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 mr1026 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
vg1006540721 sf1006556344 10 6540721 1.10E-55 3.08E-11
vg1010570787 sf1010499608 10 10570787 4.32E-51 3.44E-07
vg0407826844 sf0407822112 4 7826844 1.03E-46 NA
vg0407824609 sf0407819877 4 7824609 2.19E-46 1.92E-08
vg1008775084 sf1008703946 10 8775084 2.98E-46 3.28E-13
vg1201368299 sf1201367299 12 1368299 4.08E-45 2.33E-06
vg0719086317 sf0719085324 7 19086317 4.15E-43 NA
vg1202107188 sf1202106186 12 2107188 1.15E-42 1.38E-06
vg1006028591 sf1006045129 10 6028591 1.25E-41 1.32E-09
vg0403206873 sf0403202476 4 3206873 3.05E-40 2.02E-08
vg1007627720 sf1007643329 10 7627720 2.08E-39 3.98E-08
vg0207453789 sf0207453789 2 7453789 5.83E-39 NA
vg0528707739 sf0528645094 5 28707739 1.08E-38 2.26E-09
vg1116476110 sf1116010987 11 16476110 8.39E-36 NA
vg0142683989 sf0142682945 1 42683989 5.60E-35 8.05E-08
vg1200839145 sf1200838145 12 839145 1.24E-32 9.22E-06
vg1006522696 sf1006538319 10 6522696 NA 2.51E-09
vg1009339779 sf1009268600 10 9339779 NA 6.00E-08
vg0110929029 sf0110928005 1 10929029 NA 1.38E-07
vg1007581489 sf1007597101 10 7581489 NA 1.50E-07
vg0335543608 sf0335536477 3 35543608 NA 3.93E-07
vg0407826743 sf0407822011 4 7826743 NA 6.08E-07
vg1007555829 sf1007571441 10 7555829 NA 1.36E-06
vg0401801501 sf0401797096 4 1801501 NA 1.70E-06
vg1005691241 sf1005707779 10 5691241 NA 1.80E-06
vg0403515281 sf0403510884 4 3515281 NA 2.69E-06
vg1005820821 sf1005837359 10 5820821 NA 3.36E-06
vg1005555783 sf1005572320 10 5555783 NA 3.63E-06