 6.07E-19
vg0719136412 sf0719135419 7 19136412 2.44E-15 4.40E-08
vg1201652415 sf1201651415 12 1652415 1.06E-13 NA
vg0719136383 sf0719135390 7 19136383 2.14E-13 6.37E-07
vg1202102394 sf1202101392 12 2102394 9.86E-13 3.90E-08
vg1202414715 sf1202413716 12 2414715 3.29E-12 3.95E-06
vg0707794523 sf0707793528 7 7794523 5.10E-12 NA
vg0315179733 sf0315178380 3 15179733 1.57E-11 4.17E-06
vg0315225430 sf0315224077 3 15225430 2.40E-11 3.79E-06
vg0706547098 sf0706546103 7 6547098 1.87E-10 2.28E-06
vg0718991640 sf0718990647 7 18991640 3.16E-10 5.40E-11
vg0719153233 sf0719152240 7 19153233 7.78E-10 3.08E-08
vg0718961954 sf0718960961 7 18961954 NA 2.49E-09
vg1009450763 sf1009379584 10 9450763 NA 1.22E-07
vg0624862159 sf0624861162 6 24862159 NA 5.94E-07
vg0412457639 sf0412448354 4 12457639 NA 9.93E-07
vg0612613334 sf0612612335 6 12613334 NA 2.48E-06
vg0503840950 sf0503840927 5 3840950 NA 2.83E-06
vg0707711771 sf0707710776 7 7711771 NA 3.23E-06
vg0712904455 sf0712903462 7 12904455 NA 3.33E-06
vg1008804375 sf1008733237 10 8804375 NA 3.54E-06
vg1004296464 sf1004313002 10 4296464 NA 3.67E-06
vg0719143007 sf0719142014 7 19143007 NA 4.14E-06