RiceVarMap2

Detailed information for vg1202830783:

Variant ID: vg1202830783 (JBrowse)

Variation Type: SNP

Chromosome: chr12

Position: 2830783

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.09, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTTCGAGAATATGCCTGAGAAAACTTCAGTTACATGGAGTTCATTATTTGCAGGATTTGTGCAGAATGGTCTCCATGAAGAGGTATTGTGTTTATTTC[A/G]
GAGTACACAAAGGGAAGGAATGCAATTGACTGAATTCACTGTTTCATCTATCCTCAGCACATGTGCAAGCTTAGCATTGATAATTGAAGGAACACAGGTG

Reverse complement sequence

CACCTGTGTTCCTTCAATTATCAATGCTAAGCTTGCACATGTGCTGAGGATAGATGAAACAGTGAATTCAGTCAATTGCATTCCTTCCCTTTGTGTACTC[T/C]
GAAATAAACACAATACCTCTTCATGGAGACCATTCTGCACAAATCCTGCAAATAATGAACTCCATGTAACTGAAGTTTTCTCAGGCATATTCTCGAAAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.90%	0.10%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	0.00%	NA

Populations

Population Size

Frequency of A(primary allele)

Frequency of G(secondary allele)

Frequency of N

Frequency of DEL

Frequency of others Allele

All

4726

99.90%

0.10%

0.00%