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 mr1354 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
vg0724495741 sf0724494747 7 24495741 1.76E-29 2.13E-36
vg0724505923 sf0724504929 7 24505923 2.67E-29 6.97E-37
vg0724506609 sf0724505615 7 24506609 1.95E-26 5.05E-28
vg0724352500 sf0724351506 7 24352500 3.03E-26 4.64E-29
vg0724517571 sf0724516577 7 24517571 6.18E-26 1.67E-32
vg0724510628 sf0724509634 7 24510628 2.75E-17 9.89E-19
vg0619287097 sf0619286100 6 19287097 5.54E-16 NA
vg0724352316 sf0724351322 7 24352316 6.00E-16 1.41E-18
vg0914915290 sf0914914289 9 14915290 2.00E-13 3.48E-08
vg0618172241 sf0618171244 6 18172241 8.19E-13 NA
vg0429869745 sf0429684615 4 29869745 3.61E-11 NA
vg0724401667 sf0724400673 7 24401667 3.72E-10 7.86E-17
vg0608008401 sf0608007402 6 8008401 1.24E-08 3.52E-08
vg0724523127 sf0724522133 7 24523127 1.33E-08 3.63E-07
vg0724522889 sf0724521895 7 24522889 2.15E-08 7.68E-09
vg0218382286 sf0218376417 2 18382286 4.67E-08 1.19E-07
vg1117591563 sf1117125420 11 17591563 1.78E-07 4.21E-07
vg0724462519 sf0724461525 7 24462519 NA 1.57E-17
vg0724321079 sf0724320085 7 24321079 NA 1.29E-10
vg1205331763 sf1205330749 12 5331763 NA 2.58E-09
vg1120481623 sf1120015548 11 20481623 NA 6.42E-08
vg0608112196 sf0608111197 6 8112196 NA 1.15E-07
vg1011562893 sf1011491712 10 11562893 NA 1.37E-07
vg0331907206 sf0331900083 3 31907206 NA 1.68E-07
vg0818604778 sf0818602065 8 18604778 NA 1.95E-07
vg0319023759 sf0319022519 3 19023759 NA 2.42E-07
vg0314649425 sf0314648112 3 14649425 NA 3.11E-07
vg1011491998 sf1011420817 10 11491998 NA 5.70E-07
vg0331303645 sf0331296530 3 31303645 NA 1.17E-06