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Detailed information for vg0905906905:

Variant ID: vg0905906905 (JBrowse)	Variation Type: INDEL
Chromosome: chr09	Position: 5906905
Reference Allele: C	Alternative Allele: T,CCTTCATA
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGAAATTGAATTTTTCCTTCTCCCCACTTGGTGCTAAATCTCTTCGAAATTCCGAGACATGGTATCTTTGTCCCTTGTATGATACGAAATACCCAGGA[C/T,CCTTCATA]
GATTTGGATAGTCAACATCGATAGGATTATTGGTAGCTGTTGATATGGTTCCATGCCCTAAAGATCAATGATTAGCATCGGTATTGTGAATGTCTTCAAA

Reverse complement sequence

TTTGAAGACATTCACAATACCGATGCTAATCATTGATCTTTAGGGCATGGAACCATATCAACAGCTACCAATAATCCTATCGATGTTGACTATCCAAATC[G/A,TATGAAGG]
TCCTGGGTATTTCGTATCATACAAGGGACAAAGATACCATGTCTCGGAATTTCGAAGAGATTTAGCACCAAGTGGGGAGAAGGAAAAATTCAATTTCTTA

Allele Frequencies:

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	91.10%	5.10%	0.40%	2.94%	CCTTCATA: 0.49%
All Indica	2759	97.20%	2.80%	0.07%	0.00%	NA
All Japonica	1512	84.20%	4.20%	1.06%	9.13%	CCTTCATA: 1.46%
Aus	269	97.40%	2.20%	0.37%	0.00%	NA
Indica I	595	93.80%	5.90%	0.34%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	97.50%	2.50%	0.00%	0.00%	NA
Indica Intermediate	786	97.70%	2.30%	0.00%	0.00%	NA
Temperate Japonica	767	88.90%	3.00%	0.52%	6.78%	CCTTCATA: 0.78%
Tropical Japonica	504	82.90%	4.40%	2.18%	9.52%	CCTTCATA: 0.99%
Japonica Intermediate	241	71.80%	7.50%	0.41%	15.77%	CCTTCATA: 4.56%
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	0.00%	1.11%	CCTTCATA: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0905906905	C -> CCTTCATA	LOC_Os09g10820.1	downstream_gene_variant ; 1466.0bp to feature; MODIFIER	silent_mutation	Average:40.461; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg0905906905	C -> CCTTCATA	LOC_Os09g10830.1	downstream_gene_variant ; 64.0bp to feature; MODIFIER	silent_mutation	Average:40.461; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg0905906905	C -> CCTTCATA	LOC_Os09g10820-LOC_Os09g10830	intergenic_region ; MODIFIER	silent_mutation	Average:40.461; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg0905906905	C -> DEL	N	N	silent_mutation	Average:40.461; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg0905906905	C -> T	LOC_Os09g10820.1	downstream_gene_variant ; 1465.0bp to feature; MODIFIER	silent_mutation	Average:40.461; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg0905906905	C -> T	LOC_Os09g10830.1	downstream_gene_variant ; 65.0bp to feature; MODIFIER	silent_mutation	Average:40.461; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N
vg0905906905	C -> T	LOC_Os09g10820-LOC_Os09g10830	intergenic_region ; MODIFIER	silent_mutation	Average:40.461; most accessible tissue: Zhenshan97 young leaf, score: 57.78	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905906905	4.11E-06	4.11E-06	mr1293_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