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 mr1101 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
vg0220960199 sf0220954331 2 20960199 8.98E-10 5.32E-09
vg0221025908 sf0221020040 2 21025908 5.76E-09 7.24E-12
vg0402179876 sf0402175471 4 2179876 1.15E-08 7.24E-06
vg0628741924 sf0628740926 6 28741924 2.47E-08 NA
vg0627929341 sf0627928343 6 27929341 4.45E-08 8.96E-06
vg0222833455 sf0222827586 2 22833455 5.42E-08 4.58E-07
vg0709675216 sf0709674222 7 9675216 2.49E-07 7.50E-07
vg1127121896 sf1126650283 11 27121896 3.85E-07 1.99E-06
vg0819421680 sf0819418967 8 19421680 4.21E-07 1.15E-06
vg0108533994 sf0108532994 1 8533994 4.76E-07 1.22E-06
vg0910545581 sf0910544580 9 10545581 4.80E-07 6.83E-07
vg0727090466 sf0727089472 7 27090466 8.32E-07 5.32E-07
vg0432999273 sf0432814159 4 32999273 1.31E-06 3.97E-08
vg0805857866 sf0805856869 8 5857866 2.20E-06 2.38E-06
vg0432965430 sf0432780317 4 32965430 3.06E-06 3.94E-09
vg1110012449 sf1110007026 11 10012449 3.88E-06 NA
vg0224159749 sf0224153880 2 24159749 6.35E-06 3.56E-07
vg0906300837 sf0906299837 9 6300837 8.28E-06 1.11E-06
vg0432940473 sf0432755360 4 32940473 NA 1.08E-07
vg0121574351 sf0121573306 1 21574351 NA 3.28E-07
vg0621728622 sf0621727625 6 21728622 NA 3.37E-07
vg1222321812 sf1222288249 12 22321812 NA 4.74E-07
vg0221234344 sf0221228476 2 21234344 NA 1.27E-06
vg0903028063 sf0903027063 9 3028063 NA 2.60E-06
vg1002828516 sf1002827493 10 2828516 NA 2.67E-06
vg1110245970 sf1110240547 11 10245970 NA 4.10E-06
vg0220048340 sf0220042472 2 20048340 NA 4.19E-06