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 mr1757 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 1.52E-79 3.39E-23
vg0717004102 sf0717003109 7 17004102 1.28E-56 6.02E-11
vg0702584931 sf0702583932 7 2584931 8.10E-55 5.64E-09
vg0622627045 sf0622626048 6 22627045 1.06E-54 6.83E-09
vg0528564681 sf0528502036 5 28564681 2.07E-54 NA
vg0101083709 sf0101082709 1 1083709 9.66E-51 8.72E-09
vg1119960918 sf1119494841 11 19960918 2.71E-49 3.13E-10
vg0141203398 sf0141202355 1 41203398 4.89E-49 1.06E-07
vg0403254268 sf0403249871 4 3254268 1.94E-37 5.15E-08
vg0203130701 sf0203130699 2 3130701 1.95E-37 NA
vg0705321696 sf0705320697 7 5321696 NA 5.89E-14
vg0404591448 sf0404587051 4 4591448 NA 2.17E-10
vg1000493003 sf1000491979 10 493003 NA 1.64E-09
vg1000455258 sf1000454234 10 455258 NA 5.09E-09
vg0204657133 sf0204657130 2 4657133 NA 8.43E-09
vg0411931016 sf0411921727 4 11931016 NA 1.09E-08
vg0804804248 sf0804803251 8 4804248 NA 1.12E-08
vg0140622638 sf0140621595 1 40622638 NA 2.02E-08
vg0617983870 sf0617982873 6 17983870 NA 2.95E-08
vg1000734158 sf1000733134 10 734158 NA 3.58E-08
vg0707032320 sf0707031325 7 7032320 NA 3.97E-08
vg0709266953 sf0709265959 7 9266953 NA 4.19E-08
vg0626663016 sf0626662019 6 26663016 NA 6.12E-08
vg0124672177 sf0124671133 1 24672177 NA 6.86E-08
vg0124625557 sf0124624513 1 24625557 NA 8.60E-08
vg1202908436 sf1202907438 12 2908436 NA 9.62E-08
vg1117400025 sf1116933878 11 17400025 NA 5.53E-07
vg0514857972 sf0514800515 5 14857972 NA 4.07E-06
vg0810503248 sf0810502252 8 10503248 NA 8.12E-06