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Detailed information for vg0500377042:

Variant ID: vg0500377042 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 377042
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTACATGGTGCTCATCTGCTCAAAATATGCCTTCCCGTCATCCAAGAGAGCTAGACGGGTACACGCGCAGAGGACACCAATGAAAGTGACTTCGTCTG[G/C]
TAGCAGCCCATGTTGATCGTCTAGATCATTCCTTGAAAAGGTAGGTGTAAGATCAATAAGGAACTAGAAATAACATGGAACAAAATAAGTAGCAGGATAT

Reverse complement sequence

ATATCCTGCTACTTATTTTGTTCCATGTTATTTCTAGTTCCTTATTGATCTTACACCTACCTTTTCAAGGAATGATCTAGACGATCAACATGGGCTGCTA[C/G]
CAGACGAAGTCACTTTCATTGGTGTCCTCTGCGCGTGTACCCGTCTAGCTCTCTTGGATGACGGGAAGGCATATTTTGAGCAGATGAGCACCATGTACAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 0.90% 0.11% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 97.10% 2.60% 0.33% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 94.00% 5.00% 0.99% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 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
vg0500377042 G -> C LOC_Os05g01635.1 missense_variant ; p.Pro364Ala; MODERATE nonsynonymous_codon ; P364A Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 unknown unknown DELETERIOUS 0.00