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 mr1769 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
vg0106691928 sf0106690928 1 6691928 1.61E-122 3.35E-76
vg0106677498 sf0106676498 1 6677498 1.98E-121 3.05E-77
vg0106715029 sf0106714029 1 6715029 3.86E-32 1.83E-22
vg0106684462 sf0106683462 1 6684462 8.44E-31 2.09E-34
vg0106182662 sf0106181662 1 6182662 1.04E-26 1.31E-11
vg0106959659 sf0106958659 1 6959659 5.70E-24 7.32E-23
vg0107074175 sf0107073175 1 7074175 4.31E-22 4.13E-07
vg0106607583 sf0106606583 1 6607583 1.03E-21 5.28E-06
vg0107100004 sf0107099004 1 7100004 3.20E-21 6.00E-11
vg0107005955 sf0107004955 1 7005955 6.10E-20 2.71E-11
vg0102410486 sf0102409486 1 2410486 1.53E-17 1.18E-09
vg0826303218 sf0826300504 8 26303218 7.38E-17 2.50E-08
vg0102697328 sf0102696328 1 2697328 1.36E-16 4.23E-07
vg0235437287 sf0235431418 2 35437287 2.80E-15 3.75E-07
vg0215664387 sf0215658517 2 15664387 3.60E-15 2.53E-11
vg0106626230 sf0106625230 1 6626230 8.19E-14 4.74E-09
vg0105379062 sf0105378062 1 5379062 1.14E-13 1.78E-07
vg0106800547 sf0106799547 1 6800547 1.63E-13 1.81E-27
vg0105807534 sf0105806534 1 5807534 2.66E-13 2.79E-08
vg0106686584 sf0106685584 1 6686584 NA 2.76E-10
vg0106463385 sf0106462385 1 6463385 NA 6.14E-09
vg0106725146 sf0106724146 1 6725146 NA 9.26E-09
vg0106807221 sf0106806221 1 6807221 NA 1.29E-07
vg0106604863 sf0106603863 1 6604863 NA 2.02E-07
vg0105456074 sf0105455074 1 5456074 NA 3.10E-07