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 mr1334 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
vg1221053802 sf1221020352 12 21053802 5.30E-17 5.66E-12
vg1220249911 sf1220221353 12 20249911 7.77E-16 2.46E-11
vg1220250941 sf1220222383 12 20250941 8.12E-15 2.35E-10
vg1220567760 sf1220534308 12 20567760 4.96E-13 1.32E-08
vg1220338644 sf1220310086 12 20338644 1.86E-12 3.38E-09
vg1220301297 sf1220272739 12 20301297 2.52E-12 1.08E-09
vg1221098483 sf1221065033 12 21098483 4.91E-12 1.07E-08
vg1216192863 sf1216190159 12 16192863 1.03E-11 1.37E-08
vg1220340557 sf1220311999 12 20340557 1.50E-11 1.80E-07
vg1217240129 sf1217234084 12 17240129 1.55E-11 1.71E-08
vg0320153204 sf0320151715 3 20153204 3.50E-11 1.89E-07
vg1221096301 sf1221062851 12 21096301 4.68E-11 1.43E-08
vg1220186546 sf1220157988 12 20186546 5.75E-11 7.68E-09
vg1219966196 sf1219937666 12 19966196 6.56E-11 1.23E-08
vg0317164649 sf0317163459 3 17164649 1.43E-10 8.68E-09
vg1221031728 sf1220998278 12 21031728 6.39E-10 1.29E-07
vg1207586863 sf1207584268 12 7586863 4.48E-09 4.22E-08
vg1217439755 sf1217433710 12 17439755 9.18E-09 9.43E-08
vg1220128766 sf1220100208 12 20128766 1.08E-08 1.80E-09
vg0815172680 sf0815169966 8 15172680 2.68E-07 2.47E-06
vg1218760084 sf1218731519 12 18760084 5.38E-07 2.45E-08
vg0620536361 sf0620535364 6 20536361 1.41E-06 9.25E-08