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 mr1620 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
vg0719316520 sf0719315527 7 19316520 1.34E-23 2.03E-16
vg0719088529 sf0719087536 7 19088529 4.92E-12 2.39E-08
vg0718833591 sf0718832598 7 18833591 5.51E-12 6.40E-08
vg0719140489 sf0719139496 7 19140489 1.94E-11 1.51E-08
vg0719203725 sf0719202732 7 19203725 4.26E-10 9.89E-07
vg1201614106 sf1201613106 12 1614106 6.23E-10 NA
vg0717197101 sf0717196108 7 17197101 6.65E-10 3.72E-06
vg1201356688 sf1201355688 12 1356688 1.45E-09 1.21E-06
vg0235249589 sf0235243720 2 35249589 1.07E-08 3.10E-06
vg0820445810 sf0820443097 8 20445810 2.00E-08 3.10E-06
vg1207833484 sf1207830890 12 7833484 5.74E-08 3.06E-06
vg0718984580 sf0718983587 7 18984580 1.75E-07 1.07E-08
vg0900274248 sf0900273248 9 274248 1.87E-07 4.94E-06
vg0705751437 sf0705750438 7 5751437 1.87E-07 4.50E-06
vg0719453641 sf0719452648 7 19453641 7.18E-07 3.88E-08
vg0900730086 sf0900729086 9 730086 1.10E-06 1.32E-06
vg0719192005 sf0719191012 7 19192005 NA 1.45E-06
vg0228211407 sf0228205538 2 28211407 NA 1.66E-06
vg0715058787 sf0715057794 7 15058787 NA 2.10E-06
vg0905947134 sf0905946134 9 5947134 NA 4.07E-06
vg0319785500 sf0319784011 3 19785500 NA 4.50E-06
vg0407630134 sf0407625401 4 7630134 NA 5.51E-06
vg0212800520 sf0212800516 2 12800520 NA 7.44E-06