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 mr1119 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
vg0222673217 sf0222667348 2 22673217 1.05E-41 4.29E-18
vg0222739148 sf0222733279 2 22739148 3.56E-30 2.19E-15
vg0505964521 sf0505964460 5 5964521 5.32E-25 NA
vg1110157411 sf1110151988 11 10157411 7.45E-25 2.99E-06
vg0328992933 sf0328985985 3 28992933 1.47E-24 NA
vg0825721024 sf0825718310 8 25721024 2.03E-24 9.48E-07
vg0500664660 sf0500664660 5 664660 2.29E-24 2.37E-07
vg0825768731 sf0825766017 8 25768731 1.46E-23 9.10E-07
vg0818212763 sf0818210050 8 18212763 2.09E-23 1.87E-07
vg0306029913 sf0306028913 3 6029913 1.15E-22 3.14E-07
vg0624499979 sf0624498982 6 24499979 1.11E-21 2.95E-07
vg0434789415 sf0434604306 4 34789415 9.03E-21 6.98E-08
vg1108600295 sf1108594905 11 8600295 1.08E-20 1.20E-07
vg0434845674 sf0434660565 4 34845674 9.10E-20 2.16E-07
vg0222948971 sf0222943102 2 22948971 NA 1.58E-09
vg0222722554 sf0222716685 2 22722554 NA 8.89E-09
vg0420266563 sf0420094608 4 20266563 NA 9.58E-09
vg1209218924 sf1209216333 12 9218924 NA 6.27E-08
vg0219344371 sf0219338503 2 19344371 NA 1.54E-07
vg0506230550 sf0506230489 5 6230550 NA 1.82E-07
vg0709501453 sf0709500459 7 9501453 NA 2.03E-07
vg0801228810 sf0801227812 8 1228810 NA 2.19E-07
vg1016246436 sf1016175210 10 16246436 NA 4.80E-07
vg1006914384 sf1006930007 10 6914384 NA 6.23E-07
vg0327037726 sf0327030779 3 27037726 NA 6.67E-07
vg0121798555 sf0121797510 1 21798555 NA 9.83E-07
vg0403136311 sf0403131914 4 3136311 NA 1.04E-06
vg0914982012 sf0914981011 9 14982012 NA 1.37E-06
vg1009556200 sf1009485021 10 9556200 NA 2.60E-06