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Detailed information for vg0905621270:

Variant ID: vg0905621270 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5621270
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGTGCTATCTTCATCTTCCGGGCAATTGTAAACTCCATACTCCTGATCATGAAGCTTGTGTGGATGATACTGGAAATCTGATGACTCTAACTCCTCAT[C/T]
AAAGCGATGACGAAGCTCTCCAATGGCCACCAAAGCTGCCTCCTGACAAGCATGAATATAATCTCTTCCTCCAGCTTCAAACATCATTGATGGAAGGTCT

Reverse complement sequence

AGACCTTCCATCAATGATGTTTGAAGCTGGAGGAAGAGATTATATTCATGCTTGTCAGGAGGCAGCTTTGGTGGCCATTGGAGAGCTTCGTCATCGCTTT[G/A]
ATGAGGAGTTAGAGTCATCAGATTTCCAGTATCATCCACACAAGCTTCATGATCAGGAGTATGGAGTTTACAATTGCCCGGAAGATGAAGATAGCACCAC

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 53.60% 46.40% 0.02% 0.00% NA
All Indica  2759 88.00% 12.00% 0.00% 0.00% NA
All Japonica  1512 1.00% 98.90% 0.07% 0.00% NA
Aus  269 18.20% 81.80% 0.00% 0.00% NA
Indica I  595 92.10% 7.90% 0.00% 0.00% NA
Indica II  465 84.90% 15.10% 0.00% 0.00% NA
Indica III  913 91.10% 8.90% 0.00% 0.00% NA
Indica Intermediate  786 83.00% 17.00% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.20% 0.13% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 44.40% 55.60% 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
vg0905621270 C -> T LOC_Os09g10310.1 missense_variant ; p.Asp87Asn; MODERATE nonsynonymous_codon ; D87N Average:52.171; most accessible tissue: Zhenshan97 young leaf, score: 67.83 unknown unknown TOLERATED 0.61