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Detailed information for vg0704650033:

Variant ID: vg0704650033 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4650033
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTCACTTTAGTGAGCTCAACTAAATCCTCGGTGGCCATGTCATCGTCATCATCATTGATCATTTGTTCATTGCCTTTCGTCAAACACTTGGTAGTTGTCA[C/T]
CATGTAGAACTCATTAGTATCAACCAAGCTGATTGAATTGGCCTCATCACTGACCTCCAATGTGTTGGGGACAGATTTAGTGTTGGTGCTTTTAGCTGTC

Reverse complement sequence

GACAGCTAAAAGCACCAACACTAAATCTGTCCCCAACACATTGGAGGTCAGTGATGAGGCCAATTCAATCAGCTTGGTTGATACTAATGAGTTCTACATG[G/A]
TGACAACTACCAAGTGTTTGACGAAAGGCAATGAACAAATGATCAATGATGATGACGATGACATGGCCACCGAGGATTTAGTTGAGCTCACTAAAGTGAA

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 88.90% 11.10% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 66.70% 33.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 41.70% 58.30% 0.00% 0.00% NA
Tropical Japonica  504 96.00% 4.00% 0.00% 0.00% NA
Japonica Intermediate  241 85.10% 14.90% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0704650033 C -> T LOC_Os07g08940.1 missense_variant ; p.Val175Met; MODERATE nonsynonymous_codon ; V175M Average:48.445; most accessible tissue: Zhenshan97 young leaf, score: 69.723 unknown unknown TOLERATED 0.18