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 mr1411 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
vg0719049384 sf0719048391 7 19049384 3.92E-16 1.21E-14
vg0719156501 sf0719155508 7 19156501 7.83E-16 2.92E-18
vg0719056561 sf0719055568 7 19056561 3.46E-15 9.28E-16
vg0417642687 sf0417470728 4 17642687 7.95E-11 2.14E-09
vg1101991503 sf1101987361 11 1991503 1.28E-10 4.83E-12
vg1101911438 sf1101910439 11 1911438 2.26E-10 3.10E-13
vg0816447256 sf0816444542 8 16447256 1.04E-09 1.08E-07
vg0228933475 sf0228927606 2 28933475 7.43E-09 2.27E-08
vg1107392564 sf1107388309 11 7392564 1.23E-08 2.09E-07
vg0700559381 sf0700558381 7 559381 3.50E-08 2.11E-07
vg0804032788 sf0804031791 8 4032788 5.03E-08 7.39E-08
vg0516162890 sf0516105374 5 16162890 3.49E-07 3.27E-07
vg0707738691 sf0707737696 7 7738691 4.38E-07 3.44E-07
vg0816543049 sf0816540335 8 16543049 4.65E-07 7.73E-07
vg0432523991 sf0432338883 4 32523991 2.02E-06 3.31E-08
vg0312684585 sf0312683303 3 12684585 2.25E-06 3.99E-07
vg1125341795 sf1124875635 11 25341795 2.43E-06 3.35E-07
vg0428739520 sf0428554372 4 28739520 7.35E-06 4.04E-08
vg0421592157 sf0421420207 4 21592157 NA 2.27E-08
vg1216282751 sf1216280047 12 16282751 NA 2.01E-07
vg0123166741 sf0123165697 1 23166741 NA 2.05E-07
vg0418074959 sf0417903000 4 18074959 NA 2.08E-07
vg0909917394 sf0909916393 9 9917394 NA 4.58E-07