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 mr1264 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
vg0719064331 sf0719063338 7 19064331 1.02E-51 1.16E-19
vg0305665264 sf0305664264 3 5665264 2.17E-45 NA
vg0626833038 sf0626832041 6 26833038 6.62E-45 9.84E-07
vg0705560234 sf0705559235 7 5560234 1.28E-44 NA
vg0504619344 sf0504619321 5 4619344 3.51E-44 NA
vg0232755756 sf0232749887 2 32755756 1.79E-40 NA
vg0719091461 sf0719090468 7 19091461 NA 3.42E-14
vg0719181533 sf0719180540 7 19181533 NA 9.19E-13
vg0719145578 sf0719144585 7 19145578 NA 3.02E-12
vg0113087370 sf0113086344 1 13087370 NA 2.65E-11
vg0719065396 sf0719064403 7 19065396 NA 3.02E-08
vg0409858762 sf0409849460 4 9858762 NA 5.57E-08
vg0719436399 sf0719435406 7 19436399 NA 8.23E-08
vg0722044007 sf0722043014 7 22044007 NA 1.22E-07
vg0719452729 sf0719451736 7 19452729 NA 1.61E-07
vg0707738691 sf0707737696 7 7738691 NA 1.80E-07
vg0623760476 sf0623759479 6 23760476 NA 1.94E-07
vg0228504159 sf0228498290 2 28504159 NA 2.02E-07
vg0705591916 sf0705590917 7 5591916 NA 2.85E-07
vg1217279515 sf1217273470 12 17279515 NA 4.89E-07
vg0230220381 sf0230214512 2 30220381 NA 5.72E-07
vg0718985959 sf0718984966 7 18985959 NA 1.20E-06
vg0113081699 sf0113080673 1 13081699 NA 1.38E-06
vg0315178849 sf0315177496 3 15178849 NA 1.38E-06
vg0606430642 sf0606429643 6 6430642 NA 1.41E-06
vg0827033383 sf0827030669 8 27033383 NA 1.45E-06
vg0719060385 sf0719059392 7 19060385 NA 4.27E-06