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 mr1410 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
vg0417244171 sf0417072212 4 17244171 4.62E-44 2.42E-27
vg0519939017 sf0519876493 5 19939017 9.32E-31 1.41E-19
vg0406753488 sf0406748934 4 6753488 2.24E-30 1.07E-15
vg0211588654 sf0211588650 2 11588654 2.82E-27 1.08E-19
vg0722183786 sf0722182793 7 22183786 1.46E-26 2.97E-11
vg0707065048 sf0707064053 7 7065048 8.16E-26 2.20E-10
vg0403055424 sf0403051028 4 3055424 1.44E-25 1.65E-11
vg0905685207 sf0905684207 9 5685207 3.09E-24 1.75E-12
vg0608700390 sf0608699391 6 8700390 2.56E-23 4.97E-10
vg1013723877 sf1013652646 10 13723877 3.37E-22 9.62E-13
vg0410354028 sf0410344727 4 10354028 7.40E-22 6.38E-11
vg0817661668 sf0817658955 8 17661668 2.98E-21 1.43E-12
vg0718615443 sf0718614450 7 18615443 1.85E-20 1.35E-10
vg0317461064 sf0317459703 3 17461064 4.30E-18 2.65E-11
vg0820968372 sf0820965659 8 20968372 9.11E-18 8.06E-08
vg1015773658 sf1015702428 10 15773658 1.47E-17 3.88E-09
vg0821112264 sf0821109551 8 21112264 1.65E-17 1.28E-11
vg0419225907 sf0419053945 4 19225907 3.61E-15 1.83E-12
vg0518926914 sf0518864398 5 18926914 4.40E-14 2.36E-12
vg0718641746 sf0718640753 7 18641746 4.46E-14 1.07E-11
vg0518975375 sf0518912859 5 18975375 NA 1.69E-16
vg0514028600 sf0513971144 5 14028600 NA 5.78E-10
vg1227329837 sf1227296237 12 27329837 NA 2.86E-07