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 mr1204 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
vg0719006030 sf0719005037 7 19006030 1.94E-43 6.22E-13
vg0719049906 sf0719048913 7 19049906 5.53E-38 2.89E-21
vg0707706006 sf0707705011 7 7706006 2.36E-35 NA
vg0608639665 sf0608638666 6 8639665 2.63E-35 NA
vg0305768762 sf0305767762 3 5768762 3.16E-35 NA
vg0704624675 sf0704623676 7 4624675 3.66E-35 NA
vg0215999292 sf0215993422 2 15999292 4.36E-31 9.56E-07
vg0304989522 sf0304988524 3 4989522 2.47E-30 1.74E-07
vg0719091461 sf0719090468 7 19091461 NA 4.10E-19
vg0719323752 sf0719322759 7 19323752 NA 9.25E-14
vg0719181442 sf0719180449 7 19181442 NA 1.42E-10
vg0719140498 sf0719139505 7 19140498 NA 9.63E-10
vg0428494128 sf0428308982 4 28494128 NA 2.37E-09
vg0719067465 sf0719066472 7 19067465 NA 1.19E-08
vg0708134630 sf0708133635 7 8134630 NA 5.37E-08
vg0901040131 sf0901039131 9 1040131 NA 1.35E-07
vg0625175765 sf0625174768 6 25175765 NA 1.35E-07
vg0233012400 sf0233006531 2 33012400 NA 1.90E-07
vg1101176877 sf1101175878 11 1176877 NA 3.25E-07
vg1101198038 sf1101197039 11 1198038 NA 3.39E-07
vg0801031318 sf0801030320 8 1031318 NA 4.48E-07
vg1217045770 sf1217039724 12 17045770 NA 4.56E-07
vg0310139146 sf0310138082 3 10139146 NA 5.73E-07
vg0719618102 sf0719617109 7 19618102 NA 5.83E-07
vg0719466615 sf0719465622 7 19466615 NA 6.57E-07
vg0718883395 sf0718882402 7 18883395 NA 6.89E-07
vg0909917394 sf0909916393 9 9917394 NA 7.74E-07
vg0919718025 sf0919717615 9 19718025 NA 1.02E-06
vg0719149865 sf0719148872 7 19149865 NA 1.18E-06
vg0620513422 sf0620512425 6 20513422 NA 1.22E-06