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 mr1588 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
vg1001229450 sf1001228427 10 1229450 7.08E-13 1.47E-12
vg1001457645 sf1001456622 10 1457645 7.29E-11 9.02E-11
vg1001271744 sf1001270721 10 1271744 4.44E-10 2.18E-11
vg1001434429 sf1001433406 10 1434429 1.65E-09 1.07E-10
vg1002292707 sf1002291684 10 2292707 1.41E-08 NA
vg1001305839 sf1001304816 10 1305839 2.13E-08 1.18E-11
vg1213312673 sf1213310011 12 13312673 2.15E-08 1.99E-07
vg1214995596 sf1214992938 12 14995596 4.33E-08 3.96E-06
vg0529552096 sf0529489451 5 29552096 1.51E-07 1.27E-06
vg1001243005 sf1001241982 10 1243005 2.42E-07 1.35E-08
vg0807470225 sf0807469230 8 7470225 4.17E-07 6.10E-06
vg0707891668 sf0707890673 7 7891668 4.89E-07 7.87E-07
vg1001366206 sf1001365183 10 1366206 5.04E-07 2.88E-06
vg1001306734 sf1001305711 10 1306734 5.61E-07 1.27E-06
vg0320128318 sf0320126829 3 20128318 5.67E-07 1.84E-06
vg0403594374 sf0403589975 4 3594374 9.92E-07 2.22E-06
vg0412555488 sf0412546198 4 12555488 1.02E-06 2.59E-06
vg1002107770 sf1002106747 10 2107770 1.20E-06 3.11E-07
vg1023134528 sf1023063000 10 23134528 1.62E-06 4.64E-07
vg0319435119 sf0319433630 3 19435119 5.25E-06 2.35E-06
vg1219066039 sf1219037475 12 19066039 5.68E-06 4.55E-06
vg0821172360 sf0821169647 8 21172360 5.80E-06 4.24E-06
vg0212164216 sf0212155417 2 12164216 NA 2.28E-06
vg1217824132 sf1217795566 12 17824132 NA 2.84E-06