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Detailed information for vg0815900368:

Variant ID: vg0815900368 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 15900368
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGCCGCGAGACGACGAGCCGGCGAGGAGGAACGGTGAAGACGACGACGGACACCGGCGGCGTTCGGTCGAAGGGGAGGCGAGGCCGAGGACGACCTTGC[C/T]
GCTGTGATGCCGAAGGAGGAGATGGCGACGTTGGACGGTGCACGGGCACGGCGGAAGGGACTGCCGGAGGAGATGTCGATGAGGAGGAAGGAGAGGCCAG

Reverse complement sequence

CTGGCCTCTCCTTCCTCCTCATCGACATCTCCTCCGGCAGTCCCTTCCGCCGTGCCCGTGCACCGTCCAACGTCGCCATCTCCTCCTTCGGCATCACAGC[G/A]
GCAAGGTCGTCCTCGGCCTCGCCTCCCCTTCGACCGAACGCCGCCGGTGTCCGTCGTCGTCTTCACCGTTCCTCCTCGCCGGCTCGTCGTCTCGCGGCGC

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	67.60%	8.50%	7.68%	16.23%	NA
All Indica	2759	67.10%	0.30%	10.11%	22.51%	NA
All Japonica	1512	64.30%	25.20%	3.84%	6.68%	NA
Aus	269	80.30%	1.10%	6.32%	12.27%	NA
Indica I	595	71.30%	0.00%	12.77%	15.97%	NA
Indica II	465	40.40%	0.20%	16.13%	43.23%	NA
Indica III	913	80.30%	0.10%	5.48%	14.13%	NA
Indica Intermediate	786	64.50%	0.60%	9.92%	24.94%	NA
Temperate Japonica	767	96.10%	1.00%	1.83%	1.04%	NA
Tropical Japonica	504	22.00%	59.70%	5.56%	12.70%	NA
Japonica Intermediate	241	51.50%	29.90%	6.64%	12.03%	NA
VI/Aromatic	96	95.80%	2.10%	2.08%	0.00%	NA
Intermediate	90	70.00%	8.90%	7.78%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0815900368	C -> T	LOC_Os08g26140.1	downstream_gene_variant ; 3419.0bp to feature; MODIFIER	silent_mutation	Average:62.094; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N
vg0815900368	C -> T	LOC_Os08g26120-LOC_Os08g26140	intergenic_region ; MODIFIER	silent_mutation	Average:62.094; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N
vg0815900368	C -> DEL	N	N	silent_mutation	Average:62.094; most accessible tissue: Zhenshan97 young leaf, score: 82.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0815900368	2.54E-06	2.54E-06	mr1659	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