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 mr1542 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
vg0314567323 sf0314566010 3 14567323 4.61E-169 3.19E-78
vg0314571719 sf0314570406 3 14571719 5.47E-168 1.57E-78
vg1224601964 sf1224568418 12 24601964 9.20E-42 NA
vg0907165546 sf0907164546 9 7165546 1.05E-41 NA
vg0702564992 sf0702563993 7 2564992 1.18E-41 NA
vg1203409903 sf1203408906 12 3409903 2.20E-41 NA
vg0314573659 sf0314572346 3 14573659 NA 3.67E-46
vg0314553734 sf0314552422 3 14553734 NA 8.71E-16
vg0314570282 sf0314568969 3 14570282 NA 3.00E-15
vg0314491238 sf0314489926 3 14491238 NA 2.56E-14
vg0314860588 sf0314859235 3 14860588 NA 8.09E-12
vg0314396350 sf0314395039 3 14396350 NA 1.10E-11
vg0314727003 sf0314725690 3 14727003 NA 1.40E-09
vg0314344500 sf0314343189 3 14344500 NA 4.44E-09
vg0314911279 sf0314909926 3 14911279 NA 3.41E-08
vg0314579234 sf0314577921 3 14579234 NA 6.25E-08
vg0314825243 sf0314823930 3 14825243 NA 1.08E-07
vg0314644172 sf0314642859 3 14644172 NA 9.19E-07
vg0139714293 sf0139713250 1 39714293 NA 1.16E-06
vg0314310040 sf0314308729 3 14310040 NA 1.55E-06
vg0314584521 sf0314583208 3 14584521 NA 1.59E-06
vg0314883867 sf0314882514 3 14883867 NA 2.03E-06
vg0314864088 sf0314862735 3 14864088 NA 2.37E-06
vg0314575940 sf0314574627 3 14575940 NA 2.46E-06
vg0719259492 sf0719258499 7 19259492 NA 2.75E-06