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 mr1263 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
vg1214134657 sf1214131997 12 14134657 1.62E-11 1.02E-09
vg0821068102 sf0821065389 8 21068102 2.15E-10 NA
vg0132744722 sf0132743678 1 32744722 7.42E-10 NA
vg1217711180 sf1217705135 12 17711180 2.34E-09 NA
vg0721065888 sf0721064895 7 21065888 5.03E-09 NA
vg0220865431 sf0220859563 2 20865431 1.52E-08 7.04E-07
vg0400137352 sf0400136352 4 137352 1.77E-08 7.41E-08
vg0907577928 sf0907576928 9 7577928 2.27E-08 1.34E-06
vg0323951924 sf0323950098 3 23951924 8.22E-08 4.98E-07
vg0327810589 sf0327803643 3 27810589 2.35E-07 1.68E-07
vg0918880163 sf0918879163 9 18880163 5.14E-07 1.97E-06
vg1227491928 sf1227458328 12 27491928 6.90E-07 2.37E-06
vg0624690267 sf0624689270 6 24690267 1.31E-06 8.81E-07
vg0142100802 sf0142099759 1 42100802 2.40E-06 2.09E-07
vg0307865773 sf0307864711 3 7865773 2.64E-06 3.72E-06
vg1207667840 sf1207665244 12 7667840 4.03E-06 NA
vg0719815142 sf0719814149 7 19815142 6.61E-06 3.34E-06
vg0922205633 sf0922205152 9 22205633 8.18E-06 1.18E-06
vg0334426545 sf0334419415 3 34426545 NA 3.66E-09
vg0524168704 sf0524106123 5 24168704 NA 2.38E-08
vg0335796573 sf0335789442 3 35796573 NA 1.14E-07
vg0509819392 sf0509819321 5 9819392 NA 1.20E-07
vg0317916681 sf0317915463 3 17916681 NA 1.40E-07
vg0322631658 sf0322630147 3 22631658 NA 3.26E-07
vg0221514962 sf0221509093 2 21514962 NA 4.60E-07
vg0520397455 sf0520334927 5 20397455 NA 6.47E-07
vg0317965477 sf0317964259 3 17965477 NA 7.61E-07
vg0326004558 sf0326002578 3 26004558 NA 1.14E-06
vg0904010040 sf0904009040 9 4010040 NA 1.32E-06
vg1227329375 sf1227295775 12 27329375 NA 1.71E-06
vg1106502558 sf1106498310 11 6502558 NA 1.91E-06
vg0701224067 sf0701223067 7 1224067 NA 6.39E-06