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 mr1778 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
vg1215824234 sf1215821531 12 15824234 2.03E-118 4.51E-32
vg1215869969 sf1215867265 12 15869969 8.56E-111 5.16E-37
vg0621221946 sf0621220949 6 21221946 1.76E-88 2.85E-07
vg1013634162 sf1013562931 10 13634162 2.42E-87 NA
vg0106798403 sf0106797403 1 6798403 2.39E-86 7.72E-07
vg0112941979 sf0112940953 1 12941979 7.15E-85 NA
vg1013090320 sf1013019135 10 13090320 6.00E-78 NA
vg0916677066 sf0916676065 9 16677066 1.07E-76 8.25E-08
vg1215969757 sf1215967053 12 15969757 NA 4.76E-17
vg1215871396 sf1215868692 12 15871396 NA 9.19E-16
vg1215916036 sf1215913332 12 15916036 NA 4.52E-12
vg1215893630 sf1215890926 12 15893630 NA 1.91E-11
vg0218132013 sf0218126144 2 18132013 NA 1.09E-09
vg1215414598 sf1215411896 12 15414598 NA 1.49E-09
vg0104574233 sf0104573233 1 4574233 NA 2.18E-09
vg1215966147 sf1215963443 12 15966147 NA 6.20E-09
vg1216994915 sf1216988869 12 16994915 NA 6.35E-09
vg1215886190 sf1215883486 12 15886190 NA 9.03E-09
vg1215187066 sf1215184402 12 15187066 NA 1.22E-08
vg1215978234 sf1215975530 12 15978234 NA 1.55E-08
vg1214147913 sf1214145253 12 14147913 NA 2.12E-08
vg0702437436 sf0702436437 7 2437436 NA 3.33E-08
vg0610620315 sf0610619316 6 10620315 NA 4.66E-08
vg0918927566 sf0918926566 9 18927566 NA 4.68E-08
vg0727645219 sf0727644226 7 27645219 NA 5.22E-08
vg1216877905 sf1216871859 12 16877905 NA 7.53E-08
vg1215273070 sf1215270368 12 15273070 NA 7.66E-08
vg1216131209 sf1216128505 12 16131209 NA 8.33E-08
vg1212678410 sf1212675749 12 12678410 NA 8.36E-08
vg0104578649 sf0104577649 1 4578649 NA 9.62E-08
vg0401212486 sf0401208036 4 1212486 NA 1.01E-07
vg0104580119 sf0104579119 1 4580119 NA 1.15E-07
vg0901033665 sf0901032665 9 1033665 NA 1.29E-07
vg1216283093 sf1216280389 12 16283093 NA 1.55E-07
vg0111725377 sf0111724351 1 11725377 NA 8.05E-06