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Detailed information for vg0903742163:

Variant ID: vg0903742163 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3742163
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTTCTTGATGATGCATTTTGAGGAGTACGGTCCAGGTCTCGACTAGGGTGGGGACCGTGGGCGTCCTCGGCAACTTCGTTCTCCGTTACTCTGTCATC[G/A]
GTATGTTGTCGGGGATCTCGAGCAGGACCTTGCGGGGTTGGTTCGGCTGCGGTCAAGAAAGCAGAGTTGAGGTTGGCTATTGTCGACTATATATGTCTGA

Reverse complement sequence

TCAGACATATATAGTCGACAATAGCCAACCTCAACTCTGCTTTCTTGACCGCAGCCGAACCAACCCCGCAAGGTCCTGCTCGAGATCCCCGACAACATAC[C/T]
GATGACAGAGTAACGGAGAACGAAGTTGCCGAGGACGCCCACGGTCCCCACCCTAGTCGAGACCTGGACCGTACTCCTCAAAATGCATCATCAAGAAGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.90% 1.00% 0.04% 0.00% NA
All Indica  2759 98.20% 1.70% 0.07% 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  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 94.40% 5.20% 0.43% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.80% 0.00% 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  90 100.00% 0.00% 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
vg0903742163 G -> A LOC_Os09g07470.1 missense_variant ; p.Pro125Leu; MODERATE nonsynonymous_codon ; P125L Average:74.072; most accessible tissue: Zhenshan97 young leaf, score: 88.513 unknown unknown DELETERIOUS 0.00