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Detailed information for vg1106199277:

Variant ID: vg1106199277 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 6199277
Reference Allele: T	Alternative Allele: C,TAAATTACTACCTCCGTTTTTTAATAGATGACGC,TAAATTACTATCTCCGTTTTTTAATAGATGACGC
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:

CAATCTCCCCAATTTCCTTCTCCTCAAAGGCTCAAACACACCCTATGTTGCCATATATTGGTAACACAACTATACAACAGCCTATCAAAACTAATATATT[T/C,TAAATTACTACCTCCGTTTTTTAATAGATGACGC,TAAATTACTATCTCCGTTTTTTAATAGATGACGC]
CATTGACTTTTTCTTACATGTTTGACTATTCGTCTTATTCAAAAAATTTACGTAATTATAATTTATTTTGTTATGAGTTGTTTTATCACTCATAGTACTT

Reverse complement sequence

AAGTACTATGAGTGATAAAACAACTCATAACAAAATAAATTATAATTACGTAAATTTTTTGAATAAGACGAATAGTCAAACATGTAAGAAAAAGTCAATG[A/G,GCGTCATCTATTAAAAAACGGAGGTAGTAATTTA,GCGTCATCTATTAAAAAACGGAGATAGTAATTTA]
AATATATTAGTTTTGATAGGCTGTTGTATAGTTGTGTTACCAATATATGGCAACATAGGGTGTGTTTGAGCCTTTGAGGAGAAGGAAATTGGGGAGATTG

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	32.50%	16.10%	14.33%	36.42%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.57%; TAAATTACTATCTCCGTTTTTTAATAGATGACGC: 0.08%
All Indica	2759	4.30%	21.50%	19.14%	54.22%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.87%; TAAATTACTATCTCCGTTTTTTAATAGATGACGC: 0.04%
All Japonica	1512	85.20%	6.50%	2.98%	5.16%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.13%
Aus	269	5.20%	20.80%	31.97%	40.52%	TAAATTACTATCTCCGTTTTTTAATAGATGACGC: 1.12%; TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.37%
Indica I	595	4.70%	10.10%	12.44%	72.27%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.50%
Indica II	465	4.30%	14.00%	13.55%	67.96%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.22%
Indica III	913	2.60%	35.90%	26.07%	34.17%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 1.20%
Indica Intermediate	786	5.90%	17.70%	19.47%	55.73%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 1.15%; TAAATTACTATCTCCGTTTTTTAATAGATGACGC: 0.13%
Temperate Japonica	767	93.00%	3.90%	0.52%	2.48%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.13%
Tropical Japonica	504	73.40%	11.50%	6.94%	8.13%	NA
Japonica Intermediate	241	85.10%	4.60%	2.49%	7.47%	TAAATTACTACCTCCGTTTTTTAATAGATGACGC: 0.41%
VI/Aromatic	96	88.50%	1.00%	5.21%	5.21%	NA
Intermediate	90	33.30%	15.60%	14.44%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106199277	T -> DEL	N	N	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> TAAATTACTATCTCCGTTTTTTAATAGATG ACGC	LOC_Os11g11200.1	upstream_gene_variant ; 1534.0bp to feature; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> TAAATTACTATCTCCGTTTTTTAATAGATG ACGC	LOC_Os11g11210.1	downstream_gene_variant ; 1891.0bp to feature; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> TAAATTACTATCTCCGTTTTTTAATAGATG ACGC	LOC_Os11g11200-LOC_Os11g11210	intergenic_region ; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> TAAATTACTACCTCCGTTTTTTAATAGATG ACGC	LOC_Os11g11200.1	upstream_gene_variant ; 1534.0bp to feature; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> TAAATTACTACCTCCGTTTTTTAATAGATG ACGC	LOC_Os11g11210.1	downstream_gene_variant ; 1891.0bp to feature; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> TAAATTACTACCTCCGTTTTTTAATAGATG ACGC	LOC_Os11g11200-LOC_Os11g11210	intergenic_region ; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> C	LOC_Os11g11200.1	upstream_gene_variant ; 1533.0bp to feature; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> C	LOC_Os11g11210.1	downstream_gene_variant ; 1892.0bp to feature; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N
vg1106199277	T -> C	LOC_Os11g11200-LOC_Os11g11210	intergenic_region ; MODIFIER	silent_mutation	Average:14.969; most accessible tissue: Callus, score: 28.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106199277	2.87E-06	2.87E-06	mr1954_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