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 mr1130 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
vg0222727216 sf0222721347 2 22727216 1.07E-59 1.63E-22
vg0213988415 sf0213982545 2 13988415 7.52E-35 NA
vg1223571101 sf1223537561 12 23571101 8.01E-33 NA
vg0300648820 sf0300647818 3 648820 3.44E-32 NA
vg0208895720 sf0208895718 2 8895720 8.97E-32 NA
vg0222725003 sf0222719134 2 22725003 NA 5.90E-10
vg0130832570 sf0130831526 1 30832570 NA 3.10E-08
vg0122730398 sf0122729354 1 22730398 NA 2.49E-07
vg0223487342 sf0223481473 2 23487342 NA 4.39E-07
vg0223488998 sf0223483129 2 23488998 NA 1.32E-06
vg1125308482 sf1124842322 11 25308482 NA 2.50E-06
vg0525239875 sf0525177296 5 25239875 NA 2.60E-06
vg0224868229 sf0224862360 2 24868229 NA 2.68E-06
vg0222041029 sf0222035160 2 22041029 NA 3.13E-06
vg1127802594 sf1127330980 11 27802594 NA 3.90E-06
vg0320729993 sf0320728503 3 20729993 NA 4.29E-06
vg1125307514 sf1124841354 11 25307514 NA 4.70E-06
vg0103416441 sf0103415441 1 3416441 NA 6.28E-06