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 mr1024 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
vg1207772422 sf1207769828 12 7772422 3.76E-31 4.50E-09
vg0820974361 sf0820971648 8 20974361 1.44E-30 6.05E-07
vg0820948192 sf0820945479 8 20948192 3.35E-30 4.34E-07
vg0406268372 sf0406263812 4 6268372 1.04E-29 NA
vg1014511015 sf1014439781 10 14511015 1.41E-29 7.93E-08
vg1017244739 sf1017173512 10 17244739 4.70E-29 1.58E-07
vg1219943666 sf1219915136 12 19943666 7.05E-29 9.44E-07
vg0711805910 sf0711804916 7 11805910 1.27E-27 1.47E-06
vg1219816057 sf1219787527 12 19816057 2.62E-27 9.25E-07
vg1227356558 sf1227322958 12 27356558 6.30E-27 2.29E-08
vg0310408153 sf0310407069 3 10408153 4.26E-26 1.73E-07
vg0414482821 sf0414473534 4 14482821 6.72E-26 3.47E-06
vg0501750139 sf0501750122 5 1750139 7.99E-26 8.82E-07
vg0123104631 sf0123103587 1 23104631 2.33E-25 3.25E-08
vg1206748987 sf1206747877 12 6748987 3.98E-25 NA
vg0123100456 sf0123099412 1 23100456 1.19E-24 1.17E-07
vg1009470579 sf1009399400 10 9470579 NA 8.99E-09
vg0335210290 sf0335203159 3 35210290 NA 1.75E-08
vg1123973539 sf1123507409 11 23973539 NA 2.60E-08
vg0620558743 sf0620557746 6 20558743 NA 1.93E-07
vg0919071881 sf0919071470 9 19071881 NA 2.82E-07
vg0123089366 sf0123088322 1 23089366 NA 8.34E-07
vg1120026145 sf1119560068 11 20026145 NA 1.08E-06
vg1215972544 sf1215969840 12 15972544 NA 1.11E-06
vg1227333750 sf1227300150 12 27333750 NA 1.33E-06
vg0618973254 sf0618972257 6 18973254 NA 1.70E-06
vg0334677333 sf0334670203 3 34677333 NA 2.23E-06
vg0914487465 sf0914486464 9 14487465 NA 2.38E-06
vg1207172574 sf1207169964 12 7172574 NA 3.15E-06
vg0912154976 sf0912153975 9 12154976 NA 3.83E-06
vg0131948952 sf0131947908 1 31948952 NA 4.11E-06
vg0516439203 sf0516381685 5 16439203 NA 4.24E-06
vg0323951924 sf0323950098 3 23951924 NA 7.60E-06