RiceVarMap2

Detailed information for vg0226609031:

Variant ID: vg0226609031 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 26609031

Reference Allele: G

Alternative Allele: A

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TGACGATCTCCATCACGACGCCCTCCAGCTCGCTGATGCCGGCGACGCCGTGCGTCGGGATGGCCTACACGCGTTCGGATATCGAATTCACCGGTTAATC[G/A]
CGCTGTCCTTCTTGTCGGGAAATATATACACAGCAGTTTAAATCTAAGCCTTTAATCTATGGCGATGGTGTGCGTGCTGACCTTGCCGTGGGTGACAAAC

Reverse complement sequence

GTTTGTCACCCACGGCAAGGTCAGCACGCACACCATCGCCATAGATTAAAGGCTTAGATTTAAACTGCTGTGTATATATTTCCCGACAAGAAGGACAGCG[C/T]
GATTAACCGGTGAATTCGATATCCGAACGCGTGTAGGCCATCCCGACGCACGGCGTCGCCGGCATCAGCGAGCTGGAGGGCGTCGTGATGGAGATCGTCA

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	60.40%	39.50%	0.04%	0.00%	NA
All Indica	2759	92.00%	7.90%	0.07%	0.00%	NA
All Japonica	1512	0.60%	99.40%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	98.20%	1.80%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	83.60%	16.30%	0.11%	0.00%	NA
Indica Intermediate	786	93.60%	6.20%	0.13%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	43.30%	56.70%	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

60.40%

39.50%

0.04%