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 mr1765 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
vg0325710457 sf0325708475 3 25710457 8.11E-24 4.19E-20
vg0222035625 sf0222029756 2 22035625 3.66E-12 2.87E-08
vg1121714352 sf1121248229 11 21714352 1.06E-11 2.06E-07
vg1207091088 sf1207089978 12 7091088 1.44E-11 9.67E-07
vg1017929024 sf1017857796 10 17929024 6.51E-11 3.13E-07
vg0323177575 sf0323176063 3 23177575 1.52E-10 2.77E-06
vg0229389860 sf0229383991 2 29389860 2.08E-09 1.83E-06
vg1105209609 sf1105205420 11 5209609 2.35E-09 5.11E-07
vg0202731072 sf0202731070 2 2731072 7.72E-09 5.05E-07
vg0711956530 sf0711955536 7 11956530 8.48E-09 8.71E-07
vg0327407874 sf0327400927 3 27407874 9.89E-09 1.31E-06
vg1023111687 sf1023040159 10 23111687 1.08E-08 2.46E-06
vg0416712669 sf0416540713 4 16712669 1.78E-08 3.49E-06
vg1009343932 sf1009272753 10 9343932 3.23E-08 2.79E-07
vg1000821084 sf1000820060 10 821084 3.56E-07 2.58E-06
vg0323665466 sf0323663640 3 23665466 7.70E-06 8.42E-07
vg0907798696 sf0907797696 9 7798696 NA 8.47E-07
vg0406982385 sf0406977656 4 6982385 NA 1.51E-06
vg0220506753 sf0220500885 2 20506753 NA 4.08E-06