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 mr1949 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
vg0719064221 sf0719063228 7 19064221 1.12E-43 6.70E-31
vg0719188664 sf0719187671 7 19188664 1.67E-38 2.99E-33
vg0719231124 sf0719230131 7 19231124 1.32E-28 1.52E-07
vg0918593583 sf0918592582 9 18593583 1.95E-27 8.14E-07
vg0336402152 sf0336395022 3 36402152 2.95E-27 5.67E-08
vg0722270556 sf0722269563 7 22270556 3.06E-27 7.93E-06
vg0626932604 sf0626931607 6 26932604 6.17E-27 6.82E-06
vg0336302808 sf0336295678 3 36302808 1.70E-26 2.11E-08
vg0206262084 sf0206262084 2 6262084 1.59E-25 NA
vg0626890818 sf0626889821 6 26890818 4.16E-25 1.39E-06
vg0708011365 sf0708010370 7 8011365 1.39E-24 1.59E-06
vg0626643638 sf0626642641 6 26643638 2.24E-23 NA
vg0719057980 sf0719056987 7 19057980 NA 4.65E-22
vg0719055344 sf0719054351 7 19055344 NA 4.76E-19
vg0719056630 sf0719055637 7 19056630 NA 1.41E-15
vg0719105731 sf0719104738 7 19105731 NA 9.61E-13
vg0718961880 sf0718960887 7 18961880 NA 7.41E-12
vg0719449907 sf0719448914 7 19449907 NA 4.08E-10
vg0113087370 sf0113086344 1 13087370 NA 1.44E-07
vg0302581223 sf0302580219 3 2581223 NA 4.83E-07
vg0706310539 sf0706309542 7 6310539 NA 5.94E-07
vg0315307310 sf0315305957 3 15307310 NA 6.18E-07
vg1103514429 sf1103510332 11 3514429 NA 1.18E-06
vg1216808328 sf1216802282 12 16808328 NA 1.23E-06
vg0627197504 sf0627196507 6 27197504 NA 1.27E-06
vg0919718025 sf0919717615 9 19718025 NA 1.85E-06
vg0719618203 sf0719617210 7 19618203 NA 1.86E-06
vg0616962436 sf0616961439 6 16962436 NA 2.17E-06