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Detailed information for vg0707363161:

Variant ID: vg0707363161 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 7363161
Reference Allele: T	Alternative Allele: C,TCAGTTATGGAATTAAACATCGTGAATTGATTCC
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.59, T: 0.42, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCGCTCTCTCGTTTTGTAACGGACGGTAATAAACATGGAGAATTGATTTCGTATCAATGAACGCGTCGGTTACGGAATTAAACGTCGTGAATTGATTC[T/C,TCAGTTATGGAATTAAACATCGTGAATTGATTCC]
GTCGGTTATGGAATTAAACGCCGTGAATTGATTCCGTATTAACGAGCGCGTCGGTTATGAAATTAAACACCGCGGTTGATGACTCTGAACGTTACTCTCG

Reverse complement sequence

CGAGAGTAACGTTCAGAGTCATCAACCGCGGTGTTTAATTTCATAACCGACGCGCTCGTTAATACGGAATCAATTCACGGCGTTTAATTCCATAACCGAC[A/G,GGAATCAATTCACGATGTTTAATTCCATAACTGA]
GAATCAATTCACGACGTTTAATTCCGTAACCGACGCGTTCATTGATACGAAATCAATTCTCCATGTTTATTACCGTCCGTTACAAAACGAGAGAGCGCAG

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	39.40%	15.10%	36.35%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 9.16%
All Indica	2759	10.90%	15.20%	58.64%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 15.26%
All Japonica	1512	79.50%	16.90%	3.44%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 0.20%
Aus	269	88.10%	5.60%	4.46%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 1.86%
Indica I	595	5.40%	6.70%	77.98%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 9.92%
Indica II	465	9.50%	18.90%	55.05%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 16.56%
Indica III	913	8.70%	21.10%	50.60%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 19.61%
Indica Intermediate	786	18.60%	12.50%	55.47%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 13.49%
Temperate Japonica	767	95.70%	3.30%	0.91%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 0.13%
Tropical Japonica	504	68.10%	23.60%	8.13%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 0.20%
Japonica Intermediate	241	51.90%	46.10%	1.66%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 0.41%
VI/Aromatic	96	79.20%	13.50%	7.29%	0.00%	NA
Intermediate	90	52.20%	11.10%	32.22%	0.00%	TCAGTTATGGAATTAAACATCGTGAATTGATTCC: 4.44%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0707363161	T -> TCAGTTATGGAATTAAACATCGTGAATTGA TTCC	LOC_Os07g12850.1	upstream_gene_variant ; 379.0bp to feature; MODIFIER	silent_mutation	Average:22.661; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0707363161	T -> TCAGTTATGGAATTAAACATCGTGAATTGA TTCC	LOC_Os07g12840.1	downstream_gene_variant ; 854.0bp to feature; MODIFIER	silent_mutation	Average:22.661; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0707363161	T -> TCAGTTATGGAATTAAACATCGTGAATTGA TTCC	LOC_Os07g12840-LOC_Os07g12850	intergenic_region ; MODIFIER	silent_mutation	Average:22.661; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0707363161	T -> C	LOC_Os07g12850.1	upstream_gene_variant ; 380.0bp to feature; MODIFIER	silent_mutation	Average:22.661; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0707363161	T -> C	LOC_Os07g12840.1	downstream_gene_variant ; 853.0bp to feature; MODIFIER	silent_mutation	Average:22.661; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0707363161	T -> C	LOC_Os07g12840-LOC_Os07g12850	intergenic_region ; MODIFIER	silent_mutation	Average:22.661; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707363161	7.97E-06	NA	mr1008_2	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
vg0707363161	NA	5.41E-07	mr1064_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
vg0707363161	NA	5.02E-17	mr1457_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
vg0707363161	NA	1.39E-06	mr1559_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
vg0707363161	NA	6.97E-08	mr1680_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