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 8.84E-26 2.43E-18
vg0719011406 sf0719010413 7 19011406 3.13E-25 6.19E-20
vg0719136412 sf0719135419 7 19136412 1.48E-16 2.00E-09
vg0719136383 sf0719135390 7 19136383 6.56E-14 2.26E-07
vg1202102394 sf1202101392 12 2102394 8.79E-14 2.86E-09
vg0323468119 sf0323466293 3 23468119 8.40E-13 NA
vg0315179733 sf0315178380 3 15179733 4.50E-12 5.95E-06
vg0315045169 sf0315043816 3 15045169 1.30E-11 1.25E-06
vg0706547098 sf0706546103 7 6547098 1.41E-11 4.18E-07
vg0719076888 sf0719075895 7 19076888 5.03E-10 2.32E-10
vg1201512648 sf1201511648 12 1512648 7.85E-10 2.52E-06
vg1201451787 sf1201450787 12 1451787 1.38E-09 2.15E-06
vg0719153233 sf0719152240 7 19153233 1.40E-09 2.57E-07
vg0718985954 sf0718984961 7 18985954 NA 6.18E-10
vg1009450763 sf1009379584 10 9450763 NA 1.05E-06
vg0719209824 sf0719208831 7 19209824 NA 1.25E-06
vg0624862159 sf0624861162 6 24862159 NA 1.46E-06
vg0503840950 sf0503840927 5 3840950 NA 2.56E-06
vg0412457639 sf0412448354 4 12457639 NA 3.68E-06
vg0707711771 sf0707710776 7 7711771 NA 3.79E-06