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Detailed information for vg0610211070:

Variant ID: vg0610211070 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10211070
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTTCTTGCTGATTGCAGGATCAAATCAGCTGGCACGCCCTTGACACAATCGAGGCTAGCCTTGGACCTACACTGGAGTTATGCAGATCTCCCAATCCA[T/C]
CGTGTTGTCCGTCAACAGCTGGGTATTGTATCGGTTGGAACAGAGCATGACTTAGCCGATATGGCAAGTGGCCGATACGATATGACTTGGGCTCGATATG

Reverse complement sequence

CATATCGAGCCCAAGTCATATCGTATCGGCCACTTGCCATATCGGCTAAGTCATGCTCTGTTCCAACCGATACAATACCCAGCTGTTGACGGACAACACG[A/G]
TGGATTGGGAGATCTGCATAACTCCAGTGTAGGTCCAAGGCTAGCCTCGATTGTGTCAAGGGCGTGCCAGCTGATTTGATCCTGCAATCAGCAAGAAAGA

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	91.00%	4.70%	0.32%	4.02%	NA
All Indica	2759	88.00%	6.10%	0.33%	5.62%	NA
All Japonica	1512	97.80%	0.40%	0.40%	1.46%	NA
Aus	269	84.40%	15.20%	0.00%	0.37%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	91.40%	1.50%	1.29%	5.81%	NA
Indica III	913	76.30%	12.00%	0.11%	11.50%	NA
Indica Intermediate	786	90.60%	6.20%	0.25%	2.93%	NA
Temperate Japonica	767	97.80%	0.30%	0.52%	1.43%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	94.20%	1.70%	0.83%	3.32%	NA
VI/Aromatic	96	86.50%	5.20%	0.00%	8.33%	NA
Intermediate	90	93.30%	2.20%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610211070	T -> C	LOC_Os06g17590.1	synonymous_variant ; p.His185His; LOW	nonsynonymous_codon ; H185R	Average:46.824; most accessible tissue: Zhenshan97 young leaf, score: 83.831	unknown	unknown	DELETERIOUS	0.00
vg0610211070	T -> DEL	LOC_Os06g17590.1	N	frameshift_variant	Average:46.824; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610211070	4.10E-06	NA	mr1165_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
vg0610211070	2.39E-07	NA	mr1695_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