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 mr1526 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
vg0610608095 sf0610607096 6 10608095 4.18E-24 2.67E-15
vg0610974808 sf0610973809 6 10974808 1.63E-14 6.48E-09
vg0610545611 sf0610544612 6 10545611 4.02E-13 2.56E-07
vg0610442148 sf0610441149 6 10442148 4.25E-13 2.85E-10
vg0610390138 sf0610389139 6 10390138 4.26E-13 7.79E-11
vg0610607507 sf0610606508 6 10607507 5.91E-12 3.67E-09
vg0610421076 sf0610420077 6 10421076 1.19E-11 1.54E-10
vg0609891923 sf0609890924 6 9891923 1.20E-10 1.21E-07
vg0623229182 sf0623228185 6 23229182 2.98E-10 1.22E-06
vg0610639326 sf0610638327 6 10639326 5.00E-10 5.92E-07
vg0610143069 sf0610142070 6 10143069 7.83E-10 6.99E-08
vg0611643367 sf0611642368 6 11643367 6.26E-09 1.73E-06
vg0617636590 sf0617635593 6 17636590 2.85E-08 1.79E-06
vg0610134394 sf0610133395 6 10134394 3.17E-06 3.95E-06
vg0804123286 sf0804122289 8 4123286 NA 9.49E-07
vg0205094542 sf0205094539 2 5094542 NA 4.24E-06
vg0218320998 sf0218315129 2 18320998 NA 6.14E-06
vg0400016796 sf0400015796 4 16796 NA 8.44E-06