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 mr1309 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
vg1124335549 sf1123869393 11 24335549 4.55E-20 4.14E-17
vg1124965681 sf1124499521 11 24965681 2.26E-13 1.04E-12
vg0521578860 sf0521511524 5 21578860 4.42E-12 8.11E-10
vg0812679480 sf0812677305 8 12679480 1.35E-10 3.61E-09
vg1015983381 sf1015912153 10 15983381 5.55E-10 5.06E-09
vg1120931997 sf1120465900 11 20931997 2.39E-09 6.53E-08
vg1011368532 sf1011297351 10 11368532 4.91E-09 9.66E-07
vg0713136981 sf0713135988 7 13136981 6.37E-09 6.33E-07
vg0805902494 sf0805901497 8 5902494 1.03E-08 1.49E-06
vg0121419136 sf0121418091 1 21419136 1.24E-08 1.03E-08
vg1124463257 sf1123997097 11 24463257 1.30E-08 1.20E-07
vg1124950335 sf1124484175 11 24950335 2.03E-08 1.13E-08
vg1124348003 sf1123881847 11 24348003 2.78E-08 1.54E-07
vg1203603277 sf1203602276 12 3603277 4.89E-08 1.40E-06
vg1123640085 sf1123173955 11 23640085 5.63E-08 8.46E-08
vg1125256577 sf1124790417 11 25256577 9.30E-08 1.70E-07
vg0113026938 sf0113025912 1 13026938 9.85E-08 2.09E-06
vg0715539794 sf0715538801 7 15539794 2.07E-07 7.90E-07
vg1124340538 sf1123874382 11 24340538 2.93E-07 4.19E-08
vg1202638554 sf1202637556 12 2638554 1.80E-06 2.23E-06