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 mr1086 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
vg0719302947 sf0719301954 7 19302947 2.59E-62 1.41E-34
vg0719188664 sf0719187671 7 19188664 1.96E-60 2.01E-36
vg0719051231 sf0719050238 7 19051231 2.91E-49 4.45E-30
vg0708747195 sf0708746200 7 8747195 9.18E-36 NA
vg0719452816 sf0719451823 7 19452816 1.01E-35 NA
vg0621416163 sf0621415166 6 21416163 2.55E-35 NA
vg0705233181 sf0705232182 7 5233181 5.02E-35 NA
vg1107669372 sf1107665117 11 7669372 1.83E-34 6.99E-07
vg0719091461 sf0719090468 7 19091461 NA 5.22E-27
vg0719156563 sf0719155570 7 19156563 NA 1.22E-18
vg0719065396 sf0719064403 7 19065396 NA 4.51E-15
vg0719282436 sf0719281443 7 19282436 NA 8.03E-12
vg0719466615 sf0719465622 7 19466615 NA 1.11E-11
vg0719514240 sf0719513247 7 19514240 NA 1.41E-10
vg0719347879 sf0719346886 7 19347879 NA 1.73E-10
vg0719618102 sf0719617109 7 19618102 NA 6.02E-10
vg0718922665 sf0718921672 7 18922665 NA 8.54E-10
vg0122438890 sf0122437845 1 22438890 NA 1.89E-08
vg0418079489 sf0417907530 4 18079489 NA 2.30E-08
vg0719505870 sf0719504877 7 19505870 NA 1.33E-07
vg0421592157 sf0421420207 4 21592157 NA 1.87E-07
vg0718659061 sf0718658068 7 18659061 NA 2.16E-07
vg0719436399 sf0719435406 7 19436399 NA 2.19E-07
vg0708134630 sf0708133635 7 8134630 NA 2.39E-07
vg0329561125 sf0329554165 3 29561125 NA 7.12E-07
vg0718985745 sf0718984752 7 18985745 NA 7.96E-07
vg0224274297 sf0224268428 2 24274297 NA 9.41E-07
vg1103514429 sf1103510332 11 3514429 NA 9.87E-07
vg0432416194 sf0432231085 4 32416194 NA 1.26E-06
vg0520689110 sf0520626551 5 20689110 NA 1.45E-06
vg0625197129 sf0625196132 6 25197129 NA 1.52E-06