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 mr1917 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
vg0222887413 sf0222881544 2 22887413 1.03E-34 1.09E-14
vg0222673217 sf0222667348 2 22673217 1.37E-34 3.62E-16
vg0626309167 sf0626308170 6 26309167 8.60E-30 4.81E-06
vg0917445593 sf0917444592 9 17445593 2.02E-29 4.84E-06
vg0304690506 sf0304689508 3 4690506 7.39E-29 NA
vg0805989476 sf0805988479 8 5989476 1.16E-28 NA
vg1110591251 sf1110585796 11 10591251 2.38E-27 3.81E-08
vg0818212763 sf0818210050 8 18212763 2.68E-27 6.26E-07
vg0222734635 sf0222728766 2 22734635 3.10E-27 7.47E-08
vg0222738600 sf0222732731 2 22738600 1.04E-25 5.22E-07
vg0222952563 sf0222946694 2 22952563 NA 1.02E-08
vg0626215270 sf0626214273 6 26215270 NA 1.47E-08
vg0222722554 sf0222716685 2 22722554 NA 2.85E-08
vg1117963441 sf1117497299 11 17963441 NA 3.69E-08
vg1110033540 sf1110028117 11 10033540 NA 1.66E-07
vg0335906768 sf0335899637 3 35906768 NA 2.02E-07
vg0432750231 sf0432565117 4 32750231 NA 3.12E-07
vg1006914384 sf1006930007 10 6914384 NA 3.32E-07
vg0224158100 sf0224152231 2 24158100 NA 5.52E-07
vg0907026290 sf0907025290 9 7026290 NA 7.19E-07
vg0708623561 sf0708622566 7 8623561 NA 8.88E-07
vg0220854116 sf0220848248 2 20854116 NA 1.09E-06
vg1122328656 sf1121862527 11 22328656 NA 1.12E-06
vg0434789415 sf0434604306 4 34789415 NA 1.65E-06
vg0905697823 sf0905696823 9 5697823 NA 1.69E-06
vg0308157341 sf0308156279 3 8157341 NA 1.78E-06
vg1009556200 sf1009485021 10 9556200 NA 2.11E-06
vg0909362853 sf0909361852 9 9362853 NA 2.13E-06
vg1122364508 sf1121898379 11 22364508 NA 2.18E-06