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 mr1076 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
vg0719051231 sf0719050238 7 19051231 2.89E-39 6.44E-28
vg0719049906 sf0719048913 7 19049906 7.10E-38 2.64E-28
vg0708204553 sf0708203558 7 8204553 3.71E-31 7.28E-06
vg0608639665 sf0608638666 6 8639665 2.70E-30 NA
vg0305007501 sf0305006503 3 5007501 3.05E-30 NA
vg0917599445 sf0917598444 9 17599445 6.95E-30 NA
vg0304989522 sf0304988524 3 4989522 4.90E-27 3.93E-07
vg0719091461 sf0719090468 7 19091461 NA 4.27E-21
vg0719055344 sf0719054351 7 19055344 NA 7.22E-18
vg0719135262 sf0719134269 7 19135262 NA 1.60E-13
vg0719140498 sf0719139505 7 19140498 NA 2.91E-13
vg0719067465 sf0719066472 7 19067465 NA 4.27E-12
vg0707667722 sf0707666727 7 7667722 NA 1.28E-10
vg0329561125 sf0329554165 3 29561125 NA 1.60E-10
vg0719466615 sf0719465622 7 19466615 NA 1.61E-10
vg0719436399 sf0719435406 7 19436399 NA 6.07E-10
vg1100676096 sf1100675099 11 676096 NA 6.44E-10
vg0428494128 sf0428308982 4 28494128 NA 6.74E-10
vg0720529894 sf0720528901 7 20529894 NA 7.47E-10
vg0418071751 sf0417899792 4 18071751 NA 5.39E-09
vg0909775480 sf0909774479 9 9775480 NA 9.88E-09
vg0218618900 sf0218613031 2 18618900 NA 1.93E-08
vg0310139146 sf0310138082 3 10139146 NA 2.23E-08
vg0719452729 sf0719451736 7 19452729 NA 5.37E-08
vg0719618203 sf0719617210 7 19618203 NA 8.65E-08
vg0703539086 sf0703538087 7 3539086 NA 1.01E-07
vg1105544417 sf1105540169 11 5544417 NA 1.33E-07
vg0719139937 sf0719138944 7 19139937 NA 2.44E-07
vg0426471750 sf0426286623 4 26471750 NA 3.12E-07
vg0520660010 sf0520597451 5 20660010 NA 3.25E-07