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 mr1973 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
vg0607415578 sf0607414579 6 7415578 3.55E-174 5.00E-38
vg0428552700 sf0428367552 4 28552700 5.07E-116 NA
vg0717284816 sf0717283823 7 17284816 1.77E-115 NA
vg0306025759 sf0306024759 3 6025759 2.11E-114 NA
vg0612894297 sf0612893298 6 12894297 2.87E-114 NA
vg0607502729 sf0607501730 6 7502729 1.41E-105 1.64E-19
vg0235583404 sf0235577535 2 35583404 1.53E-103 1.97E-06
vg0122602553 sf0122601508 1 22602553 8.00E-103 4.97E-06
vg0617272557 sf0617271560 6 17272557 1.50E-102 1.18E-06
vg0607252722 sf0607251723 6 7252722 NA 5.63E-23
vg0607242219 sf0607241220 6 7242219 NA 6.67E-18
vg1201691997 sf1201690995 12 1691997 NA 6.62E-10
vg0607310239 sf0607309240 6 7310239 NA 7.40E-10
vg0607008709 sf0607007710 6 7008709 NA 8.48E-10
vg0607019063 sf0607018064 6 7019063 NA 8.64E-09
vg0607385204 sf0607384205 6 7385204 NA 2.90E-08
vg0131651142 sf0131650098 1 31651142 NA 6.75E-08
vg0317210715 sf0317209525 3 17210715 NA 7.08E-08
vg0102402484 sf0102401484 1 2402484 NA 2.96E-07
vg0908369264 sf0908368264 9 8369264 NA 3.72E-07
vg0606970149 sf0606969150 6 6970149 NA 4.91E-07
vg0607450753 sf0607449754 6 7450753 NA 6.58E-07
vg0502391941 sf0502391917 5 2391941 NA 7.13E-07
vg0500745591 sf0500745591 5 745591 NA 9.28E-07
vg0514396497 sf0514339040 5 14396497 NA 1.01E-06
vg0131952630 sf0131951586 1 31952630 NA 1.11E-06
vg0822651774 sf0822649061 8 22651774 NA 2.06E-06
vg0103824036 sf0103823036 1 3824036 NA 4.32E-06