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 mr1055 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
vg1215976937 sf1215974233 12 15976937 3.61E-75 1.29E-33
vg1215854444 sf1215851740 12 15854444 3.64E-75 9.88E-34
vg1215854982 sf1215852278 12 15854982 9.21E-73 1.35E-34
vg1209571445 sf1209568854 12 9571445 3.68E-59 1.55E-22
vg1223872806 sf1223839259 12 23872806 2.90E-39 8.32E-06
vg1212726422 sf1212723761 12 12726422 2.26E-27 2.10E-08
vg1212938220 sf1212935559 12 12938220 2.29E-25 2.63E-09
vg0410423427 sf0410414126 4 10423427 1.07E-24 NA
vg1017847198 sf1017775971 10 17847198 3.19E-23 4.01E-07
vg1212129784 sf1212127120 12 12129784 1.07E-19 1.93E-08
vg1100799396 sf1100798397 11 799396 9.88E-19 1.14E-07
vg0217462843 sf0217456973 2 17462843 2.75E-18 1.66E-07
vg1217924678 sf1217896112 12 17924678 6.63E-18 4.62E-07
vg1223876846 sf1223843299 12 23876846 1.22E-17 4.07E-07
vg1216192507 sf1216189803 12 16192507 1.00E-15 8.50E-11
vg1215916353 sf1215913649 12 15916353 1.12E-15 3.50E-09
vg0315454216 sf0315452863 3 15454216 2.71E-15 2.28E-07
vg1207827697 sf1207825103 12 7827697 7.03E-15 1.06E-11
vg1215983666 sf1215980962 12 15983666 9.54E-15 3.79E-07
vg1214847524 sf1214844865 12 14847524 1.11E-13 2.01E-14
vg0526374490 sf0526311853 5 26374490 1.72E-13 2.09E-07
vg0327914592 sf0327907646 3 27914592 NA 1.58E-08
vg1216278238 sf1216275534 12 16278238 NA 1.76E-08
vg1215683048 sf1215680345 12 15683048 NA 4.01E-08
vg0404657697 sf0404653136 4 4657697 NA 4.75E-07