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 mr1033 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
vg0613566824 sf0613565825 6 13566824 3.06E-19 NA
vg0613607173 sf0613606174 6 13607173 4.55E-19 3.00E-08
vg0617693637 sf0617692640 6 17693637 2.42E-17 9.38E-10
vg0613552011 sf0613551012 6 13552011 2.87E-17 NA
vg0619651371 sf0619650374 6 19651371 3.50E-16 3.14E-06
vg0617841825 sf0617840828 6 17841825 4.80E-16 NA
vg0612828976 sf0612827977 6 12828976 1.55E-15 4.97E-08
vg1100738560 sf1100737562 11 738560 1.88E-15 6.98E-07
vg0613547532 sf0613546533 6 13547532 6.55E-15 2.80E-07
vg0613553868 sf0613552869 6 13553868 7.34E-15 NA
vg0918923160 sf0918922160 9 18923160 2.00E-14 3.37E-08
vg0613383622 sf0613382623 6 13383622 2.21E-14 1.81E-06
vg0619710656 sf0619709659 6 19710656 7.66E-14 2.31E-06
vg0613550597 sf0613549598 6 13550597 2.53E-12 3.63E-06
vg0707077541 sf0707076546 7 7077541 4.31E-12 2.23E-07
vg0611857510 sf0611856511 6 11857510 NA 2.09E-08
vg0404541420 sf0404537023 4 4541420 NA 3.35E-07
vg0405072995 sf0405068434 4 5072995 NA 5.84E-07
vg0612033836 sf0612032837 6 12033836 NA 5.89E-07
vg0401332098 sf0401327648 4 1332098 NA 1.20E-06
vg0825753695 sf0825750981 8 25753695 NA 2.17E-06
vg1204327553 sf1204326541 12 4327553 NA 3.54E-06
vg0401334644 sf0401330194 4 1334644 NA 7.14E-06