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 mr1191 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
vg1125545839 sf1125079678 11 25545839 2.51E-75 6.95E-59
vg1125582889 sf1125116728 11 25582889 1.82E-46 1.01E-24
vg1125812120 sf1125346041 11 25812120 1.06E-36 1.76E-23
vg0507714473 sf0507714414 5 7714473 3.09E-36 1.63E-14
vg1125078873 sf1124612713 11 25078873 2.93E-33 2.84E-09
vg1125609610 sf1125143449 11 25609610 5.56E-33 3.44E-29
vg1125234228 sf1124768068 11 25234228 3.00E-32 1.10E-16
vg1124938370 sf1124472210 11 24938370 1.47E-31 1.06E-13
vg1125576537 sf1125110376 11 25576537 1.35E-30 2.53E-23
vg1125881170 sf1125415089 11 25881170 3.92E-26 2.10E-11
vg1126531677 sf1126060092 11 26531677 3.45E-23 1.00E-11
vg0224605253 sf0224599384 2 24605253 1.13E-22 6.94E-14
vg1125943983 sf1125472397 11 25943983 5.74E-22 3.77E-13
vg1125569375 sf1125103214 11 25569375 1.67E-20 5.81E-22
vg1125605039 sf1125138878 11 25605039 3.92E-17 3.16E-11
vg1125221937 sf1124755777 11 25221937 2.05E-16 1.44E-22
vg1125791323 sf1125325244 11 25791323 2.07E-13 2.95E-12
vg1125582069 sf1125115908 11 25582069 5.05E-13 6.20E-09
vg1125945479 sf1125473893 11 25945479 6.12E-13 7.14E-14
vg1125589582 sf1125123421 11 25589582 NA 1.30E-17
vg1125545040 sf1125078879 11 25545040 NA 1.46E-13
vg1125203416 sf1124737256 11 25203416 NA 1.67E-13
vg0204429559 sf0204429556 2 4429559 NA 9.77E-12
vg1125566004 sf1125099843 11 25566004 NA 5.35E-10