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Detailed information for vg0903742586:

Variant ID: vg0903742586 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3742586
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGAAGATTCCTGGTCATCTAAGTTGTGAAGGACGGAAGGATCGATGTCGATGAATCCGACCAGGCGATCTGCAGTTCCCATTTCGCATATCTTCCACG[G/A]
ATGCATCTCAAGGTTGCTCTCGGCGTTGGTGGATCGGATAGCAAGGGACATGGATCATGGATCCAGTAATCTCTAGAAGATCTTACAGCCGGTAAGTAGG

Reverse complement sequence

CCTACTTACCGGCTGTAAGATCTTCTAGAGATTACTGGATCCATGATCCATGTCCCTTGCTATCCGATCCACCAACGCCGAGAGCAACCTTGAGATGCAT[C/T]
CGTGGAAGATATGCGAAATGGGAACTGCAGATCGCCTGGTCGGATTCATCGACATCGATCCTTCCGTCCTTCACAACTTAGATGACCAGGAATCTTCAGG

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 98.80% 1.20% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 47.90% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0903742586 G -> A LOC_Os09g07470.1 missense_variant ; p.Pro18Ser; MODERATE nonsynonymous_codon ; P18S Average:61.906; most accessible tissue: Zhenshan97 young leaf, score: 81.353 unknown unknown DELETERIOUS 0.00