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Detailed information for vg0408104657:

Variant ID: vg0408104657 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8104657
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATTCCTGAATTTACCAAGTTTAGTGGTGAGGATAGTAGGACTACATGCGAGCATGTAGACCAATTCTTAGTGCAATGTGGTAGGGTTAATAGTGATA[T/C]
TTTTAAATTGCGCTTGTTTTCTTTATCTTTGTCCGGTACTGCTTTTACATGGTTTATTTCTTTACCGGCAAATTCTGTTAGTACTTGGGCTCAAATAGAA

Reverse complement sequence

TTCTATTTGAGCCCAAGTACTAACAGAATTTGCCGGTAAAGAAATAAACCATGTAAAAGCAGTACCGGACAAAGATAAAGAAAACAAGCGCAATTTAAAA[A/G]
TATCACTATTAACCCTACCACATTGCACTAAGAATTGGTCTACATGCTCGCATGTAGTCCTACTATCCTCACCACTAAACTTGGTAAATTCAGGAATTTT

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	40.30%	0.30%	14.45%	44.96%	NA
All Indica	2759	26.10%	0.30%	19.64%	54.01%	NA
All Japonica	1512	67.70%	0.40%	6.02%	25.93%	NA
Aus	269	27.10%	0.00%	13.01%	59.85%	NA
Indica I	595	20.20%	0.20%	8.40%	71.26%	NA
Indica II	465	31.20%	0.90%	20.86%	47.10%	NA
Indica III	913	25.40%	0.10%	29.24%	45.24%	NA
Indica Intermediate	786	28.20%	0.30%	16.28%	55.22%	NA
Temperate Japonica	767	96.30%	0.00%	0.78%	2.87%	NA
Tropical Japonica	504	19.20%	1.20%	14.29%	65.28%	NA
Japonica Intermediate	241	77.60%	0.00%	5.39%	17.01%	NA
VI/Aromatic	96	44.80%	1.00%	8.33%	45.83%	NA
Intermediate	90	50.00%	0.00%	7.78%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408104657	T -> C	LOC_Os04g14480.1	upstream_gene_variant ; 2553.0bp to feature; MODIFIER	silent_mutation	Average:9.944; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0408104657	T -> C	LOC_Os04g14490.1	intron_variant ; MODIFIER	silent_mutation	Average:9.944; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0408104657	T -> DEL	N	N	silent_mutation	Average:9.944; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408104657	NA	4.44E-07	mr1133	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
vg0408104657	NA	8.45E-06	mr1450	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
vg0408104657	2.23E-06	NA	mr1769	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
vg0408104657	NA	1.54E-07	mr1808_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