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Detailed information for vg0704650105:

Variant ID: vg0704650105 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4650105
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTTCGTCAAACACTTGGTAGTTGTCACCATGTAGAACTCATTAGTATCAACCAAGCTGATTGAATTGGCCTCATCACTGACCTCCAATGTGTTGGGGA[C/T]
AGATTTAGTGTTGGTGCTTTTAGCTGTCACCACTCTGGTGATACCAACGCTCGTGATTGACTCAAGCTTGATGTTGCGGCATGTCACAAGCATGTTGTTG

Reverse complement sequence

CAACAACATGCTTGTGACATGCCGCAACATCAAGCTTGAGTCAATCACGAGCGTTGGTATCACCAGAGTGGTGACAGCTAAAAGCACCAACACTAAATCT[G/A]
TCCCCAACACATTGGAGGTCAGTGATGAGGCCAATTCAATCAGCTTGGTTGATACTAATGAGTTCTACATGGTGACAACTACCAAGTGTTTGACGAAAGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 2.50% 0.74% 0.00% NA
All Indica  2759 94.50% 4.30% 1.20% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.60% 2.20% 3.19% 0.00% NA
Indica II  465 94.60% 4.30% 1.08% 0.00% NA
Indica III  913 91.70% 8.10% 0.22% 0.00% NA
Indica Intermediate  786 97.60% 1.50% 0.89% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 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 98.90% 0.00% 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
vg0704650105 C -> T LOC_Os07g08940.1 missense_variant ; p.Val151Ile; MODERATE nonsynonymous_codon ; V151I Average:46.279; most accessible tissue: Zhenshan97 young leaf, score: 67.83 unknown unknown TOLERATED 0.14