Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1022609740:

Variant ID: vg1022609740 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 22609740
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATGCCGACGAGAGGGGTCCCAGACCAACAACAGGTTAGGTCCCAGACCATACTGTGCCAGGAAGCCCAGGGGTCCTCCCCGACACCACCCCGGCGAAT[T/C]
CACATGTCTCTCGGCATCAAGGCTCCCCTGATAAGCTAGTTACTCAGCTAGGGGTGTCCCATTCCACCCATGTGGTCGTACTTGTCTTATGTTTAGATGA

Reverse complement sequence

TCATCTAAACATAAGACAAGTACGACCACATGGGTGGAATGGGACACCCCTAGCTGAGTAACTAGCTTATCAGGGGAGCCTTGATGCCGAGAGACATGTG[A/G]
ATTCGCCGGGGTGGTGTCGGGGAGGACCCCTGGGCTTCCTGGCACAGTATGGTCTGGGACCTAACCTGTTGTTGGTCTGGGACCCCTCTCGTCGGCATAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	19.10%	16.90%	3.17%	60.85%	NA
All Indica	2759	3.80%	0.10%	2.79%	93.22%	NA
All Japonica	1512	43.70%	51.50%	3.77%	1.06%	NA
Aus	269	9.70%	0.00%	2.60%	87.73%	NA
Indica I	595	4.50%	0.00%	1.68%	93.78%	NA
Indica II	465	3.20%	0.60%	1.94%	94.19%	NA
Indica III	913	2.00%	0.10%	3.40%	94.52%	NA
Indica Intermediate	786	5.90%	0.00%	3.44%	90.71%	NA
Temperate Japonica	767	49.50%	48.90%	0.52%	1.04%	NA
Tropical Japonica	504	42.90%	45.40%	10.32%	1.39%	NA
Japonica Intermediate	241	26.60%	72.60%	0.41%	0.41%	NA
VI/Aromatic	96	79.20%	7.30%	3.12%	10.42%	NA
Intermediate	90	37.80%	8.90%	6.67%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1022609740	T -> C	LOC_Os10g42050.1	upstream_gene_variant ; 4607.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022609740	T -> C	LOC_Os10g42040.1	downstream_gene_variant ; 1038.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022609740	T -> C	LOC_Os10g42040-LOC_Os10g42050	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022609740	T -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1022609740	NA	8.28E-12	Grain_weight	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1022609740	NA	5.05E-06	mr1293	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	5.53E-06	mr1373	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	1.39E-06	mr1392	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	3.18E-06	mr1418	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	4.33E-06	mr1507	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	1.22E-07	mr1604	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	1.42E-06	mr1633	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	2.62E-07	mr1810	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	1.36E-10	mr1921	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	2.09E-06	mr1060_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	8.74E-06	mr1164_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	NA	7.07E-06	mr1296_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1022609740	7.23E-07	7.23E-07	mr1360_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251