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 mr1107 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
vg0719064221 sf0719063228 7 19064221 3.44E-63 4.06E-44
vg0719209499 sf0719208506 7 19209499 1.65E-43 1.10E-12
vg0626833038 sf0626832041 6 26833038 4.61E-42 3.92E-09
vg0305665264 sf0305664264 3 5665264 1.02E-41 NA
vg0705593826 sf0705592827 7 5593826 1.76E-41 9.50E-06
vg0917918788 sf0917917787 9 17918788 1.85E-40 NA
vg0719091461 sf0719090468 7 19091461 NA 1.30E-32
vg0719065396 sf0719064403 7 19065396 NA 3.30E-32
vg0719055344 sf0719054351 7 19055344 NA 3.27E-27
vg0719192174 sf0719191181 7 19192174 NA 2.69E-24
vg0719436399 sf0719435406 7 19436399 NA 6.83E-15
vg0828401472 sf0828398758 8 28401472 NA 3.41E-14
vg0707667722 sf0707666727 7 7667722 NA 4.38E-14
vg0719466615 sf0719465622 7 19466615 NA 4.92E-14
vg0704482336 sf0704481337 7 4482336 NA 1.42E-13
vg0422489098 sf0422303985 4 22489098 NA 1.12E-12
vg0719452729 sf0719451736 7 19452729 NA 1.69E-12
vg0919718025 sf0919717615 9 19718025 NA 1.23E-11
vg0302581223 sf0302580219 3 2581223 NA 2.47E-11
vg1104364582 sf1104360484 11 4364582 NA 2.82E-11
vg1103515104 sf1103511007 11 3515104 NA 2.95E-11
vg0419906517 sf0419734553 4 19906517 NA 6.36E-11
vg1217054183 sf1217048137 12 17054183 NA 9.40E-11
vg0309319838 sf0309318774 3 9319838 NA 4.19E-10
vg0803630208 sf0803629211 8 3630208 NA 9.64E-10
vg0113087370 sf0113086344 1 13087370 NA 1.13E-09
vg0718664463 sf0718663470 7 18664463 NA 1.42E-09
vg0112079946 sf0112078920 1 12079946 NA 1.78E-09
vg0801178662 sf0801177664 8 1178662 NA 1.55E-08
vg0719074812 sf0719073819 7 19074812 NA 3.05E-06