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 mr1035 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
vg0405641604 sf0405637044 4 5641604 1.65E-33 3.61E-21
vg0411120101 sf0411110802 4 11120101 1.67E-18 1.64E-07
vg0805194471 sf0805193474 8 5194471 8.33E-18 2.35E-07
vg0428201379 sf0428016242 4 28201379 3.58E-16 NA
vg0400435492 sf0400434490 4 435492 5.39E-16 NA
vg0431913003 sf0431727898 4 31913003 1.47E-15 1.52E-07
vg0411655204 sf0411645910 4 11655204 2.54E-15 4.85E-09
vg0326477186 sf0326470280 3 26477186 5.03E-14 4.55E-07
vg0121948219 sf0121947174 1 21948219 1.02E-13 8.58E-07
vg0409044552 sf0409039827 4 9044552 1.03E-13 9.55E-08
vg0401719886 sf0401715435 4 1719886 4.07E-13 6.55E-07
vg0406279898 sf0406275338 4 6279898 6.44E-13 1.21E-06
vg0114502200 sf0114501174 1 14502200 7.12E-13 5.08E-07
vg0405603570 sf0405599011 4 5603570 NA 2.32E-16
vg0405682716 sf0405678155 4 5682716 NA 1.82E-13
vg0409425501 sf0409416200 4 9425501 NA 1.23E-07
vg0134118800 sf0134117756 1 34118800 NA 7.44E-07
vg0228555399 sf0228549530 2 28555399 NA 7.84E-07
vg0710325080 sf0710324086 7 10325080 NA 8.76E-07
vg0405973917 sf0405969358 4 5973917 NA 9.60E-07
vg0137296183 sf0137295140 1 37296183 NA 1.00E-06
vg0921555207 sf0921554726 9 21555207 NA 1.10E-06
vg0405244442 sf0405239883 4 5244442 NA 1.16E-06