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 mr1495 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
vg1006839627 sf1006855250 10 6839627 3.21E-41 8.60E-10
vg1007030937 sf1007046560 10 7030937 2.47E-36 9.11E-15
vg1008348646 sf1008277508 10 8348646 2.17E-33 3.91E-15
vg1008512380 sf1008441242 10 8512380 8.59E-30 3.75E-15
vg0407825052 sf0407820320 4 7825052 1.63E-29 3.42E-07
vg1009704536 sf1009633357 10 9704536 1.59E-28 2.16E-12
vg1009620429 sf1009549250 10 9620429 1.24E-27 NA
vg0403206782 sf0403202385 4 3206782 5.90E-27 7.74E-06
vg0407826743 sf0407822011 4 7826743 7.08E-26 6.44E-11
vg1216843191 sf1216837145 12 16843191 7.50E-25 1.72E-09
vg1005872232 sf1005888770 10 5872232 8.45E-25 1.11E-11
vg1202107188 sf1202106186 12 2107188 3.28E-23 4.20E-06
vg0813652209 sf0813649494 8 13652209 1.33E-22 3.40E-06
vg0110929029 sf0110928005 1 10929029 1.76E-22 4.28E-08
vg0222729493 sf0222723624 2 22729493 7.94E-21 1.97E-12
vg1202107576 sf1202106574 12 2107576 1.44E-20 3.05E-08
vg1005666781 sf1005683319 10 5666781 3.35E-20 9.75E-07
vg0905249361 sf0905248361 9 5249361 3.37E-18 8.95E-09
vg0528706863 sf0528644218 5 28706863 9.57E-18 8.48E-07
vg0412853605 sf0412844314 4 12853605 4.28E-17 3.46E-06
vg1010652163 sf1010580984 10 10652163 1.10E-16 1.57E-06
vg0716827828 sf0716826835 7 16827828 1.13E-16 2.09E-06
vg0221945123 sf0221939254 2 21945123 8.34E-13 3.21E-07
vg1011829118 sf1011757933 10 11829118 NA 5.45E-07