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Detailed information for vg0909301676:

Variant ID: vg0909301676 (JBrowse)	Variation Type: INDEL
Chromosome: chr09	Position: 9301676
Reference Allele: A	Alternative Allele: G,AGTTG
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCTATTATCACGAAACTACAGGTCAATGCTAAAACCTGTAGTTTTGTGATAATGAAGACACTAAACTTGTAGTTTTGGGATAAATGAAGATATTAAATCT[A/G,AGTTG]
TAGTTTTGTGAAACAAATTCTTAAATATGTAATTTTGTGAAATATTGTACAAAGTCCATGTAGTTTTGTGATAAACGAAGGCACTGAATCTGTAGTTTTG

Reverse complement sequence

CAAAACTACAGATTCAGTGCCTTCGTTTATCACAAAACTACATGGACTTTGTACAATATTTCACAAAATTACATATTTAAGAATTTGTTTCACAAAACTA[T/C,CAACT]
AGATTTAATATCTTCATTTATCCCAAAACTACAAGTTTAGTGTCTTCATTATCACAAAACTACAGGTTTTAGCATTGACCTGTAGTTTCGTGATAATAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.70%	29.80%	0.34%	0.00%	AGTTG: 2.16%
All Indica	2759	90.90%	8.40%	0.54%	0.00%	AGTTG: 0.07%
All Japonica	1512	25.90%	74.00%	0.00%	0.00%	AGTTG: 0.13%
Aus	269	85.90%	2.20%	0.00%	0.00%	AGTTG: 11.90%
Indica I	595	92.60%	6.40%	1.01%	0.00%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	83.60%	16.00%	0.44%	0.00%	NA
Indica Intermediate	786	93.90%	5.30%	0.51%	0.00%	AGTTG: 0.25%
Temperate Japonica	767	12.90%	87.10%	0.00%	0.00%	NA
Tropical Japonica	504	37.70%	62.30%	0.00%	0.00%	NA
Japonica Intermediate	241	42.30%	56.80%	0.00%	0.00%	AGTTG: 0.83%
VI/Aromatic	96	24.00%	16.70%	0.00%	0.00%	AGTTG: 59.38%
Intermediate	90	48.90%	40.00%	1.11%	0.00%	AGTTG: 10.00%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909301676	A -> G	LOC_Os09g15260-LOC_Os09g15270	intergenic_region ; MODIFIER	silent_mutation	Average:23.144; most accessible tissue: Callus, score: 46.034	N	N	N	N
vg0909301676	A -> AGTTG	LOC_Os09g15260-LOC_Os09g15270	intergenic_region ; MODIFIER	silent_mutation	Average:23.144; most accessible tissue: Callus, score: 46.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909301676	3.13E-06	NA	mr1133_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
vg0909301676	1.06E-06	NA	mr1133_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
vg0909301676	NA	9.10E-07	mr1263_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
vg0909301676	NA	1.63E-07	mr1727_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