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 mr1107 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
vg0719302947 sf0719301954 7 19302947 6.95E-56 4.77E-32
vg0719064221 sf0719063228 7 19064221 4.89E-53 8.98E-36
vg0215804066 sf0215798196 2 15804066 2.02E-35 NA
vg0305138684 sf0305137686 3 5138684 6.12E-35 4.49E-06
vg0708201428 sf0708200433 7 8201428 7.06E-35 NA
vg0717192350 sf0717191357 7 17192350 8.01E-35 2.98E-06
vg0719316841 sf0719315848 7 19316841 7.64E-34 1.27E-09
vg0719091461 sf0719090468 7 19091461 NA 1.00E-25
vg0719057980 sf0719056987 7 19057980 NA 7.80E-25
vg0719055344 sf0719054351 7 19055344 NA 1.31E-22
vg0719065396 sf0719064403 7 19065396 NA 5.05E-15
vg0719192174 sf0719191181 7 19192174 NA 9.50E-15
vg0705591916 sf0705590917 7 5591916 NA 4.70E-11
vg0801031318 sf0801030320 8 1031318 NA 6.74E-11
vg0719466615 sf0719465622 7 19466615 NA 1.29E-10
vg0607478609 sf0607477610 6 7478609 NA 5.25E-10
vg0708220481 sf0708219486 7 8220481 NA 1.14E-09
vg0719505870 sf0719504877 7 19505870 NA 1.26E-09
vg1101516781 sf1101515782 11 1516781 NA 2.47E-09
vg0919718025 sf0919717615 9 19718025 NA 8.28E-09
vg0113011816 sf0113010790 1 13011816 NA 8.79E-09
vg0631160329 sf0631159331 6 31160329 NA 1.24E-08
vg1100721323 sf1100720326 11 721323 NA 1.35E-08
vg0130826614 sf0130825570 1 30826614 NA 1.64E-08
vg0428494128 sf0428308982 4 28494128 NA 1.91E-08
vg0130828230 sf0130827186 1 30828230 NA 2.26E-08
vg0720528667 sf0720527674 7 20528667 NA 3.97E-08
vg0718961965 sf0718960972 7 18961965 NA 4.28E-08
vg1103515499 sf1103511402 11 3515499 NA 5.20E-08
vg1104364656 sf1104360558 11 4364656 NA 6.90E-08
vg0718999754 sf0718998761 7 18999754 NA 3.90E-07