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 mr1071 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
vg0406526555 sf0406521998 4 6526555 1.53E-142 3.08E-32
vg0411344776 sf0411335479 4 11344776 2.95E-107 NA
vg0305431587 sf0305430587 3 5431587 3.43E-105 NA
vg1017228554 sf1017157327 10 17228554 4.97E-105 1.48E-06
vg1016528662 sf1016457435 10 16528662 9.77E-104 3.73E-07
vg0122842459 sf0122841415 1 22842459 1.28E-103 NA
vg1122454208 sf1121988079 11 22454208 5.46E-98 1.46E-06
vg0614107939 sf0614106940 6 14107939 1.12E-97 1.96E-08
vg0406521772 sf0406517215 4 6521772 NA 9.93E-10
vg0619719272 sf0619718275 6 19719272 NA 3.75E-09
vg0407576542 sf0407571810 4 7576542 NA 1.49E-08
vg0720714007 sf0720713014 7 20714007 NA 1.50E-08
vg0411635497 sf0411626203 4 11635497 NA 2.35E-08
vg0713947405 sf0713946412 7 13947405 NA 2.15E-07
vg1020493966 sf1020422445 10 20493966 NA 2.34E-07
vg0406356097 sf0406351537 4 6356097 NA 3.22E-07
vg0618247340 sf0618246343 6 18247340 NA 3.55E-07
vg0722680756 sf0722679763 7 22680756 NA 5.38E-07
vg0123406453 sf0123405409 1 23406453 NA 7.14E-07
vg1011221880 sf1011150700 10 11221880 NA 7.55E-07
vg0123800969 sf0123799925 1 23800969 NA 8.23E-07
vg0124267851 sf0124266807 1 24267851 NA 9.11E-07
vg0412479470 sf0412470185 4 12479470 NA 9.16E-07
vg0522637550 sf0522574993 5 22637550 NA 1.57E-06
vg0406489536 sf0406484979 4 6489536 NA 1.66E-06
vg0406373952 sf0406369392 4 6373952 NA 2.15E-06