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 mr1959 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
vg1000459276 sf1000458252 10 459276 1.74E-35 1.02E-24
vg1000443925 sf1000442901 10 443925 2.02E-35 5.71E-25
vg1011122210 sf1011051030 10 11122210 6.73E-21 4.89E-09
vg0330850428 sf0330843315 3 30850428 2.12E-20 1.10E-10
vg0330834913 sf0330827800 3 30834913 3.96E-20 7.79E-11
vg1008207053 sf1008135915 10 8207053 9.24E-20 5.36E-08
vg1124714538 sf1124248378 11 24714538 1.78E-19 5.50E-07
vg1125100181 sf1124634021 11 25100181 4.68E-18 1.96E-08
vg0142257399 sf0142256355 1 42257399 8.68E-18 3.78E-07
vg0528162167 sf0528099522 5 28162167 1.35E-17 1.40E-08
vg1004262572 sf1004279110 10 4262572 1.63E-17 5.79E-07
vg1214648997 sf1214646337 12 14648997 4.35E-17 6.22E-08
vg0606407151 sf0606406152 6 6407151 1.97E-13 8.79E-07
vg1125046291 sf1124580131 11 25046291 NA 1.96E-13
vg1124986395 sf1124520235 11 24986395 NA 8.06E-12
vg1128161380 sf1127638159 11 28161380 NA 1.30E-09
vg0328637867 sf0328630920 3 28637867 NA 1.78E-08
vg1000740409 sf1000739385 10 740409 NA 2.78E-08
vg1011012939 sf1010941759 10 11012939 NA 1.47E-07
vg0528218584 sf0528155939 5 28218584 NA 3.06E-07
vg1002061060 sf1002060037 10 2061060 NA 3.94E-07
vg1010576466 sf1010505287 10 10576466 NA 4.74E-07
vg1000551614 sf1000550590 10 551614 NA 4.74E-07
vg1000738126 sf1000737102 10 738126 NA 5.12E-07
vg0607242294 sf0607241295 6 7242294 NA 5.44E-07
vg0818530563 sf0818527850 8 18530563 NA 9.48E-07
vg0106771127 sf0106770127 1 6771127 NA 1.36E-06
vg0606540226 sf0606539227 6 6540226 NA 1.73E-06