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 mr1211 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
vg0610687764 sf0610686765 6 10687764 1.61E-17 1.67E-16
vg0610060451 sf0610059452 6 10060451 7.31E-11 2.66E-08
vg0610649207 sf0610648208 6 10649207 2.89E-10 1.65E-08
vg0403922278 sf0403917884 4 3922278 1.99E-09 1.04E-07
vg1126273958 sf1125802371 11 26273958 8.08E-09 3.59E-06
vg1126274190 sf1125802603 11 26274190 9.40E-09 3.22E-06
vg1123389478 sf1122923348 11 23389478 1.80E-08 3.48E-06
vg0610322269 sf0610321270 6 10322269 5.11E-08 3.88E-07
vg0612767306 sf0612766307 6 12767306 6.73E-08 3.14E-07
vg0616129303 sf0616128305 6 16129303 1.49E-07 2.56E-07
vg1105749725 sf1105745477 11 5749725 1.54E-07 5.17E-07
vg0718051702 sf0718050709 7 18051702 2.71E-07 7.86E-07
vg1001052701 sf1001051677 10 1052701 5.56E-07 2.45E-06
vg0402677786 sf0402673390 4 2677786 6.19E-07 1.22E-06
vg1123359940 sf1122893810 11 23359940 6.47E-07 1.12E-06
vg0915069345 sf0915068344 9 15069345 5.60E-06 NA
vg1123222536 sf1122756407 11 23222536 NA 3.77E-06
vg1220092619 sf1220064061 12 20092619 NA 5.10E-06