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 mr1128 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
vg0135821566 sf0135820523 1 35821566 2.80E-20 2.93E-07
vg0130815902 sf0130814858 1 30815902 6.61E-20 9.47E-06
vg0229918346 sf0229912477 2 29918346 3.58E-18 NA
vg0726172831 sf0726171837 7 26172831 1.64E-17 NA
vg0213825024 sf0213819154 2 13825024 2.06E-16 NA
vg0130736753 sf0130735709 1 30736753 5.45E-14 NA
vg0726396706 sf0726395712 7 26396706 7.34E-14 2.40E-06
vg0130732040 sf0130730996 1 30732040 NA 1.15E-13
vg1009321592 sf1009250413 10 9321592 NA 3.73E-08
vg0130856412 sf0130855368 1 30856412 NA 9.84E-08
vg1226927430 sf1226893829 12 26927430 NA 1.32E-07
vg1009412063 sf1009340884 10 9412063 NA 1.33E-07
vg0113096184 sf0113095158 1 13096184 NA 6.01E-07
vg0401720667 sf0401716216 4 1720667 NA 7.17E-07
vg0131033386 sf0131032342 1 31033386 NA 1.42E-06
vg1009450795 sf1009379616 10 9450795 NA 2.84E-06
vg1009262901 sf1009191722 10 9262901 NA 2.95E-06
vg0601365150 sf0601364151 6 1365150 NA 3.09E-06
vg0130651782 sf0130650738 1 30651782 NA 3.13E-06
vg1200418022 sf1200417022 12 418022 NA 3.14E-06
vg0716785759 sf0716784766 7 16785759 NA 3.46E-06
vg1009312105 sf1009240926 10 9312105 NA 4.21E-06
vg1009327905 sf1009256726 10 9327905 NA 4.30E-06
vg0115899007 sf0115897981 1 15899007 NA 4.87E-06
vg0423752653 sf0423567510 4 23752653 NA 9.32E-06