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 mr1855 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
vg0217033687 sf0217027817 2 17033687 1.57E-129 2.34E-70
vg0217095683 sf0217089813 2 17095683 3.80E-125 2.40E-71
vg1108225523 sf1108220133 11 8225523 8.57E-42 4.44E-06
vg1128516527 sf1127993306 11 28516527 4.25E-36 3.24E-14
vg1220336317 sf1220307759 12 20336317 5.28E-36 4.53E-11
vg1015182556 sf1015111324 10 15182556 1.71E-32 2.22E-07
vg1005364284 sf1005380821 10 5364284 7.29E-27 1.68E-07
vg1216728961 sf1216722915 12 16728961 1.58E-25 3.64E-09
vg0213586076 sf0213586072 2 13586076 1.57E-23 7.78E-12
vg0212875961 sf0212875957 2 12875961 2.36E-23 6.28E-09
vg0216957423 sf0216951553 2 16957423 2.19E-21 1.71E-13
vg1226816127 sf1226782526 12 26816127 8.70E-19 1.58E-07
vg0213911062 sf0213905192 2 13911062 6.10E-18 1.51E-14
vg0218330515 sf0218324646 2 18330515 7.70E-17 4.74E-07
vg0218796566 sf0218790697 2 18796566 3.15E-16 1.57E-06
vg0216394881 sf0216389011 2 16394881 6.47E-15 3.45E-09
vg0216246251 sf0216240381 2 16246251 3.03E-14 1.10E-07
vg0217461610 sf0217455740 2 17461610 6.46E-14 2.16E-09
vg0216627913 sf0216622043 2 16627913 2.63E-10 4.70E-12
vg1206939533 sf1206938423 12 6939533 NA 7.10E-07
vg0819576434 sf0819573721 8 19576434 NA 7.74E-07
vg0820115562 sf0820112849 8 20115562 NA 1.27E-06