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 mr1849 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
vg1102677343 sf1102673247 11 2677343 4.55E-10 1.16E-08
vg0921699962 sf0921699481 9 21699962 4.08E-09 1.10E-08
vg1213717963 sf1213715301 12 13717963 4.11E-09 6.49E-09
vg0329957015 sf0329950054 3 29957015 5.82E-08 3.86E-06
vg0803532222 sf0803531225 8 3532222 9.58E-08 3.30E-06
vg0125628571 sf0125627527 1 25628571 1.02E-07 1.27E-06
vg0207729665 sf0207729664 2 7729665 1.25E-07 1.64E-06
vg1214782030 sf1214779371 12 14782030 1.94E-07 9.11E-07
vg0921539163 sf0921538682 9 21539163 2.23E-07 2.74E-07
vg0414249582 sf0414240295 4 14249582 7.00E-06 5.12E-08
vg0406525139 sf0406520582 4 6525139 NA 1.67E-07
vg0432876148 sf0432691035 4 32876148 NA 3.49E-06
vg0916049005 sf0916048004 9 16049005 NA 3.64E-06
vg0223262220 sf0223256351 2 23262220 NA 3.79E-06
vg1115925850 sf1115460720 11 15925850 NA 3.92E-06
vg0713426232 sf0713425239 7 13426232 NA 4.39E-06