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Detailed information for vg0629061095:

Variant ID: vg0629061095 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29061095
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


CTCATATCTCTGTGCTGGTCATGCAGGCCAAGGCCGCTAAGAAACAAGTTAGTTTCTAGCACCAGCAATTGCTGCCAATATTTTCATCCAGAAGGCCAGA[G/A]
CACATTTCAGTACCATGTTAGCAATAAAATTGAAAAAAGGGAATCAAGTCAAAGAACTAACCTCATAAGTCAATTCATCATCTTGTTCAATCCTGTCCAA

Reverse complement sequence

TTGGACAGGATTGAACAAGATGATGAATTGACTTATGAGGTTAGTTCTTTGACTTGATTCCCTTTTTTCAATTTTATTGCTAACATGGTACTGAAATGTG[C/T]
TCTGGCCTTCTGGATGAAAATATTGGCAGCAATTGCTGGTGCTAGAAACTAACTTGTTTCTTAGCGGCCTTGGCCTGCATGACCAGCACAGAGATATGAG

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 99.80% 0.20% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 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
vg0629061095 G -> A LOC_Os06g48040.1 intron_variant ; MODIFIER N Average:64.55; most accessible tissue: Minghui63 young leaf, score: 85.028 N N N N