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 mr1865 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
vg0922428117 sf0922427636 9 22428117 2.93E-28 2.58E-26
vg0922221136 sf0922220655 9 22221136 1.68E-26 1.55E-26
vg0922436617 sf0922436136 9 22436617 8.51E-24 6.48E-20
vg0922498959 sf0922498478 9 22498959 3.94E-21 1.38E-18
vg0922634062 sf0922633581 9 22634062 9.87E-18 8.18E-15
vg0922415488 sf0922415007 9 22415488 4.66E-17 2.85E-16
vg0922610630 sf0922610149 9 22610630 6.39E-17 3.99E-15
vg0922156063 sf0922155582 9 22156063 1.02E-16 1.92E-16
vg0922172112 sf0922171631 9 22172112 1.61E-14 6.37E-17
vg0922495561 sf0922495080 9 22495561 3.64E-12 2.07E-09
vg0904740928 sf0904739928 9 4740928 1.72E-10 6.97E-08
vg0922486287 sf0922485806 9 22486287 1.19E-09 6.50E-09
vg0922436360 sf0922435879 9 22436360 1.70E-09 3.51E-10
vg0912946767 sf0912945766 9 12946767 2.66E-08 4.51E-07
vg0922374834 sf0922374353 9 22374834 5.26E-08 9.85E-09
vg0922661467 sf0922660986 9 22661467 7.84E-08 2.57E-06
vg0403323241 sf0403318844 4 3323241 2.38E-07 4.73E-08
vg0922202326 sf0922201845 9 22202326 7.35E-07 1.73E-06
vg0922373958 sf0922373477 9 22373958 3.27E-06 4.53E-06
vg0804660474 sf0804659477 8 4660474 NA 1.19E-06
vg0922141239 sf0922140758 9 22141239 NA 1.42E-06
vg0913451651 sf0913450650 9 13451651 NA 2.49E-06
vg0922485010 sf0922484529 9 22485010 NA 2.95E-06
vg1217863597 sf1217835031 12 17863597 NA 3.38E-06
vg0922141898 sf0922141417 9 22141898 NA 3.86E-06