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Detailed information for vg0719012268:

Variant ID: vg0719012268 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19012268
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGGGGTAGCGTCAAATTCTCGCCGACTAAGTGCGATGGGTTTCGTTTCTGGCATCGACGACTTCGCCTTCCCCCCGGGCAGGCGTTCCGGTTCGGCAGC[T/C]
TCAACTTCATCACCAATGACTTCGGCAAGATCTCTCTCCTTGACTCGGATTCAAACCAGTCGGGGAGAGACCAGGTCCCCGTGCCATTCGGTATTCCGAA

Reverse complement sequence

TTCGGAATACCGAATGGCACGGGGACCTGGTCTCTCCCCGACTGGTTTGAATCCGAGTCAAGGAGAGAGATCTTGCCGAAGTCATTGGTGATGAAGTTGA[A/G]
GCTGCCGAACCGGAACGCCTGCCCGGGGGGAAGGCGAAGTCGTCGATGCCAGAAACGAAACCCATCGCACTTAGTCGGCGAGAATTTGACGCTACCCCTA

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	56.90%	0.30%	7.96%	34.91%	NA
All Indica	2759	47.70%	0.40%	11.67%	40.20%	NA
All Japonica	1512	74.70%	0.00%	2.91%	22.42%	NA
Aus	269	56.90%	0.00%	0.37%	42.75%	NA
Indica I	595	34.10%	0.20%	11.76%	53.95%	NA
Indica II	465	37.80%	0.20%	9.68%	52.26%	NA
Indica III	913	62.70%	0.80%	10.51%	26.07%	NA
Indica Intermediate	786	46.60%	0.30%	14.12%	39.06%	NA
Temperate Japonica	767	96.70%	0.00%	0.00%	3.26%	NA
Tropical Japonica	504	45.20%	0.00%	7.94%	46.83%	NA
Japonica Intermediate	241	66.00%	0.00%	1.66%	32.37%	NA
VI/Aromatic	96	40.60%	0.00%	1.04%	58.33%	NA
Intermediate	90	55.60%	1.10%	8.89%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719012268	T -> DEL	N	N	silent_mutation	Average:12.71; most accessible tissue: Callus, score: 42.878	N	N	N	N
vg0719012268	T -> C	LOC_Os07g31960.1	upstream_gene_variant ; 2623.0bp to feature; MODIFIER	silent_mutation	Average:12.71; most accessible tissue: Callus, score: 42.878	N	N	N	N
vg0719012268	T -> C	LOC_Os07g31960-LOC_Os07g31980	intergenic_region ; MODIFIER	silent_mutation	Average:12.71; most accessible tissue: Callus, score: 42.878	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719012268	NA	4.87E-12	mr1155	Ind_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
vg0719012268	NA	1.28E-07	mr1213	Ind_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
vg0719012268	3.15E-09	NA	mr1155_2	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
vg0719012268	2.18E-08	1.63E-13	mr1155_2	Ind_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