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 mr1211 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 4.80E-102 2.92E-43
vg0610642844 sf0610641845 6 10642844 2.61E-96 1.15E-35
vg0615016614 sf0615015615 6 15016614 1.81E-57 NA
vg0717210175 sf0717209182 7 17210175 4.93E-57 4.29E-06
vg0709045792 sf0709044798 7 9045792 1.11E-55 NA
vg0613854532 sf0613853533 6 13854532 9.47E-55 3.40E-07
vg0410124644 sf0410115341 4 10124644 4.01E-54 NA
vg0610539571 sf0610538572 6 10539571 5.84E-52 1.07E-46
vg0610685711 sf0610684712 6 10685711 NA 5.75E-20
vg0610733548 sf0610732549 6 10733548 NA 8.17E-18
vg0609926308 sf0609925309 6 9926308 NA 5.97E-12
vg0610763769 sf0610762770 6 10763769 NA 2.17E-11
vg0610645391 sf0610644392 6 10645391 NA 8.32E-11
vg0610564653 sf0610563654 6 10564653 NA 3.09E-10
vg0610539400 sf0610538401 6 10539400 NA 5.00E-10
vg0403922278 sf0403917884 4 3922278 NA 1.92E-09
vg0610118930 sf0610117931 6 10118930 NA 2.12E-09
vg0610442278 sf0610441279 6 10442278 NA 5.27E-09
vg0615907055 sf0615906057 6 15907055 NA 5.89E-09
vg0610533263 sf0610532264 6 10533263 NA 9.28E-09
vg0610446203 sf0610445204 6 10446203 NA 2.32E-08
vg0609930953 sf0609929954 6 9930953 NA 8.55E-08
vg0606988364 sf0606987365 6 6988364 NA 9.96E-08
vg0618930430 sf0618929433 6 18930430 NA 1.98E-07
vg0610495466 sf0610494467 6 10495466 NA 2.38E-07
vg0610116683 sf0610115684 6 10116683 NA 3.86E-07
vg0715843139 sf0715842146 7 15843139 NA 9.28E-06