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 mr1334 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
vg1220789540 sf1220756088 12 20789540 3.90E-164 2.39E-51
vg1220404630 sf1220376072 12 20404630 2.39E-163 5.56E-51
vg1220731451 sf1220697999 12 20731451 2.11E-162 6.18E-55
vg1217257899 sf1217251854 12 17257899 7.09E-113 5.88E-12
vg0805444625 sf0805443628 8 5444625 5.80E-109 4.67E-14
vg1217236598 sf1217230553 12 17236598 1.18E-107 2.66E-12
vg0128263030 sf0128261986 1 28263030 1.02E-106 1.06E-06
vg0311732301 sf0311731019 3 11732301 1.96E-97 NA
vg1224749159 sf1224715613 12 24749159 4.14E-92 3.30E-10
vg1220173627 sf1220145069 12 20173627 NA 9.78E-14
vg0223104206 sf0223098337 2 23104206 NA 1.16E-13
vg1220730650 sf1220697198 12 20730650 NA 3.33E-13
vg1220793865 sf1220760413 12 20793865 NA 1.64E-11
vg1220827723 sf1220794272 12 20827723 NA 4.48E-11
vg1220174021 sf1220145463 12 20174021 NA 4.46E-10
vg1220093627 sf1220065069 12 20093627 NA 2.16E-09
vg0218341130 sf0218335261 2 18341130 NA 1.74E-08
vg1220907449 sf1220873998 12 20907449 NA 3.13E-08
vg0604320261 sf0604319262 6 4320261 NA 6.48E-08
vg0223104293 sf0223098424 2 23104293 NA 9.02E-08
vg0903033282 sf0903032282 9 3033282 NA 1.32E-07
vg1213458584 sf1213455922 12 13458584 NA 1.61E-07
vg0521146809 sf0521084250 5 21146809 NA 2.79E-07
vg1224769193 sf1224735647 12 24769193 NA 4.15E-07
vg0211277323 sf0211277320 2 11277323 NA 4.70E-07
vg0905069340 sf0905068340 9 5069340 NA 7.56E-07
vg0207179397 sf0207179397 2 7179397 NA 7.76E-07
vg1220360753 sf1220332195 12 20360753 NA 7.91E-07
vg0207184033 sf0207184033 2 7184033 NA 3.07E-06
vg1003996421 sf1003995397 10 3996421 NA 3.17E-06