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 mr1233 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
vg0719302457 sf0719301464 7 19302457 2.57E-47 1.48E-27
vg0719051231 sf0719050238 7 19051231 3.03E-47 2.29E-30
vg0719188664 sf0719187671 7 19188664 3.94E-44 2.37E-34
vg0336302800 sf0336295670 3 36302800 4.51E-33 3.11E-09
vg0722275405 sf0722274412 7 22275405 2.03E-29 7.52E-06
vg0917918788 sf0917917787 9 17918788 6.06E-29 NA
vg0627145476 sf0627144479 6 27145476 4.18E-28 NA
vg0304997671 sf0304996673 3 4997671 2.22E-26 3.19E-06
vg0719057980 sf0719056987 7 19057980 NA 1.84E-23
vg0719091461 sf0719090468 7 19091461 NA 1.61E-21
vg0719156649 sf0719155656 7 19156649 NA 7.56E-20
vg0719105731 sf0719104738 7 19105731 NA 4.32E-13
vg0718961880 sf0718960887 7 18961880 NA 5.36E-13
vg0719154140 sf0719153147 7 19154140 NA 3.53E-12
vg0719140918 sf0719139925 7 19140918 NA 1.90E-08
vg0503827315 sf0503827292 5 3827315 NA 1.67E-07
vg0820524101 sf0820521388 8 20524101 NA 2.03E-07
vg1222822194 sf1222788633 12 22822194 NA 2.14E-07
vg0302581223 sf0302580219 3 2581223 NA 2.34E-07
vg0719449907 sf0719448914 7 19449907 NA 6.45E-07
vg0315307310 sf0315305957 3 15307310 NA 6.53E-07
vg0336337217 sf0336330087 3 36337217 NA 8.74E-07
vg0315231624 sf0315230271 3 15231624 NA 9.00E-07
vg0719618203 sf0719617210 7 19618203 NA 1.44E-06
vg0720146822 sf0720145829 7 20146822 NA 1.73E-06
vg0820093448 sf0820090735 8 20093448 NA 1.86E-06
vg0631160329 sf0631159331 6 31160329 NA 2.19E-06
vg1001349943 sf1001348920 10 1349943 NA 2.51E-06
vg1103514429 sf1103510332 11 3514429 NA 3.08E-06