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 mr1562 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
vg1102677343 sf1102673247 11 2677343 3.41E-09 3.41E-09
vg0217857667 sf0217851798 2 17857667 4.46E-09 4.46E-09
vg0921699962 sf0921699481 9 21699962 5.52E-09 5.52E-09
vg0418087588 sf0417915629 4 18087588 3.72E-08 3.73E-08
vg1213717956 sf1213715294 12 13717956 3.73E-08 3.73E-08
vg0330295614 sf0330288653 3 30295614 5.95E-08 5.95E-08
vg0605460208 sf0605459209 6 5460208 1.15E-07 1.15E-07
vg0223262220 sf0223256351 2 23262220 1.76E-07 1.76E-07
vg0125628571 sf0125627527 1 25628571 2.01E-07 2.01E-07
vg0413509258 sf0413499972 4 13509258 2.14E-07 2.14E-07
vg0313902394 sf0313901111 3 13902394 2.50E-07 2.50E-07
vg0706910489 sf0706909494 7 6910489 2.66E-07 2.66E-07
vg0812614441 sf0812612266 8 12614441 3.03E-07 3.03E-07
vg0918918596 sf0918917596 9 18918596 5.77E-07 5.77E-07
vg1208274233 sf1208271639 12 8274233 6.05E-07 6.05E-07
vg1117567414 sf1117101270 11 17567414 7.03E-07 7.03E-07
vg1220408794 sf1220380236 12 20408794 7.88E-07 7.89E-07
vg0609213350 sf0609212351 6 9213350 9.59E-07 9.60E-07
vg0729495328 sf0729494336 7 29495328 1.23E-06 1.23E-06
vg0303752606 sf0303751602 3 3752606 1.23E-06 1.23E-06