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 mr1549 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
vg0705451627 sf0705450628 7 5451627 3.41E-70 1.25E-16
vg0529192490 sf0529129845 5 29192490 5.61E-55 1.26E-09
vg0500746368 sf0500746368 5 746368 2.91E-53 NA
vg0701229450 sf0701228450 7 1229450 3.04E-53 NA
vg0728355419 sf0728354427 7 28355419 4.51E-53 NA
vg0702584931 sf0702583932 7 2584931 2.87E-52 2.68E-08
vg0141203398 sf0141202355 1 41203398 8.70E-52 3.90E-09
vg0622627045 sf0622626048 6 22627045 1.47E-50 2.77E-08
vg0717004102 sf0717003109 7 17004102 2.32E-49 2.70E-08
vg0305879043 sf0305878043 3 5879043 5.02E-49 1.60E-08
vg1226720029 sf1226686427 12 26720029 2.07E-48 1.71E-07
vg1119960918 sf1119494841 11 19960918 1.26E-46 6.96E-11
vg1202743447 sf1202742449 12 2743447 1.64E-44 3.31E-09
vg0819146214 sf0819143501 8 19146214 5.92E-40 9.50E-08
vg0332722597 sf0332715468 3 32722597 3.99E-38 NA
vg0710123448 sf0710122454 7 10123448 NA 4.32E-09
vg0705321696 sf0705320697 7 5321696 NA 5.67E-09
vg0412976900 sf0412967610 4 12976900 NA 7.37E-09
vg0401293916 sf0401289466 4 1293916 NA 2.28E-08
vg0720401570 sf0720400577 7 20401570 NA 2.33E-08
vg0712641791 sf0712640798 7 12641791 NA 4.89E-08
vg0412918734 sf0412909442 4 12918734 NA 5.14E-08
vg0617983870 sf0617982873 6 17983870 NA 5.85E-08
vg0709500958 sf0709499964 7 9500958 NA 1.85E-07
vg0204657133 sf0204657130 2 4657133 NA 5.28E-07
vg0401701280 sf0401696829 4 1701280 NA 5.66E-07
vg1000454826 sf1000453802 10 454826 NA 6.82E-07
vg1202482303 sf1202481305 12 2482303 NA 1.00E-06
vg1125606899 sf1125140738 11 25606899 NA 1.01E-06
vg0140622638 sf0140621595 1 40622638 NA 1.22E-06
vg0414476036 sf0414466749 4 14476036 NA 7.08E-06