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 mr1829 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
vg0724516475 sf0724515481 7 24516475 5.28E-56 2.08E-55
vg0724495741 sf0724494747 7 24495741 2.61E-55 1.00E-55
vg0724417110 sf0724416116 7 24417110 3.21E-37 8.88E-36
vg0331232428 sf0331225313 3 31232428 1.05E-22 1.32E-11
vg0331303645 sf0331296530 3 31303645 4.79E-22 7.93E-12
vg0331001535 sf0330994422 3 31001535 1.50E-21 NA
vg0722530382 sf0722529389 7 22530382 1.72E-21 6.62E-08
vg0400999452 sf0400995004 4 999452 4.37E-21 1.04E-13
vg0331091486 sf0331084373 3 31091486 4.19E-19 2.27E-08
vg0724515873 sf0724514879 7 24515873 6.80E-18 1.08E-16
vg1000389182 sf1000388182 10 389182 2.19E-17 1.54E-09
vg0725312603 sf0725311609 7 25312603 1.69E-16 1.57E-13
vg1117595503 sf1117129360 11 17595503 2.76E-16 1.50E-11
vg0724532089 sf0724531095 7 24532089 2.63E-15 3.71E-34
vg0101040689 sf0101039689 1 1040689 8.21E-15 2.48E-09
vg0722707172 sf0722706179 7 22707172 7.47E-14 1.27E-08
vg0419794296 sf0419622333 4 19794296 8.29E-13 1.27E-09
vg0724381738 sf0724380744 7 24381738 5.79E-12 9.79E-15
vg0724510628 sf0724509634 7 24510628 3.99E-09 1.38E-16
vg1005832870 sf1005849408 10 5832870 5.52E-09 1.62E-09
vg1201219940 sf1201218940 12 1219940 1.56E-08 3.89E-09
vg0607952570 sf0607951571 6 7952570 1.88E-08 8.10E-10
vg0724424690 sf0724423696 7 24424690 NA 7.00E-21
vg0724536144 sf0724535150 7 24536144 NA 4.27E-16
vg0724226199 sf0724225205 7 24226199 NA 3.56E-12
vg0608011454 sf0608010455 6 8011454 NA 9.72E-11
vg0233123079 sf0233117210 2 33123079 NA 1.04E-10
vg0914828139 sf0914827138 9 14828139 NA 4.76E-10
vg0620955421 sf0620954424 6 20955421 NA 1.26E-09
vg0101034362 sf0101033362 1 1034362 NA 2.27E-08
vg1109563062 sf1109557639 11 9563062 NA 2.20E-06
vg0608272886 sf0608271887 6 8272886 NA 2.79E-06