RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0105931184:

Variant ID: vg0105931184 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5931184
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTGAACACGATTGAATTCACCAGAAGAAATTCCACCAATGATTGCATTTCTTGCACGATAATTAAAATCAACCTGAGCCATATTTGCAGGCGTGATGT[C/T]
AGCATCATCGGGCACAGTGTAAGGTGATTTAACCTTATTCCACACATTATGCCCTTGCGACTGGAGGTAGGCCTCCATTCGTGCCTTCCAAATGACAAAA

Reverse complement sequence

TTTTGTCATTTGGAAGGCACGAATGGAGGCCTACCTCCAGTCGCAAGGGCATAATGTGTGGAATAAGGTTAAATCACCTTACACTGTGCCCGATGATGCT[G/A]
ACATCACGCCTGCAAATATGGCTCAGGTTGATTTTAATTATCGTGCAAGAAATGCAATCATTGGTGGAATTTCTTCTGGTGAATTCAATCGTGTTCAACA

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	96.30%	3.70%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	88.90%	11.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	97.30%	2.70%	0.00%	0.00%	NA
Tropical Japonica	504	93.50%	6.50%	0.00%	0.00%	NA
Japonica Intermediate	241	52.70%	47.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0105931184	C -> T	LOC_Os01g11120.1	downstream_gene_variant ; 3389.0bp to feature; MODIFIER	silent_mutation	Average:32.213; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0105931184	C -> T	LOC_Os01g11110.2	intron_variant ; MODIFIER	silent_mutation	Average:32.213; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105931184	NA	2.16E-06	mr1114	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
vg0105931184	NA	5.00E-08	mr1117	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
vg0105931184	NA	9.41E-08	mr1118	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
vg0105931184	NA	8.95E-07	mr1119	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
vg0105931184	NA	8.47E-06	mr1120	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
vg0105931184	NA	2.48E-09	mr1123	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
vg0105931184	NA	4.63E-06	mr1240	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
vg0105931184	NA	1.07E-07	mr1242	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
vg0105931184	NA	3.01E-08	mr1247	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
vg0105931184	NA	1.48E-07	mr1496	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

Showing 1 to 10 of 28 entries

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Search for Variation information by Variation ID:

Detailed information for vg0105931184:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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