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Detailed information for vg0403314769:

Variant ID: vg0403314769 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3314769
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCGCCCCGTGCCCGTTGTGCGGTTGTCGACCCCGGTACCCGTGTACCGGTGTCGGTAGTCGTTTGTGTGTGCGTGTGGTGACCGTGTTAGCGTGCTCG[T/C]
TCGGTAGCTGTCACGCCCAGAAATTTAACCTAAATTTCCAGACTATTTCGTGTATTAAATCCCTGTCCAGGACCAGTTAGGGTACACAAAACGACAAGTA

Reverse complement sequence

TACTTGTCGTTTTGTGTACCCTAACTGGTCCTGGACAGGGATTTAATACACGAAATAGTCTGGAAATTTAGGTTAAATTTCTGGGCGTGACAGCTACCGA[A/G]
CGAGCACGCTAACACGGTCACCACACGCACACACAAACGACTACCGACACCGGTACACGGGTACCGGGGTCGACAACCGCACAACGGGCACGGGGCGACA

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	40.70%	14.60%	1.63%	43.02%	NA
All Indica	2759	28.60%	3.20%	2.54%	65.64%	NA
All Japonica	1512	60.80%	29.70%	0.26%	9.26%	NA
Aus	269	45.70%	50.60%	0.74%	2.97%	NA
Indica I	595	22.90%	0.30%	1.85%	74.96%	NA
Indica II	465	37.40%	6.20%	2.80%	53.55%	NA
Indica III	913	25.00%	2.60%	2.52%	69.88%	NA
Indica Intermediate	786	32.10%	4.20%	2.93%	60.81%	NA
Temperate Japonica	767	88.00%	7.70%	0.00%	4.30%	NA
Tropical Japonica	504	26.60%	61.90%	0.20%	11.31%	NA
Japonica Intermediate	241	45.60%	32.40%	1.24%	20.75%	NA
VI/Aromatic	96	57.30%	4.20%	0.00%	38.54%	NA
Intermediate	90	41.10%	16.70%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403314769	T -> C	LOC_Os04g06340.1	upstream_gene_variant ; 3938.0bp to feature; MODIFIER	silent_mutation	Average:38.143; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0403314769	T -> C	LOC_Os04g06350.1	downstream_gene_variant ; 2079.0bp to feature; MODIFIER	silent_mutation	Average:38.143; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0403314769	T -> C	LOC_Os04g06360.1	intron_variant ; MODIFIER	silent_mutation	Average:38.143; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0403314769	T -> DEL	N	N	silent_mutation	Average:38.143; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403314769	NA	7.80E-06	mr1648	Ind_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
vg0403314769	NA	4.34E-08	mr1563_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