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Detailed information for vg1200353813:

Variant ID: vg1200353813 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 353813
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

ATCCCTGGCTGCCAGGGAAGGGTCTGTTCCAATGGCTGGCTATGAGATATGTTTGCAAGTGTGGCTAACGATTTCTCTACTCAATGATGCACTAGCTCTT[G/T]
CTGGTCAGGTGTGTACATTTACAGGAACAGACCTTTAGTTTCTAGCCTCTAATTGTGTTCACTTGTAAAGTGTTCATAATATAATGCAGGCTCTACTTGC

Reverse complement sequence

GCAAGTAGAGCCTGCATTATATTATGAACACTTTACAAGTGAACACAATTAGAGGCTAGAAACTAAAGGTCTGTTCCTGTAAATGTACACACCTGACCAG[C/A]
AAGAGCTAGTGCATCATTGAGTAGAGAAATCGTTAGCCACACTTGCAAACATATCTCATAGCCAGCCATTGGAACAGACCCTTCCCTGGCAGCCAGGGAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.90%	19.90%	0.11%	0.15%	NA
All Indica	2759	68.00%	31.70%	0.14%	0.22%	NA
All Japonica	1512	96.80%	3.10%	0.00%	0.07%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	94.80%	5.20%	0.00%	0.00%	NA
Indica II	465	26.70%	72.50%	0.00%	0.86%	NA
Indica III	913	72.70%	27.10%	0.22%	0.00%	NA
Indica Intermediate	786	66.50%	33.00%	0.25%	0.25%	NA
Temperate Japonica	767	95.40%	4.60%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg1200353813	G -> DEL	LOC_Os12g01580.2	N	frameshift_variant	Average:66.181; most accessible tissue: Callus, score: 84.591	N	N	N	N
vg1200353813	G -> DEL	LOC_Os12g01580.1	N	frameshift_variant	Average:66.181; most accessible tissue: Callus, score: 84.591	N	N	N	N
vg1200353813	G -> T	LOC_Os12g01580.1	missense_variant ; p.Ala396Ser; MODERATE	nonsynonymous_codon ; A396S	Average:66.181; most accessible tissue: Callus, score: 84.591	unknown	unknown	TOLERATED	0.15
vg1200353813	G -> T	LOC_Os12g01580.2	missense_variant ; p.Ala185Ser; MODERATE	nonsynonymous_codon ; A185S	Average:66.181; most accessible tissue: Callus, score: 84.591	unknown	unknown	TOLERATED	0.28

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200353813	NA	9.99E-17	Grain_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1200353813	NA	8.33E-18	Grain_length	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1200353813	NA	6.59E-09	mr1174	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