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 mr1644 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
vg1125519768 sf1125053607 11 25519768 1.39E-74 6.00E-50
vg1125545839 sf1125079678 11 25545839 1.34E-56 3.08E-41
vg1125227929 sf1124761769 11 25227929 4.79E-35 9.77E-22
vg1125233498 sf1124767338 11 25233498 9.13E-34 3.60E-24
vg1125234228 sf1124768068 11 25234228 9.08E-29 5.31E-20
vg1125863852 sf1125397771 11 25863852 2.44E-27 3.86E-16
vg1125854393 sf1125388312 11 25854393 6.99E-27 8.99E-17
vg1125583842 sf1125117681 11 25583842 7.34E-27 1.92E-22
vg1125569375 sf1125103214 11 25569375 9.81E-25 1.40E-19
vg1125252953 sf1124786793 11 25252953 1.79E-23 5.33E-20
vg0507714473 sf0507714414 5 7714473 3.86E-22 7.37E-12
vg1125434571 sf1124968410 11 25434571 8.15E-20 6.97E-14
vg1125605977 sf1125139816 11 25605977 1.33E-19 3.42E-16
vg1125893344 sf1125427263 11 25893344 1.46E-19 7.48E-19
vg1125162956 sf1124696796 11 25162956 1.18E-18 1.72E-13
vg1125566004 sf1125099843 11 25566004 1.66E-18 3.39E-16
vg0224605253 sf0224599384 2 24605253 1.26E-15 1.10E-12
vg1125605039 sf1125138878 11 25605039 1.67E-15 3.15E-11
vg1125245538 sf1124779378 11 25245538 2.19E-15 1.41E-20
vg1125607563 sf1125141402 11 25607563 3.53E-15 1.85E-15
vg1125544943 sf1125078782 11 25544943 1.11E-14 1.30E-14
vg1125960837 sf1125489251 11 25960837 1.68E-14 7.72E-14
vg1125581911 sf1125115750 11 25581911 2.31E-14 2.55E-11
vg1125520645 sf1125054484 11 25520645 7.17E-13 1.04E-11
vg1125153506 sf1124687346 11 25153506 1.64E-11 5.94E-14
vg1125571040 sf1125104879 11 25571040 NA 6.20E-14