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 mr1778 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
vg1215824234 sf1215821531 12 15824234 1.40E-123 4.06E-31
vg1215869969 sf1215867265 12 15869969 1.16E-113 1.39E-34
vg0621221946 sf0621220949 6 21221946 4.30E-91 9.96E-08
vg0129570224 sf0129569179 1 29570224 2.51E-86 NA
vg0113354243 sf0113353217 1 13354243 9.04E-86 NA
vg1018643913 sf1018572470 10 18643913 2.41E-85 1.80E-07
vg1018571610 sf1018500167 10 18571610 4.95E-85 5.39E-08
vg0916677066 sf0916676065 9 16677066 9.05E-78 1.26E-09
vg0807183892 sf0807182897 8 7183892 1.50E-77 1.48E-07
vg0133494604 sf0133493560 1 33494604 1.07E-75 3.06E-10
vg1215969757 sf1215967053 12 15969757 NA 2.80E-16
vg1215981299 sf1215978595 12 15981299 NA 1.50E-15
vg1216993003 sf1216986957 12 16993003 NA 3.71E-12
vg1216281909 sf1216279205 12 16281909 NA 1.09E-11
vg1215894346 sf1215891642 12 15894346 NA 5.96E-11
vg1216298496 sf1216066554 12 16298496 NA 3.14E-10
vg1215397261 sf1215394559 12 15397261 NA 1.50E-09
vg1223681739 sf1223648192 12 23681739 NA 2.52E-09
vg1215321806 sf1215319104 12 15321806 NA 7.27E-09
vg1216023976 sf1216021272 12 16023976 NA 9.67E-09
vg0702437436 sf0702436437 7 2437436 NA 1.20E-08
vg1216514861 sf1216512154 12 16514861 NA 2.39E-08
vg1109319597 sf1109314174 11 9319597 NA 2.75E-08
vg1109270791 sf1109265368 11 9270791 NA 2.93E-08
vg1216492299 sf1216489592 12 16492299 NA 3.02E-08
vg1215216489 sf1215213786 12 15216489 NA 6.37E-08
vg0408410897 sf0408406171 4 8410897 NA 1.18E-07
vg1216319054 sf1216316350 12 16319054 NA 1.19E-07
vg1215129394 sf1215126730 12 15129394 NA 1.55E-07
vg0134802811 sf0134801768 1 34802811 NA 1.71E-07
vg0315351032 sf0315349679 3 15351032 NA 5.03E-07
vg0515954806 sf0515897313 5 15954806 NA 2.79E-06
vg1203045015 sf1203044017 12 3045015 NA 3.29E-06