RiceVarMap2

Detailed information for vg0431565329:

Variant ID: vg0431565329 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 31565329

Reference Allele: C

Alternative Allele: A,T

Primary Allele: C

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCATCTCCGCTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATATCATCCATTCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTT[C/A,T]
GGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATTAAAGTTCAGGGTTGCCCCAAACTGATACCGTTGTTGGTGAGTGGTAAGATGG

Reverse complement sequence

CCATCTTACCACTCACCAACAACGGTATCAGTTTGGGGCAACCCTGAACTTTAATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACC[G/T,A]
AACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGAATGGATGATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAGCGGAGATGGAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.90%	25.70%	11.79%	19.59%	T: 0.06%
All Indica	2759	23.00%	33.40%	13.30%	30.23%	T: 0.04%
All Japonica	1512	76.10%	10.00%	9.33%	4.50%	T: 0.07%
Aus	269	55.80%	29.70%	11.52%	2.60%	T: 0.37%
Indica I	595	28.10%	22.40%	18.99%	30.59%	NA
Indica II	465	25.80%	28.20%	16.77%	29.25%	NA
Indica III	913	13.50%	47.50%	7.78%	31.11%	T: 0.11%
Indica Intermediate	786	28.60%	28.50%	13.36%	29.52%	NA
Temperate Japonica	767	93.60%	2.30%	3.39%	0.65%	NA
Tropical Japonica	504	45.00%	23.60%	20.04%	11.11%	T: 0.20%
Japonica Intermediate	241	85.50%	5.80%	5.81%	2.90%	NA
VI/Aromatic	96	40.60%	42.70%	11.46%	5.21%	NA
Intermediate	90	57.80%	21.10%	7.78%	13.33%	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
vg0431565329	C -> DEL	LOC_Os04g53000.1	N	frameshift_variant	Average:50.26; most accessible tissue: Callus, score: 73.976	N	N	N	N
vg0431565329	C -> A	LOC_Os04g53000.1	missense_variant ; p.Phe62Leu; MODERATE	nonsynonymous_codon ; F62L	Average:50.26; most accessible tissue: Callus, score: 73.976	benign	-0.23	TOLERATED	0.13
vg0431565329	C -> T	LOC_Os04g53000.1	synonymous_variant ; p.Phe62Phe; LOW	synonymous_codon	Average:50.26; most accessible tissue: Callus, score: 73.976	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431565329	NA	3.00E-08	mr1940_2	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

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Detailed information for vg0431565329:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

RiceVarMap v2.0

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