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 mr1695 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
vg0610022110 sf0610021111 6 10022110 5.16E-27 2.69E-25
vg0610146210 sf0610145211 6 10146210 1.38E-24 4.91E-24
vg0610073155 sf0610072156 6 10073155 1.47E-21 1.86E-14
vg0610058798 sf0610057799 6 10058798 2.01E-20 3.12E-16
vg0609894917 sf0609893918 6 9894917 3.36E-18 2.37E-12
vg0610108790 sf0610107791 6 10108790 4.61E-18 3.94E-20
vg0610135808 sf0610134809 6 10135808 1.08E-15 8.80E-17
vg0609889578 sf0609888579 6 9889578 4.94E-14 1.71E-15
vg0609912063 sf0609911064 6 9912063 1.25E-13 4.74E-16
vg0610453680 sf0610452681 6 10453680 1.14E-12 9.28E-09
vg0610367407 sf0610366408 6 10367407 1.22E-12 1.11E-12
vg0621488776 sf0621487779 6 21488776 2.41E-12 2.78E-11
vg0611621075 sf0611620076 6 11621075 7.89E-12 1.01E-09
vg0618067784 sf0618066787 6 18067784 1.53E-11 1.94E-08
vg0611642002 sf0611641003 6 11642002 1.90E-11 4.41E-10
vg0610901670 sf0610900671 6 10901670 5.45E-11 1.86E-11
vg0620971322 sf0620970325 6 20971322 6.78E-11 6.33E-10
vg0610554368 sf0610553369 6 10554368 8.41E-11 5.46E-12
vg0610211069 sf0610210070 6 10211069 2.45E-09 2.67E-07
vg0404086232 sf0404081839 4 4086232 1.58E-08 2.35E-08
vg0611292337 sf0611291338 6 11292337 5.75E-07 5.64E-09
vg0609889408 sf0609888409 6 9889408 5.58E-06 2.24E-09
vg0601047105 sf0600959740 6 1047105 NA 5.92E-07
vg0321869681 sf0321868191 3 21869681 NA 7.31E-07