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 mr1795 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
vg0406390054 sf0406385494 4 6390054 3.60E-25 1.03E-19
vg0817436608 sf0817433894 8 17436608 2.39E-14 7.16E-11
vg0912864929 sf0912863928 9 12864929 8.90E-14 1.99E-08
vg0900549563 sf0900548563 9 549563 1.11E-11 NA
vg1116633939 sf1116168817 11 16633939 2.49E-11 1.34E-08
vg0406165696 sf0406161136 4 6165696 4.03E-11 1.22E-06
vg0116676710 sf0116675684 1 16676710 1.26E-10 1.47E-07
vg0503312521 sf0503312497 5 3312521 1.29E-10 2.39E-08
vg0823019901 sf0823017188 8 23019901 1.59E-10 2.21E-08
vg1125096005 sf1124629845 11 25096005 1.89E-10 1.61E-08
vg1116629534 sf1116164412 11 16629534 2.86E-10 1.63E-09
vg0500806382 sf0500806364 5 806382 1.26E-09 1.20E-06
vg0709773820 sf0709772826 7 9773820 4.12E-09 7.18E-07
vg1004380487 sf1004397025 10 4380487 4.14E-09 5.90E-07
vg0605983029 sf0605982030 6 5983029 9.93E-09 1.58E-07
vg0900591523 sf0900590523 9 591523 1.11E-08 6.12E-07
vg0819654266 sf0819651553 8 19654266 1.78E-08 4.61E-07
vg0912195797 sf0912194796 9 12195797 9.08E-08 2.12E-06
vg0234169418 sf0234163549 2 34169418 2.03E-07 1.53E-06
vg0313192451 sf0313191169 3 13192451 2.80E-07 4.01E-08
vg0817157608 sf0817154894 8 17157608 3.07E-07 6.00E-07
vg1216568438 sf1216565731 12 16568438 4.59E-07 1.06E-07
vg1214929592 sf1214926934 12 14929592 5.63E-07 1.80E-07