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Detailed information for vg0825998501:

Variant ID: vg0825998501 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25998501
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:


TCTATAGAGCTATTCTTTGCACAGAGTGAAGATGGTTTACCATCTTTGTTCATCAAGAAGACCTCAAAGATAACATTGATCTTGGGGTCGATCTCAGTAA[G/T]
CAGCAGGAAGACAGCGATGTACTCACCATTACGGCCCTCACATCCACGCGGGAATAACAAAATCGTCGCATTGTGCTCCCCGGCCGAGATTCTTATTCCG

Reverse complement sequence

CGGAATAAGAATCTCGGCCGGGGAGCACAATGCGACGATTTTGTTATTCCCGCGTGGATGTGAGGGCCGTAATGGTGAGTACATCGCTGTCTTCCTGCTG[C/A]
TTACTGAGATCGACCCCAAGATCAATGTTATCTTTGAGGTCTTCTTGATGAACAAAGATGGTAAACCATCTTCACTCTGTGCAAAGAATAGCTCTATAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 4.30% 1.52% 0.00% NA
All Indica  2759 90.10% 7.40% 2.50% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 93.30% 1.20% 5.55% 0.00% NA
Indica II  465 94.60% 3.20% 2.15% 0.00% NA
Indica III  913 83.80% 15.00% 1.20% 0.00% NA
Indica Intermediate  786 92.50% 5.60% 1.91% 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 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0825998501 G -> T LOC_Os08g41150.1 missense_variant ; p.Leu67Ile; MODERATE nonsynonymous_codon ; L67I Average:55.713; most accessible tissue: Zhenshan97 young leaf, score: 65.28 unknown unknown TOLERATED 0.22