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Detailed information for vg1001332178:

Variant ID: vg1001332178 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1332178
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGCGAGGATTTGTGTTGCCTTGATGCTTCTCTCCGTTGGAACTGGCGGGTTGGTTGGCCATCTTCTTCGTCAGCAGAAAACTGAATTGACAATCTTTT[A/G]
GTACATGATCAGTTCCTTCACAAAAGAAACAAGTGATCCTGCTCGTTGGACACCTGTCGGGTGGATGGTCTTCCTCACAATGAACGCATGTAGTGGCACA

Reverse complement sequence

TGTGCCACTACATGCGTTCATTGTGAGGAAGACCATCCACCCGACAGGTGTCCAACGAGCAGGATCACTTGTTTCTTTTGTGAAGGAACTGATCATGTAC[T/C]
AAAAGATTGTCAATTCAGTTTTCTGCTGACGAAGAAGATGGCCAACCAACCCGCCAGTTCCAACGGAGAGAAGCATCAAGGCAACACAAATCCTCGCCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.70%	13.30%	2.29%	11.72%	NA
All Indica	2759	98.90%	0.90%	0.18%	0.07%	NA
All Japonica	1512	22.20%	38.60%	3.24%	35.98%	NA
Aus	269	97.80%	1.50%	0.37%	0.37%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	98.50%	1.30%	0.22%	0.00%	NA
Indica III	913	99.10%	0.70%	0.22%	0.00%	NA
Indica Intermediate	786	98.70%	0.80%	0.25%	0.25%	NA
Temperate Japonica	767	2.90%	71.10%	1.30%	24.77%	NA
Tropical Japonica	504	53.00%	1.60%	5.75%	39.68%	NA
Japonica Intermediate	241	19.10%	12.90%	4.15%	63.90%	NA
VI/Aromatic	96	42.70%	3.10%	52.08%	2.08%	NA
Intermediate	90	74.40%	16.70%	3.33%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001332178	A -> G	LOC_Os10g03160.1	downstream_gene_variant ; 4724.0bp to feature; MODIFIER	silent_mutation	Average:9.483; most accessible tissue: Callus, score: 12.817	N	N	N	N
vg1001332178	A -> G	LOC_Os10g03150.1	intron_variant ; MODIFIER	silent_mutation	Average:9.483; most accessible tissue: Callus, score: 12.817	N	N	N	N
vg1001332178	A -> DEL	N	N	silent_mutation	Average:9.483; most accessible tissue: Callus, score: 12.817	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001332178	NA	6.41E-07	mr1212_2	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
vg1001332178	NA	2.91E-12	mr1216_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