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 mr1139 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
vg0719011406 sf0719010413 7 19011406 8.82E-60 2.37E-18
vg0719051231 sf0719050238 7 19051231 7.80E-55 1.18E-23
vg0305273083 sf0305272083 3 5273083 7.37E-48 1.58E-06
vg0708221201 sf0708220206 7 8221201 1.71E-46 NA
vg0215991693 sf0215985823 2 15991693 6.52E-45 NA
vg0705562659 sf0705561660 7 5562659 1.16E-44 NA
vg0216352293 sf0216346423 2 16352293 7.71E-42 1.15E-06
vg0315197792 sf0315196439 3 15197792 6.84E-41 1.16E-07
vg0305026293 sf0305025295 3 5026293 9.91E-40 7.35E-07
vg0719091461 sf0719090468 7 19091461 NA 1.61E-21
vg0719153604 sf0719152611 7 19153604 NA 1.41E-13
vg0718985745 sf0718984752 7 18985745 NA 7.95E-11
vg0719192174 sf0719191181 7 19192174 NA 1.49E-09
vg0718922665 sf0718921672 7 18922665 NA 7.70E-09
vg0719466615 sf0719465622 7 19466615 NA 1.03E-07
vg0719417652 sf0719416659 7 19417652 NA 1.10E-07
vg0329561125 sf0329554165 3 29561125 NA 1.20E-07
vg0719316841 sf0719315848 7 19316841 NA 1.37E-06
vg0702977077 sf0702976078 7 2977077 NA 2.09E-06
vg0315178849 sf0315177496 3 15178849 NA 2.96E-06
vg0315356844 sf0315355491 3 15356844 NA 3.03E-06
vg1001966691 sf1001965668 10 1966691 NA 3.30E-06
vg0719346699 sf0719345706 7 19346699 NA 3.86E-06
vg0719618102 sf0719617109 7 19618102 NA 4.50E-06
vg1121617585 sf1121151462 11 21617585 NA 9.13E-06