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 mr1068 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
vg0610608095 sf0610607096 6 10608095 7.08E-168 1.30E-64
vg0610480621 sf0610479622 6 10480621 1.46E-166 3.45E-65
vg0610584513 sf0610583514 6 10584513 3.02E-157 2.44E-57
vg0610365898 sf0610364899 6 10365898 3.72E-136 1.16E-52
vg0610359961 sf0610358962 6 10359961 6.53E-133 3.93E-45
vg0708553753 sf0708552758 7 8553753 1.47E-74 NA
vg0304920678 sf0304919680 3 4920678 1.58E-74 NA
vg0233932146 sf0233926277 2 33932146 1.26E-73 NA
vg0615150907 sf0615149908 6 15150907 3.39E-73 6.96E-06
vg0617821393 sf0617820396 6 17821393 1.93E-64 2.92E-07
vg0610532672 sf0610531673 6 10532672 NA 3.05E-36
vg0610763769 sf0610762770 6 10763769 NA 8.91E-22
vg0610444069 sf0610443070 6 10444069 NA 4.96E-18
vg0610685711 sf0610684712 6 10685711 NA 3.09E-14
vg0610134394 sf0610133395 6 10134394 NA 8.21E-13
vg0610886339 sf0610885340 6 10886339 NA 1.17E-12
vg0610533048 sf0610532049 6 10533048 NA 1.06E-11
vg0611127784 sf0611126785 6 11127784 NA 4.21E-11
vg0609929059 sf0609928060 6 9929059 NA 6.16E-11
vg0610281727 sf0610280728 6 10281727 NA 7.10E-11
vg0615907055 sf0615906057 6 15907055 NA 1.31E-08
vg0610723836 sf0610722837 6 10723836 NA 1.75E-08
vg0613057898 sf0613056899 6 13057898 NA 5.70E-08
vg0610957761 sf0610956762 6 10957761 NA 6.04E-08
vg0610082555 sf0610081556 6 10082555 NA 8.90E-08
vg0613809145 sf0613808146 6 13809145 NA 1.21E-07
vg0617639143 sf0617638146 6 17639143 NA 1.27E-07
vg0206556033 sf0206556033 2 6556033 NA 1.27E-07
vg0610456976 sf0610455977 6 10456976 NA 1.57E-07
vg0610495466 sf0610494467 6 10495466 NA 2.77E-07
vg0612257913 sf0612256914 6 12257913 NA 4.10E-07
vg0613071268 sf0613070269 6 13071268 NA 5.81E-07