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 mr1945 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
vg1124468452 sf1124002292 11 24468452 4.08E-13 4.08E-13
vg1127797000 sf1127325386 11 27797000 1.44E-09 1.44E-09
vg1206990413 sf1206989303 12 6990413 7.07E-09 7.07E-09
vg1124342509 sf1123876353 11 24342509 1.58E-08 1.58E-08
vg0815631643 sf0815628929 8 15631643 2.39E-08 2.39E-08
vg1126207622 sf1125736036 11 26207622 5.33E-07 5.33E-07
vg1125108494 sf1124642334 11 25108494 8.69E-07 8.69E-07
vg1125105982 sf1124639822 11 25105982 9.02E-07 9.02E-07
vg1125157024 sf1124690864 11 25157024 9.60E-07 9.60E-07
vg1015982479 sf1015911251 10 15982479 1.42E-06 1.42E-06
vg0802371527 sf0802370530 8 2371527 1.57E-06 1.57E-06
vg0820968946 sf0820966233 8 20968946 1.68E-06 1.68E-06
vg0518262212 sf0518201698 5 18262212 2.14E-06 2.14E-06
vg0709361289 sf0709360295 7 9361289 2.70E-06 2.70E-06
vg1216192863 sf1216190159 12 16192863 3.06E-06 3.07E-06
vg0141918301 sf0141917258 1 41918301 3.66E-06 3.66E-06
vg1123834453 sf1123368323 11 23834453 4.44E-06 4.45E-06
vg0811459294 sf0811458299 8 11459294 4.50E-06 4.50E-06
vg0102329091 sf0102328091 1 2329091 4.56E-06 4.56E-06