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 mr1945 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
vg1125118463 sf1124652303 11 25118463 4.45E-17 8.18E-12
vg1124958705 sf1124492545 11 24958705 1.95E-13 1.46E-06
vg0727628077 sf0727627083 7 27628077 1.99E-13 5.94E-07
vg0124266409 sf0124265365 1 24266409 2.11E-13 1.85E-06
vg0123784118 sf0123783074 1 23784118 3.55E-13 8.67E-07
vg0105138368 sf0105137368 1 5138368 5.32E-13 1.28E-06
vg0717147271 sf0717146278 7 17147271 7.04E-13 1.23E-06
vg1125603928 sf1125137767 11 25603928 6.06E-12 1.31E-06
vg1124989458 sf1124523298 11 24989458 1.86E-11 1.37E-08
vg0728918648 sf0728917656 7 28918648 5.51E-11 6.12E-06
vg1125468181 sf1125002020 11 25468181 5.81E-11 2.58E-06
vg1125390548 sf1124924387 11 25390548 1.04E-10 4.19E-07
vg0716931835 sf0716930842 7 16931835 4.41E-10 2.25E-06
vg1124972080 sf1124505920 11 24972080 NA 1.32E-07
vg1125121722 sf1124655562 11 25121722 NA 5.41E-07
vg0704635310 sf0704634311 7 4635310 NA 1.77E-06
vg1122225663 sf1121759534 11 22225663 NA 2.90E-06
vg1125113390 sf1124647230 11 25113390 NA 3.59E-06
vg1124963624 sf1124497464 11 24963624 NA 4.55E-06
vg1006723044 sf1006738667 10 6723044 NA 4.62E-06
vg0804426635 sf0804425638 8 4426635 NA 4.73E-06