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 mr1583 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
vg0610274952 sf0610273953 6 10274952 1.53E-32 5.45E-13
vg0610271987 sf0610270988 6 10271987 3.43E-32 3.99E-13
vg0621535653 sf0621534656 6 21535653 1.03E-25 2.74E-06
vg0719601158 sf0719600165 7 19601158 4.59E-23 NA
vg0232879689 sf0232873820 2 32879689 1.06E-20 NA
vg0612914787 sf0612913788 6 12914787 2.61E-20 NA
vg0403221112 sf0403216715 4 3221112 8.40E-19 3.72E-06
vg0611974346 sf0611973347 6 11974346 4.98E-15 4.06E-08
vg0616930764 sf0616929767 6 16930764 9.51E-15 2.75E-06
vg1120967952 sf1120501825 11 20967952 1.95E-14 3.56E-06
vg0610760999 sf0610760000 6 10760999 NA 3.39E-10
vg0610110374 sf0610109375 6 10110374 NA 3.91E-09
vg0610590127 sf0610589128 6 10590127 NA 5.17E-09
vg0916030541 sf0916029540 9 16030541 NA 1.54E-07
vg0910350606 sf0910349605 9 10350606 NA 4.36E-07
vg0412960919 sf0412951630 4 12960919 NA 5.64E-07
vg1215582510 sf1215579807 12 15582510 NA 1.08E-06
vg0610849223 sf0610848224 6 10849223 NA 2.24E-06
vg0610487099 sf0610486100 6 10487099 NA 2.45E-06
vg0116398776 sf0116397750 1 16398776 NA 2.66E-06
vg0403922278 sf0403917884 4 3922278 NA 3.81E-06
vg1222204534 sf1222171081 12 22204534 NA 3.95E-06
vg0431615949 sf0431430844 4 31615949 NA 4.44E-06