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 mr1099 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
vg0222743508 sf0222737639 2 22743508 1.20E-54 9.48E-34
vg0222747179 sf0222741310 2 22747179 1.10E-53 7.35E-34
vg0906971590 sf0906970590 9 6971590 1.64E-40 1.28E-06
vg0702448220 sf0702447221 7 2448220 1.95E-37 NA
vg0529002068 sf0528939423 5 29002068 6.90E-37 3.82E-06
vg0526142842 sf0526080262 5 26142842 5.84E-36 NA
vg0222679274 sf0222673405 2 22679274 3.83E-35 4.00E-10
vg0500664660 sf0500664660 5 664660 9.97E-35 2.76E-06
vg0222630367 sf0222624498 2 22630367 3.92E-29 6.52E-11
vg0819074999 sf0819072286 8 19074999 2.65E-28 3.16E-06
vg0222725003 sf0222719134 2 22725003 NA 5.84E-14
vg0224532813 sf0224526944 2 24532813 NA 5.43E-08
vg0232358383 sf0232352514 2 32358383 NA 8.27E-08
vg0222961186 sf0222955317 2 22961186 NA 1.40E-07
vg0224832469 sf0224826600 2 24832469 NA 2.54E-07
vg0222672641 sf0222666772 2 22672641 NA 9.43E-07
vg0224019660 sf0224013791 2 24019660 NA 1.42E-06
vg0222677953 sf0222672084 2 22677953 NA 2.10E-06
vg0610463015 sf0610462016 6 10463015 NA 2.44E-06
vg0222730936 sf0222725067 2 22730936 NA 3.01E-06
vg1200551682 sf1200550682 12 551682 NA 3.35E-06
vg0224239570 sf0224233701 2 24239570 NA 3.92E-06
vg0224870622 sf0224864753 2 24870622 NA 4.24E-06