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 mr1676 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
vg0919836694 sf0919836213 9 19836694 1.43E-28 1.21E-15
vg0920140858 sf0920140377 9 20140858 1.60E-24 9.62E-21
vg0305233552 sf0305232552 3 5233552 7.17E-16 1.53E-09
vg0607464839 sf0607463840 6 7464839 1.04E-13 3.15E-06
vg0920176499 sf0920176018 9 20176499 5.36E-13 3.40E-08
vg0918701888 sf0918700887 9 18701888 1.74E-12 1.45E-08
vg0920305662 sf0920305181 9 20305662 2.43E-12 1.81E-08
vg1002208168 sf1002207145 10 2208168 2.56E-12 3.21E-06
vg0919843915 sf0919843434 9 19843915 3.35E-12 1.99E-07
vg1222170941 sf1222137488 12 22170941 1.03E-11 3.98E-07
vg0718873374 sf0718872381 7 18873374 1.09E-11 3.98E-07
vg0726399988 sf0726398994 7 26399988 2.79E-11 8.55E-08
vg0400894219 sf0400893219 4 894219 1.86E-10 2.05E-06
vg0142573739 sf0142572695 1 42573739 2.71E-10 7.46E-07
vg0142970300 sf0142969256 1 42970300 2.52E-08 6.65E-07
vg0205808842 sf0205808842 2 5808842 5.08E-08 8.19E-06
vg0501188064 sf0501188048 5 1188064 6.23E-08 NA
vg0719227901 sf0719226908 7 19227901 7.03E-08 2.33E-06
vg0820422849 sf0820420136 8 20422849 2.58E-07 6.89E-07
vg0719306112 sf0719305119 7 19306112 2.83E-07 2.15E-06
vg1118089667 sf1117623525 11 18089667 9.32E-07 9.07E-07
vg0919531759 sf0919531349 9 19531759 5.27E-06 4.71E-06
vg1010284480 sf1010213301 10 10284480 NA 1.14E-06