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 mr1546 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
vg1209242642 sf1209240051 12 9242642 2.13E-61 5.13E-07
vg0526274314 sf0526211678 5 26274314 4.75E-57 NA
vg0216045329 sf0216039459 2 16045329 3.13E-54 NA
vg1223859443 sf1223825896 12 23859443 5.55E-53 NA
vg0620322305 sf0620321308 6 20322305 1.93E-52 NA
vg0112821395 sf0112820369 1 12821395 4.33E-50 4.90E-06
vg1215977007 sf1215974303 12 15977007 4.06E-48 8.02E-08
vg1219717603 sf1219689073 12 19717603 NA 1.70E-08
vg1022748280 sf1022676754 10 22748280 NA 9.32E-08
vg1224025383 sf1223991836 12 24025383 NA 1.07E-07
vg0223115199 sf0223109330 2 23115199 NA 2.10E-07
vg0229312349 sf0229306480 2 29312349 NA 2.19E-07
vg0702669541 sf0702668542 7 2669541 NA 2.73E-07
vg0918951541 sf0918950541 9 18951541 NA 3.94E-07
vg1215992528 sf1215989824 12 15992528 NA 8.24E-07
vg1022756524 sf1022684997 10 22756524 NA 1.23E-06
vg0616302182 sf0616301184 6 16302182 NA 1.39E-06
vg0323808792 sf0323806966 3 23808792 NA 1.71E-06
vg0426596087 sf0426410960 4 26596087 NA 2.34E-06
vg1013054571 sf1012983386 10 13054571 NA 3.00E-06
vg1010382960 sf1010311781 10 10382960 NA 3.95E-06
vg0904255240 sf0904254240 9 4255240 NA 4.07E-06
vg1103886177 sf1103882079 11 3886177 NA 4.47E-06
vg1216590670 sf1216587963 12 16590670 NA 5.84E-06