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 mr1118 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
vg1006839627 sf1006855250 10 6839627 1.34E-39 9.31E-12
vg1007525105 sf1007540727 10 7525105 2.20E-35 1.12E-15
vg0407823811 sf0407819079 4 7823811 1.38E-28 1.47E-06
vg0407825052 sf0407820320 4 7825052 1.55E-28 5.62E-07
vg1009341357 sf1009270178 10 9341357 3.62E-28 1.17E-13
vg1009540574 sf1009469395 10 9540574 2.43E-27 1.60E-12
vg0403205317 sf0403200920 4 3205317 3.46E-26 5.88E-06
vg0813652209 sf0813649494 8 13652209 7.64E-26 9.64E-08
vg1005872232 sf1005888770 10 5872232 1.13E-25 3.80E-14
vg1202107668 sf1202106666 12 2107668 6.39E-25 4.72E-07
vg1006738188 sf1006753811 10 6738188 4.10E-23 2.85E-06
vg0407826743 sf0407822011 4 7826743 1.41E-22 5.56E-10
vg1216843191 sf1216837145 12 16843191 3.92E-21 8.83E-08
vg1005691354 sf1005707892 10 5691354 1.03E-20 5.32E-12
vg0110929029 sf0110928005 1 10929029 5.82E-19 2.48E-06
vg1010655699 sf1010584520 10 10655699 1.88E-18 1.49E-06
vg1005555827 sf1005572364 10 5555827 4.17E-16 1.40E-07
vg0407782850 sf0407778118 4 7782850 4.51E-15 1.66E-06
vg0905249361 sf0905248361 9 5249361 1.84E-14 2.45E-07
vg0315246434 sf0315245081 3 15246434 NA 4.19E-07
vg0710985476 sf0710984482 7 10985476 NA 2.96E-06
vg1127281051 sf1126809438 11 27281051 NA 3.61E-06