RiceVarMap2

Phenotype and GWAS Information:

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 mr1118 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 ID	Variation ID V6	Chromosome	Position	LR P-value	LMM P-value
vg1006839627	sf1006855250	10	6839627	1.34E-39	9.31E-12
vg1007525105	sf1007540727	10	7525105	2.20E-35	1.12E-15
vg0407823811	sf0407819079	4	7823811	1.38E-28	1.47E-06
vg0407825052	sf0407820320	4	7825052	1.55E-28	5.62E-07
vg1009341357	sf1009270178	10	9341357	3.62E-28	1.17E-13
vg1009540574	sf1009469395	10	9540574	2.43E-27	1.60E-12
vg0403205317	sf0403200920	4	3205317	3.46E-26	5.88E-06
vg0813652209	sf0813649494	8	13652209	7.64E-26	9.64E-08
vg1005872232	sf1005888770	10	5872232	1.13E-25	3.80E-14
vg1202107668	sf1202106666	12	2107668	6.39E-25	4.72E-07
vg1006738188	sf1006753811	10	6738188	4.10E-23	2.85E-06
vg0407826743	sf0407822011	4	7826743	1.41E-22	5.56E-10
vg1216843191	sf1216837145	12	16843191	3.92E-21	8.83E-08
vg1005691354	sf1005707892	10	5691354	1.03E-20	5.32E-12
vg0110929029	sf0110928005	1	10929029	5.82E-19	2.48E-06
vg1010655699	sf1010584520	10	10655699	1.88E-18	1.49E-06
vg1005555827	sf1005572364	10	5555827	4.17E-16	1.40E-07
vg0407782850	sf0407778118	4	7782850	4.51E-15	1.66E-06
vg0905249361	sf0905248361	9	5249361	1.84E-14	2.45E-07
vg0315246434	sf0315245081	3	15246434	NA	4.19E-07
vg0710985476	sf0710984482	7	10985476	NA	2.96E-06
vg1127281051	sf1126809438	11	27281051	NA	3.61E-06

Variation ID

Variation ID V6

Chromosome

Position

LR P-value

LMM P-value

vg1006839627

sf1006855250

6839627

1.34E-39

9.31E-12

vg1007525105