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 mr1691 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
vg0216078062 sf0216072192 2 16078062 3.27E-14 2.33E-07
vg0215982412 sf0215976542 2 15982412 1.77E-12 8.36E-07
vg0917087568 sf0917086567 9 17087568 3.53E-12 1.06E-06
vg0519502040 sf0519439524 5 19502040 3.96E-11 2.63E-06
vg1221901937 sf1221868484 12 21901937 7.42E-11 NA
vg0132263132 sf0132262088 1 32263132 9.15E-11 NA
vg0302378820 sf0302377816 3 2378820 3.88E-10 2.12E-06
vg0138594460 sf0138593417 1 38594460 1.08E-09 3.75E-06
vg0718182723 sf0718181730 7 18182723 1.36E-09 4.77E-07
vg1206394368 sf1206393258 12 6394368 1.16E-08 5.37E-07
vg0221202752 sf0221196884 2 21202752 1.28E-08 4.02E-06
vg1204671441 sf1204670429 12 4671441 1.70E-07 9.68E-08
vg0107540499 sf0107539499 1 7540499 2.44E-07 NA
vg0127208150 sf0127207106 1 27208150 5.86E-07 NA
vg0200505558 sf0200505558 2 505558 1.71E-06 NA
vg1204657395 sf1204656383 12 4657395 NA 2.40E-08
vg0720593494 sf0720592501 7 20593494 NA 2.45E-08
vg0724216200 sf0724215206 7 24216200 NA 9.24E-08
vg0724166441 sf0724165447 7 24166441 NA 2.22E-07
vg1004675667 sf1004692204 10 4675667 NA 5.51E-07
vg0723091591 sf0723090598 7 23091591 NA 9.01E-07
vg0335115022 sf0335107892 3 35115022 NA 1.30E-06
vg0900852151 sf0900851151 9 852151 NA 2.17E-06
vg0714165056 sf0714164063 7 14165056 NA 2.58E-06
vg1128161380 sf1127638159 11 28161380 NA 2.85E-06
vg0905539417 sf0905538417 9 5539417 NA 3.80E-06
vg0623601535 sf0623600538 6 23601535 NA 3.83E-06
vg1000880358 sf1000879334 10 880358 NA 4.16E-06
vg1003801826 sf1003800802 10 3801826 NA 4.52E-06