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 mr1335 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
vg0126776565 sf0126775521 1 26776565 1.35E-07 1.35E-07
vg0901410990 sf0901409990 9 1410990 1.61E-07 1.61E-07
vg0307132377 sf0307131375 3 7132377 2.18E-07 2.18E-07
vg0818341901 sf0818339188 8 18341901 3.49E-07 3.50E-07
vg0715139529 sf0715138536 7 15139529 4.13E-07 4.14E-07
vg0509233251 sf0509233180 5 9233251 7.25E-07 7.26E-07
vg0332463518 sf0332456391 3 32463518 9.07E-07 9.07E-07
vg0301215623 sf0301214621 3 1215623 1.09E-06 1.09E-06
vg0816086900 sf0816084186 8 16086900 1.11E-06 1.11E-06
vg0709483572 sf0709482578 7 9483572 1.25E-06 1.25E-06
vg0606257199 sf0606256200 6 6257199 1.37E-06 1.37E-06
vg0321811921 sf0321810431 3 21811921 1.75E-06 1.75E-06
vg0722131045 sf0722130052 7 22131045 1.83E-06 1.83E-06
vg0706732811 sf0706731816 7 6732811 1.88E-06 1.88E-06
vg0607084144 sf0607083145 6 7084144 2.01E-06 2.01E-06
vg0317372993 sf0317371803 3 17372993 2.10E-06 2.10E-06
vg1216567539 sf1216564832 12 16567539 2.15E-06 2.15E-06
vg0805900956 sf0805899959 8 5900956 2.22E-06 2.22E-06
vg0131498286 sf0131497242 1 31498286 2.66E-06 2.67E-06
vg1008957832 sf1008886693 10 8957832 2.83E-06 2.84E-06