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 mr1489 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
vg1215869969 sf1215867265 12 15869969 4.88E-158 9.21E-59
vg1210219854 sf1210217266 12 10219854 2.88E-83 3.37E-07
vg1210354222 sf1210351679 12 10354222 3.79E-79 1.13E-08
vg0621221946 sf0621220949 6 21221946 3.84E-79 4.50E-06
vg1013634162 sf1013562931 10 13634162 2.11E-77 NA
vg1018567403 sf1018495960 10 18567403 3.57E-76 NA
vg1221903729 sf1221870276 12 21903729 4.93E-75 3.22E-08
vg1212938220 sf1212935559 12 12938220 1.18E-74 3.33E-10
vg1215871396 sf1215868692 12 15871396 NA 8.12E-25
vg1215970855 sf1215968151 12 15970855 NA 2.27E-17
vg1215893630 sf1215890926 12 15893630 NA 4.93E-13
vg0610620315 sf0610619316 6 10620315 NA 1.34E-12
vg0218132013 sf0218126144 2 18132013 NA 6.69E-12
vg1215976560 sf1215973856 12 15976560 NA 2.20E-11
vg0104574233 sf0104573233 1 4574233 NA 8.01E-10
vg1216411230 sf1216408523 12 16411230 NA 4.23E-09
vg1215414598 sf1215411896 12 15414598 NA 4.34E-09
vg1216019827 sf1216017123 12 16019827 NA 4.61E-09
vg1216212155 sf1216209451 12 16212155 NA 5.81E-09
vg0918927566 sf0918926566 9 18927566 NA 8.56E-09
vg1216413575 sf1216410868 12 16413575 NA 9.16E-09
vg0102116003 sf0102115003 1 2116003 NA 1.21E-08
vg0901048761 sf0901047761 9 1048761 NA 1.22E-08
vg1216994915 sf1216988869 12 16994915 NA 1.40E-08
vg1215273070 sf1215270368 12 15273070 NA 2.62E-08
vg1216062863 sf1216060159 12 16062863 NA 3.48E-08
vg1216346285 sf1216343581 12 16346285 NA 4.18E-08
vg1216151894 sf1216149190 12 16151894 NA 6.36E-08
vg0104579209 sf0104578209 1 4579209 NA 1.11E-07
vg0630161553 sf0630160555 6 30161553 NA 3.38E-06