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Detailed information for vg0911196891:

Variant ID: vg0911196891 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11196891
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAAATACCTTCCGGAGATGTAGCTAGGGAGACTTCAAGCGACAAATCCGAAGCAGGGACTAGCTCTGCGCAGGTGGCCGGTCTGACCGCCGGCCCCATA[T/C]
GGATTTGACCGAGCCTTCTGGCCGGTCTGACCCGGTGGTCTTCATCCGGTCTGACCGGGCTCCAGCACCGGTTTGACAGAAGATTCACGAAGGGTAGCTT

Reverse complement sequence

AAGCTACCCTTCGTGAATCTTCTGTCAAACCGGTGCTGGAGCCCGGTCAGACCGGATGAAGACCACCGGGTCAGACCGGCCAGAAGGCTCGGTCAAATCC[A/G]
TATGGGGCCGGCGGTCAGACCGGCCACCTGCGCAGAGCTAGTCCCTGCTTCGGATTTGTCGCTTGAAGTCTCCCTAGCTACATCTCCGGAAGGTATTTGC

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	54.00%	21.80%	1.93%	22.28%	NA
All Indica	2759	63.90%	2.90%	2.86%	30.37%	NA
All Japonica	1512	30.50%	59.90%	0.66%	8.99%	NA
Aus	269	98.50%	1.10%	0.00%	0.37%	NA
Indica I	595	84.20%	2.70%	0.50%	12.61%	NA
Indica II	465	43.90%	6.00%	3.44%	46.67%	NA
Indica III	913	62.20%	0.30%	4.05%	33.41%	NA
Indica Intermediate	786	62.30%	4.10%	2.93%	30.66%	NA
Temperate Japonica	767	28.00%	63.50%	0.91%	7.56%	NA
Tropical Japonica	504	40.70%	54.60%	0.20%	4.56%	NA
Japonica Intermediate	241	17.00%	59.30%	0.83%	22.82%	NA
VI/Aromatic	96	28.10%	13.50%	1.04%	57.29%	NA
Intermediate	90	40.00%	33.30%	1.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911196891	T -> DEL	N	N	silent_mutation	Average:53.816; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N
vg0911196891	T -> C	LOC_Os09g18250.1	downstream_gene_variant ; 4604.0bp to feature; MODIFIER	silent_mutation	Average:53.816; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N
vg0911196891	T -> C	LOC_Os09g18240.1	intron_variant ; MODIFIER	silent_mutation	Average:53.816; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911196891	2.02E-06	2.02E-06	mr1430_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