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 mr1211 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
vg0610480621 sf0610479622 6 10480621 3.85E-120 7.08E-55
vg0610608095 sf0610607096 6 10608095 5.13E-120 1.60E-56
vg0610871994 sf0610870995 6 10871994 2.19E-73 1.18E-11
vg0614491664 sf0614490665 6 14491664 8.07E-62 NA
vg0709217528 sf0709216534 7 9217528 1.91E-61 NA
vg0916815493 sf0916814492 9 16815493 3.72E-60 NA
vg0412175142 sf0412165853 4 12175142 3.89E-60 NA
vg0610557648 sf0610556649 6 10557648 4.81E-56 3.18E-14
vg0610539571 sf0610538572 6 10539571 6.61E-55 4.12E-59
vg0610532672 sf0610531673 6 10532672 3.77E-54 2.14E-59
vg0610685711 sf0610684712 6 10685711 NA 2.35E-20
vg0610723836 sf0610722837 6 10723836 NA 2.42E-15
vg0610118930 sf0610117931 6 10118930 NA 2.65E-15
vg0610444069 sf0610443070 6 10444069 NA 1.59E-12
vg0610763769 sf0610762770 6 10763769 NA 4.35E-12
vg0403922278 sf0403917884 4 3922278 NA 1.49E-10
vg0609926308 sf0609925309 6 9926308 NA 2.73E-10
vg0610802239 sf0610801240 6 10802239 NA 3.27E-10
vg0610564653 sf0610563654 6 10564653 NA 7.58E-10
vg0611081410 sf0611080411 6 11081410 NA 7.17E-09
vg0610281727 sf0610280728 6 10281727 NA 8.64E-09
vg0611127784 sf0611126785 6 11127784 NA 1.12E-08
vg0610465783 sf0610464784 6 10465783 NA 2.15E-08
vg0610645391 sf0610644392 6 10645391 NA 2.32E-08
vg0610495466 sf0610494467 6 10495466 NA 2.47E-08
vg0610145935 sf0610144936 6 10145935 NA 2.91E-08
vg1017279652 sf1017208425 10 17279652 NA 5.29E-08
vg0610197477 sf0610196478 6 10197477 NA 5.82E-08
vg0615907055 sf0615906057 6 15907055 NA 6.05E-08
vg0609929059 sf0609928060 6 9929059 NA 1.35E-07
vg0609585936 sf0609584937 6 9585936 NA 2.30E-07
vg0610886339 sf0610885340 6 10886339 NA 1.85E-06
vg0610772052 sf0610771053 6 10772052 NA 4.30E-06
vg0318014283 sf0318013065 3 18014283 NA 6.50E-06