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Detailed information for vg0103300358:

Variant ID: vg0103300358 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3300358
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAGCAAGCTAATAAAAACATAAAAAATTTACAACACAATCACACAAGAGCAACAGCAATTAAAACAGAAACACAAAAGAACCACGTATCCACCGTCCAA[T/C]
TATAATTCCATGCCTCCTGAATTGATGAAATGCGCAACTGTGCAAGTGTAAGTGTTACAAATGCAGGCATTTTTATAGGGTGCCTAGTGCTTAGGAGGGC

Reverse complement sequence

GCCCTCCTAAGCACTAGGCACCCTATAAAAATGCCTGCATTTGTAACACTTACACTTGCACAGTTGCGCATTTCATCAATTCAGGAGGCATGGAATTATA[A/G]
TTGGACGGTGGATACGTGGTTCTTTTGTGTTTCTGTTTTAATTGCTGTTGCTCTTGTGTGATTGTGTTGTAAATTTTTTATGTTTTTATTAGCTTGCTGC

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	32.50%	32.20%	34.47%	0.85%	NA
All Indica	2759	28.80%	26.20%	43.97%	1.05%	NA
All Japonica	1512	25.90%	49.20%	24.27%	0.66%	NA
Aus	269	85.10%	7.10%	7.81%	0.00%	NA
Indica I	595	27.90%	12.80%	58.66%	0.67%	NA
Indica II	465	38.10%	20.20%	40.65%	1.08%	NA
Indica III	913	22.90%	38.40%	37.68%	0.99%	NA
Indica Intermediate	786	30.80%	25.70%	42.11%	1.40%	NA
Temperate Japonica	767	39.00%	25.80%	35.07%	0.13%	NA
Tropical Japonica	504	5.40%	82.70%	10.12%	1.79%	NA
Japonica Intermediate	241	27.00%	53.50%	19.50%	0.00%	NA
VI/Aromatic	96	92.70%	4.20%	3.12%	0.00%	NA
Intermediate	90	36.70%	34.40%	27.78%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103300358	T -> DEL	N	N	silent_mutation	Average:17.992; most accessible tissue: Callus, score: 39.49	N	N	N	N
vg0103300358	T -> C	LOC_Os01g06990.1	upstream_gene_variant ; 1948.0bp to feature; MODIFIER	silent_mutation	Average:17.992; most accessible tissue: Callus, score: 39.49	N	N	N	N
vg0103300358	T -> C	LOC_Os01g07000.1	downstream_gene_variant ; 84.0bp to feature; MODIFIER	silent_mutation	Average:17.992; most accessible tissue: Callus, score: 39.49	N	N	N	N
vg0103300358	T -> C	LOC_Os01g07010.1	downstream_gene_variant ; 3165.0bp to feature; MODIFIER	silent_mutation	Average:17.992; most accessible tissue: Callus, score: 39.49	N	N	N	N
vg0103300358	T -> C	LOC_Os01g06990-LOC_Os01g07000	intergenic_region ; MODIFIER	silent_mutation	Average:17.992; most accessible tissue: Callus, score: 39.49	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103300358	2.53E-06	2.53E-06	mr1703	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