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 mr1274 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
vg0605299881 sf0605298882 6 5299881 2.80E-43 1.83E-22
vg0605299036 sf0605298037 6 5299036 8.63E-40 2.16E-20
vg0605274340 sf0605273341 6 5274340 1.05E-36 1.49E-24
vg0604984887 sf0604983888 6 4984887 3.84E-24 6.84E-13
vg0605448742 sf0605447743 6 5448742 2.94E-22 4.58E-11
vg0605270755 sf0605269756 6 5270755 3.39E-19 3.32E-09
vg0605415219 sf0605414220 6 5415219 1.19E-18 5.91E-09
vg0600826406 sf0600825407 6 826406 9.69E-16 NA
vg1104739877 sf1104735779 11 4739877 1.89E-14 NA
vg0604778086 sf0604777087 6 4778086 3.06E-14 9.11E-07
vg0605917767 sf0605916768 6 5917767 4.38E-13 1.89E-07
vg0605181590 sf0605180591 6 5181590 1.55E-12 2.88E-07
vg0605311849 sf0605310850 6 5311849 7.29E-10 2.86E-21
vg0605322089 sf0605321090 6 5322089 3.44E-08 1.33E-10
vg0501314676 sf0501314660 5 1314676 3.96E-07 2.20E-06
vg0605259601 sf0605258602 6 5259601 NA 1.53E-07
vg0401042995 sf0401038547 4 1042995 NA 7.62E-07
vg0225646452 sf0225640583 2 25646452 NA 2.12E-06
vg0604840256 sf0604839257 6 4840256 NA 3.26E-06
vg0209885622 sf0209885620 2 9885622 NA 3.98E-06
vg1211536647 sf1211533983 12 11536647 NA 4.78E-06