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 mr1174 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
vg0429923292 sf0429738159 4 29923292 6.05E-33 1.42E-14
vg0102741030 sf0102740030 1 2741030 9.96E-16 NA
vg0132158684 sf0132157640 1 32158684 1.07E-15 NA
vg1014784092 sf1014712858 10 14784092 2.03E-15 NA
vg1103770986 sf1103766888 11 3770986 2.89E-15 NA
vg0430036961 sf0429851832 4 30036961 1.44E-14 3.89E-10
vg0804315269 sf0804314272 8 4315269 6.75E-14 2.68E-16
vg0724567323 sf0724566329 7 24567323 5.86E-13 9.71E-09
vg0401198560 sf0401194110 4 1198560 2.77E-12 NA
vg0804327523 sf0804326526 8 4327523 NA 9.01E-16
vg0724528623 sf0724527629 7 24528623 NA 2.14E-08
vg0400676401 sf0400675400 4 676401 NA 3.68E-08
vg0804435056 sf0804434059 8 4435056 NA 6.89E-08
vg0332031704 sf0332024581 3 32031704 NA 1.37E-07
vg0310791558 sf0310790276 3 10791558 NA 1.38E-07
vg0727650948 sf0727649955 7 27650948 NA 1.46E-07
vg0331480345 sf0331473230 3 31480345 NA 2.42E-07
vg0429773519 sf0429588388 4 29773519 NA 2.65E-07
vg0620632643 sf0620631646 6 20632643 NA 4.47E-07
vg0722235878 sf0722234885 7 22235878 NA 6.50E-07
vg0322407127 sf0322405616 3 22407127 NA 6.70E-07
vg0208321255 sf0208321254 2 8321255 NA 7.00E-07
vg0332922670 sf0332915540 3 32922670 NA 7.17E-07
vg0332988748 sf0332981618 3 32988748 NA 9.34E-07
vg0310787372 sf0310786288 3 10787372 NA 9.75E-07
vg0722241548 sf0722240555 7 22241548 NA 1.07E-06
vg0519154442 sf0519091926 5 19154442 NA 1.22E-06
vg1224060006 sf1224026460 12 24060006 NA 2.67E-06
vg0729066829 sf0729065837 7 29066829 NA 3.88E-06
vg0401443541 sf0401439091 4 1443541 NA 4.59E-06
vg0725407361 sf0725406367 7 25407361 NA 4.92E-06