RiceVarMap2

Detailed information for vg1119375564:

Variant ID: vg1119375564 (JBrowse)

Variation Type: SNP

Chromosome: chr11

Position: 19375564

Reference Allele: T

Alternative Allele: C

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

ACACTGTTGGTTGTGACTTGTATGTTAATAATCCGTCATATTGCTATCTGTATGAAGTAGATGGTAACAAATCCGAGTCATCGGCACCTGCATGCGCCGC[T/C]
GCTGCCGCCTGCACGTAGAGACACCCTGACGCCACCGCATGACGTATTCCCCTTTGTCAATGGTTGCCGAATCAATCCAGACCTGTCCTTGTCGATCCGC

Reverse complement sequence

GCGGATCGACAAGGACAGGTCTGGATTGATTCGGCAACCATTGACAAAGGGGAATACGTCATGCGGTGGCGTCAGGGTGTCTCTACGTGCAGGCGGCAGC[A/G]
GCGGCGCATGCAGGTGCCGATGACTCGGATTTGTTACCATCTACTTCATACAGATAGCAATATGACGGATTATTAACATACAAGTCACAACCAACAGTGT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.20%	32.40%	0.30%	3.15%	NA
All Indica	2759	94.70%	1.40%	0.25%	3.55%	NA
All Japonica	1512	8.00%	90.90%	0.40%	0.66%	NA
Aus	269	79.20%	5.20%	0.37%	15.24%	NA
Indica I	595	96.50%	1.50%	0.34%	1.68%	NA
Indica II	465	91.60%	0.20%	0.43%	7.74%	NA
Indica III	913	97.70%	1.00%	0.00%	1.31%	NA
Indica Intermediate	786	91.90%	2.70%	0.38%	5.09%	NA
Temperate Japonica	767	4.20%	93.70%	0.78%	1.30%	NA
Tropical Japonica	504	11.10%	88.90%	0.00%	0.00%	NA
Japonica Intermediate	241	13.70%	86.30%	0.00%	0.00%	NA
VI/Aromatic	96	29.20%	70.80%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119375564	T -> DEL	LOC_Os11g32800.1	N	frameshift_variant	Average:32.228; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg1119375564	T -> C	LOC_Os11g32800.1	missense_variant ; p.Gln115Arg; MODERATE	nonsynonymous_codon ; Q115R	Average:32.228; most accessible tissue: Zhenshan97 root, score: 72.188	unknown	unknown	TOLERATED	1.00

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119375564	1.99E-06	1.99E-06	mr1187_2	Ind_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
vg1119375564	NA	5.16E-07	mr1354_2	Ind_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

Showing 1 to 2 of 2 entries

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Detailed information for vg1119375564:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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