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Detailed information for vg1127402824:

Variant ID: vg1127402824 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27402824
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTGTTTACTTACGAATGTTCATGTGCATAATTAGAAAAAAAATGAGGGAGAAATAATCTATTAATTGCCTGAATTGCCTGCTATATGCATACGGGCAC[T/C]
GTTCTGTTTTTCTAATAGATATACTTCTTTCCATGTTTGACCAAACAGGTTCTTGTGGAACAGTGTATCATGCTCTGTGGTATGGTTCGGTATGTATGCC

Reverse complement sequence

GGCATACATACCGAACCATACCACAGAGCATGATACACTGTTCCACAAGAACCTGTTTGGTCAAACATGGAAAGAAGTATATCTATTAGAAAAACAGAAC[A/G]
GTGCCCGTATGCATATAGCAGGCAATTCAGGCAATTAATAGATTATTTCTCCCTCATTTTTTTTCTAATTATGCACATGAACATTCGTAAGTAAACAAAA

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	90.90%	8.40%	0.63%	0.00%	NA
All Indica	2759	97.60%	1.90%	0.47%	0.00%	NA
All Japonica	1512	77.40%	21.60%	0.99%	0.00%	NA
Aus	269	95.50%	4.10%	0.37%	0.00%	NA
Indica I	595	97.80%	1.70%	0.50%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	98.40%	1.60%	0.00%	0.00%	NA
Indica Intermediate	786	95.80%	2.90%	1.27%	0.00%	NA
Temperate Japonica	767	68.10%	30.20%	1.69%	0.00%	NA
Tropical Japonica	504	90.70%	9.30%	0.00%	0.00%	NA
Japonica Intermediate	241	79.70%	19.50%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	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
vg1127402824	T -> C	LOC_Os11g45280.1	intron_variant ; MODIFIER	silent_mutation	Average:57.728; most accessible tissue: Zhenshan97 young leaf, score: 78.347	N	N	N	N
vg1127402824	T -> C	LOC_Os11g45280.2	intron_variant ; MODIFIER	silent_mutation	Average:57.728; most accessible tissue: Zhenshan97 young leaf, score: 78.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127402824	1.21E-06	NA	Spikelet_length	All	YES	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