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Detailed information for vg0710362097:

Variant ID: vg0710362097 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10362097
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCGCAGCAGGAAAACAGTGTTTGATATGGTTAAAGATCTTAAAGTAATGTTCGAAAAGGGGCCTGGAAGCCAGCCTATAGAGAGCGAAGATGGTCACG[C/T]
GGCGATGTGGAAAAAGAACTCTATATTTTGGGAGTTATCCTATTGGGAATTCTTGGATGTCCGCCACACAATTGACGTGATGCACCTCACTAAGACCTTT

Reverse complement sequence

AAAGGTCTTAGTGAGGTGCATCACGTCAATTGTGTGGCGGACATCCAAGAATTCCCAATAGGATAACTCCCAAAATATAGAGTTCTTTTTCCACATCGCC[G/A]
CGTGACCATCTTCGCTCTCTATAGGCTGGCTTCCAGGCCCCTTTTCGAACATTACTTTAAGATCTTTAACCATATCAAACACTGTTTTCCTGCTGCGATG

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	94.20%	4.60%	0.06%	1.21%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	88.00%	9.20%	0.00%	2.78%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	82.80%	17.20%	0.00%	0.00%	NA
Tropical Japonica	504	91.50%	0.40%	0.00%	8.13%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	24.00%	59.40%	1.04%	15.62%	NA
Intermediate	90	93.30%	4.40%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710362097	C -> DEL	N	N	silent_mutation	Average:19.042; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0710362097	C -> T	LOC_Os07g17530.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:19.042; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0710362097	C -> T	LOC_Os07g17540.1	upstream_gene_variant ; 4922.0bp to feature; MODIFIER	silent_mutation	Average:19.042; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710362097	3.59E-06	NA	mr1395	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
vg0710362097	NA	6.08E-06	mr1631_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