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 mr1560 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
vg0719006525 sf0719005532 7 19006525 4.74E-13 3.98E-12
vg0417642687 sf0417470728 4 17642687 5.80E-09 2.20E-06
vg0719271739 sf0719270746 7 19271739 1.10E-08 7.12E-14
vg0430102469 sf0429917340 4 30102469 1.88E-08 5.81E-06
vg1128579692 sf1128056471 11 28579692 2.21E-08 NA
vg0707738691 sf0707737696 7 7738691 2.91E-08 1.86E-06
vg0428494128 sf0428308982 4 28494128 3.87E-08 1.73E-06
vg0112713543 sf0112712517 1 12713543 1.42E-07 2.56E-06
vg1101911438 sf1101910439 11 1911438 2.07E-07 3.68E-07
vg1117099141 sf1116632993 11 17099141 2.14E-07 4.58E-07
vg0432630329 sf0432445218 4 32630329 2.38E-07 3.87E-06
vg0719052876 sf0719051883 7 19052876 3.13E-07 4.49E-11
vg0218610194 sf0218604325 2 18610194 3.71E-07 4.60E-06
vg0404665746 sf0404661185 4 4665746 2.00E-06 NA
vg0900544466 sf0900543466 9 544466 NA 2.09E-06
vg0421592157 sf0421420207 4 21592157 NA 2.12E-06
vg0811122650 sf0811121655 8 11122650 NA 2.17E-06
vg0811336981 sf0811335986 8 11336981 NA 2.45E-06
vg0813109769 sf0813107329 8 13109769 NA 2.58E-06
vg1119110596 sf1118644284 11 19110596 NA 2.82E-06
vg0124647921 sf0124646877 1 24647921 NA 2.90E-06
vg0421968989 sf0421797040 4 21968989 NA 3.21E-06
vg1208207975 sf1208205380 12 8207975 NA 3.57E-06