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 mr1977 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
vg0235068385 sf0235062516 2 35068385 8.88E-11 NA
vg0300781584 sf0300780582 3 781584 9.90E-11 NA
vg0818657655 sf0818654942 8 18657655 1.10E-10 NA
vg0827102972 sf0827100258 8 27102972 1.20E-10 6.58E-08
vg0609892121 sf0609891122 6 9892121 1.34E-10 NA
vg0227474066 sf0227468197 2 27474066 1.76E-10 2.53E-07
vg0609583002 sf0609582003 6 9583002 3.23E-10 1.14E-06
vg0123526774 sf0123525730 1 23526774 4.39E-10 5.16E-08
vg0202488699 sf0202488697 2 2488699 9.33E-10 4.55E-07
vg0802071791 sf0802070794 8 2071791 7.05E-09 1.88E-06
vg0628643421 sf0628642423 6 28643421 8.79E-09 1.12E-06
vg0107648672 sf0107647672 1 7648672 9.73E-09 1.04E-06
vg0232481318 sf0232475449 2 32481318 2.39E-08 2.20E-07
vg0233254450 sf0233248581 2 33254450 2.49E-08 2.77E-06
vg0233306848 sf0233300979 2 33306848 2.59E-08 6.02E-07
vg0233028845 sf0233022976 2 33028845 3.30E-08 1.18E-07
vg0802266533 sf0802265536 8 2266533 6.93E-08 NA
vg0140815392 sf0140814349 1 40815392 NA 1.28E-08
vg0628725900 sf0628724902 6 28725900 NA 8.82E-08
vg0221240541 sf0221234673 2 21240541 NA 5.55E-07
vg0123529738 sf0123528694 1 23529738 NA 8.81E-07
vg0819150140 sf0819147427 8 19150140 NA 2.39E-06
vg1000501145 sf1000500121 10 501145 NA 4.43E-06