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 mr1390 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
vg1215967035 sf1215964331 12 15967035 4.87E-47 1.03E-24
vg1215343863 sf1215341161 12 15343863 1.86E-23 5.86E-10
vg0500829493 sf0500829475 5 829493 1.81E-17 NA
vg1212873997 sf1212871336 12 12873997 3.20E-17 1.59E-06
vg1011512136 sf1011440955 10 11512136 1.34E-16 3.08E-07
vg1004851571 sf1004868108 10 4851571 6.99E-15 7.85E-06
vg1005031656 sf1005048193 10 5031656 4.02E-14 1.90E-06
vg1018579412 sf1018507969 10 18579412 6.14E-13 3.13E-06
vg1218663003 sf1218634438 12 18663003 9.72E-12 1.94E-07
vg1215876237 sf1215873533 12 15876237 1.84E-11 6.61E-07
vg1006587700 sf1006603323 10 6587700 2.19E-11 1.87E-07
vg1215852700 sf1215849996 12 15852700 NA 2.33E-11
vg1022588644 sf1022517118 10 22588644 NA 3.48E-09
vg1216463200 sf1216460493 12 16463200 NA 5.77E-08
vg1206197673 sf1206196564 12 6197673 NA 1.87E-07
vg1208048502 sf1208045908 12 8048502 NA 2.34E-07
vg1209876216 sf1209873626 12 9876216 NA 1.18E-06
vg0901555655 sf0901554655 9 1555655 NA 1.54E-06
vg1018220310 sf1018148869 10 18220310 NA 1.94E-06
vg0612563711 sf0612562712 6 12563711 NA 2.06E-06
vg0616129303 sf0616128305 6 16129303 NA 2.88E-06
vg1117078119 sf1116611971 11 17078119 NA 3.33E-06
vg0902575416 sf0902574416 9 2575416 NA 3.45E-06
vg1213186520 sf1213183858 12 13186520 NA 3.53E-06