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 mr1129 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
vg0216800422 sf0216794552 2 16800422 1.76E-92 8.78E-36
vg0719968935 sf0719967942 7 19968935 3.82E-46 NA
vg0900336799 sf0900335799 9 336799 6.88E-45 3.31E-11
vg0216681021 sf0216675151 2 16681021 6.47E-44 9.61E-13
vg0900337327 sf0900336327 9 337327 6.54E-44 3.13E-11
vg0216889955 sf0216884085 2 16889955 7.32E-44 6.26E-13
vg0129124737 sf0129123692 1 29124737 1.30E-42 NA
vg0213525745 sf0213525741 2 13525745 2.30E-42 1.84E-09
vg0216767790 sf0216761920 2 16767790 3.14E-40 2.56E-07
vg0217612860 sf0217606990 2 17612860 3.07E-39 1.29E-09
vg1114473442 sf1114009759 11 14473442 2.41E-38 1.27E-07
vg0525571168 sf0525508589 5 25571168 5.19E-38 3.97E-06
vg0812023942 sf0812022947 8 12023942 1.45E-37 1.23E-07
vg0217232931 sf0217227061 2 17232931 NA 1.33E-18
vg0216381408 sf0216375538 2 16381408 NA 5.93E-09
vg0130736176 sf0130735132 1 30736176 NA 3.19E-08
vg0217271139 sf0217265269 2 17271139 NA 4.53E-08
vg0130697648 sf0130696604 1 30697648 NA 7.37E-08
vg0217810600 sf0217804731 2 17810600 NA 1.95E-07
vg1220237342 sf1220208784 12 20237342 NA 4.56E-07
vg0217027146 sf0217021276 2 17027146 NA 7.78E-07
vg0402172542 sf0402168137 4 2172542 NA 8.07E-07
vg0210765712 sf0210765710 2 10765712 NA 1.75E-06
vg1005364262 sf1005380799 10 5364262 NA 1.93E-06
vg1213797573 sf1213794911 12 13797573 NA 3.23E-06
vg1000028798 sf1000027798 10 28798 NA 4.84E-06