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 mr1676 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
vg0919851501 sf0919851020 9 19851501 2.20E-36 7.44E-14
vg0305233552 sf0305232552 3 5233552 2.77E-28 4.45E-08
vg0107047780 sf0107046780 1 7047780 3.92E-28 6.00E-10
vg0719242312 sf0719241319 7 19242312 1.20E-26 1.63E-06
vg1226236616 sf1226203010 12 26236616 2.11E-25 NA
vg0608680831 sf0608679832 6 8680831 1.14E-22 4.32E-06
vg0815656712 sf0815653998 8 15656712 3.55E-22 1.61E-06
vg1122935128 sf1122468999 11 22935128 1.17E-21 1.11E-07
vg0805970880 sf0805969883 8 5970880 5.67E-21 3.39E-06
vg0918886513 sf0918885513 9 18886513 NA 8.79E-09
vg0106797241 sf0106796241 1 6797241 NA 1.39E-07
vg0107031520 sf0107030520 1 7031520 NA 2.39E-07
vg0124418602 sf0124417558 1 24418602 NA 2.96E-07
vg0129276978 sf0129275933 1 29276978 NA 3.64E-07
vg0129289299 sf0129288254 1 29289299 NA 4.45E-07
vg0316269069 sf0316267716 3 16269069 NA 4.83E-07
vg0316308734 sf0316307381 3 16308734 NA 6.98E-07
vg0617709303 sf0617708306 6 17709303 NA 1.05E-06
vg1122958251 sf1122492122 11 22958251 NA 2.06E-06
vg0316103102 sf0316101749 3 16103102 NA 2.25E-06
vg0919033371 sf0919032371 9 19033371 NA 2.77E-06
vg0142245153 sf0142244109 1 42245153 NA 3.12E-06
vg0400867538 sf0400866538 4 867538 NA 3.22E-06
vg1117954021 sf1117487879 11 17954021 NA 4.25E-06