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 mr1758 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
vg1115917664 sf1115452534 11 15917664 1.58E-14 1.11E-06
vg0128496994 sf0128495949 1 28496994 2.64E-13 NA
vg0125906058 sf0125905014 1 25906058 2.49E-12 NA
vg1200841195 sf1200840195 12 841195 2.98E-12 NA
vg0131535738 sf0131534694 1 31535738 4.20E-12 NA
vg1105459786 sf1105455537 11 5459786 4.63E-11 NA
vg0112504974 sf0112503948 1 12504974 4.03E-10 4.82E-06
vg1114515282 sf1114051599 11 14515282 4.98E-10 3.36E-08
vg1111473925 sf1111468242 11 11473925 1.75E-09 2.68E-10
vg0801466220 sf0801465222 8 1466220 1.58E-08 7.90E-06
vg1112966318 sf1112502639 11 12966318 NA 5.80E-07
vg1115590193 sf1115126505 11 15590193 NA 1.13E-06
vg1110727944 sf1110722489 11 10727944 NA 3.04E-06
vg1014230261 sf1014159027 10 14230261 NA 4.60E-06
vg1112964378 sf1112500699 11 12964378 NA 6.96E-06