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Detailed information for vg0226608626:

Variant ID: vg0226608626 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26608626
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCCTGTGAACGTATCACACACGACGAATATCAAATCAAGCAAACGTACGATGCATGCAAACTGACACGGATACTTCAATTAATTCGGTTCATCCACTT[T/C]
TAAGCGTAGTCCTGGTCGGCAACGGGCTGGTATGAGCCGATGAACACGTCGCCGTACACGAGCCCGGCGAGGCCGCCGCCGATCAGCGGGCCGACCCAGT

Reverse complement sequence

ACTGGGTCGGCCCGCTGATCGGCGGCGGCCTCGCCGGGCTCGTGTACGGCGACGTGTTCATCGGCTCATACCAGCCCGTTGCCGACCAGGACTACGCTTA[A/G]
AAGTGGATGAACCGAATTAATTGAAGTATCCGTGTCAGTTTGCATGCATCGTACGTTTGCTTGATTTGATATTCGTCGTGTGTGATACGTTCACAGGCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 1.00% 0.02% 0.00% NA
All Indica  2759 98.40% 1.60% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.80% 0.13% 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

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0226608626 T -> C LOC_Os02g44080.1 stop_retained_variant ; p.Ter249Ter; LOW N Average:71.6; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N