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 mr1023 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 9.79E-157 6.34E-53
vg1215967035 sf1215964331 12 15967035 2.55E-139 4.58E-45
vg1210219854 sf1210217266 12 10219854 7.43E-81 3.30E-06
vg1210372109 sf1210369522 12 10372109 5.94E-74 4.88E-07
vg1212938220 sf1212935559 12 12938220 2.04E-73 1.52E-09
vg1224007541 sf1223973994 12 24007541 1.17E-67 NA
vg0217092666 sf0217086796 2 17092666 1.73E-67 NA
vg1018579412 sf1018507969 10 18579412 1.38E-62 5.82E-07
vg1215871396 sf1215868692 12 15871396 NA 6.92E-24
vg1215970855 sf1215968151 12 15970855 NA 5.23E-16
vg1215966147 sf1215963443 12 15966147 NA 1.97E-12
vg0610620315 sf0610619316 6 10620315 NA 2.90E-10
vg1215976560 sf1215973856 12 15976560 NA 3.03E-10
vg1216165822 sf1216163118 12 16165822 NA 2.23E-09
vg0218132013 sf0218126144 2 18132013 NA 3.50E-09
vg0102116003 sf0102115003 1 2116003 NA 7.77E-09
vg1216411230 sf1216408523 12 16411230 NA 3.08E-08
vg0901048761 sf0901047761 9 1048761 NA 4.58E-08
vg1216413575 sf1216410868 12 16413575 NA 4.72E-08
vg0901033665 sf0901032665 9 1033665 NA 6.80E-08
vg1216273753 sf1216271049 12 16273753 NA 9.57E-08
vg0104590396 sf0104589396 1 4590396 NA 1.92E-07
vg1216492299 sf1216489592 12 16492299 NA 1.97E-07
vg1216019827 sf1216017123 12 16019827 NA 2.35E-07
vg1216284064 sf1216281360 12 16284064 NA 2.39E-07
vg1104366840 sf1104362742 11 4366840 NA 3.94E-07
vg1216156576 sf1216153872 12 16156576 NA 4.80E-07
vg1216151894 sf1216149190 12 16151894 NA 6.08E-07
vg1119431785 sf1118965473 11 19431785 NA 6.26E-07