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Detailed information for vg0714437365:

Variant ID: vg0714437365 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14437365
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, C: 0.23, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

GCAAGGAACTGTATGGTTGGGTGAGAGAATCTGTGTCCCAGATAACAAAGATTTGAAAGATGCAATTCTAAAGGAAGCCCATTATACGTTATACTCCATT[G/C]
ACCCTGGTAGTACTAAGATGTACCAGGATCTCAAGGAAAGATTTTGGTGGGCAAGTATGAAGCGTGAGATCGCAGAATATGTAGCGGTATGTGACGTTTG

Reverse complement sequence

CAAACGTCACATACCGCTACATATTCTGCGATCTCACGCTTCATACTTGCCCACCAAAATCTTTCCTTGAGATCCTGGTACATCTTAGTACTACCAGGGT[C/G]
AATGGAGTATAACGTATAATGGGCTTCCTTTAGAATTGCATCTTTCAAATCTTTGTTATCTGGGACACAGATTCTCTCACCCAACCATACAGTTCCTTGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.40%	2.30%	28.61%	26.64%	NA
All Indica	2759	20.90%	2.00%	38.53%	38.56%	NA
All Japonica	1512	81.90%	2.90%	10.98%	4.23%	NA
Aus	269	20.80%	3.00%	36.06%	40.15%	NA
Indica I	595	42.00%	2.20%	15.97%	39.83%	NA
Indica II	465	24.30%	0.20%	44.52%	30.97%	NA
Indica III	913	3.00%	3.00%	46.99%	47.10%	NA
Indica Intermediate	786	23.70%	1.90%	42.24%	32.19%	NA
Temperate Japonica	767	81.40%	4.40%	12.39%	1.83%	NA
Tropical Japonica	504	93.10%	0.00%	3.77%	3.17%	NA
Japonica Intermediate	241	60.20%	4.10%	21.58%	14.11%	NA
VI/Aromatic	96	83.30%	1.00%	8.33%	7.29%	NA
Intermediate	90	61.10%	1.10%	20.00%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714437365	G -> DEL	N	N	silent_mutation	Average:11.478; most accessible tissue: Callus, score: 26.58	N	N	N	N
vg0714437365	G -> C	LOC_Os07g25280.1	downstream_gene_variant ; 2899.0bp to feature; MODIFIER	silent_mutation	Average:11.478; most accessible tissue: Callus, score: 26.58	N	N	N	N
vg0714437365	G -> C	LOC_Os07g25270.1	intron_variant ; MODIFIER	silent_mutation	Average:11.478; most accessible tissue: Callus, score: 26.58	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714437365	NA	5.46E-07	mr1554	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
vg0714437365	9.51E-07	6.74E-07	mr1758	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
vg0714437365	NA	4.53E-06	mr1118_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
vg0714437365	NA	4.30E-07	mr1733_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