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Detailed information for vg0629060923:

Variant ID: vg0629060923 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 29060923
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATAGTTCCTGAGCAAATGAAAAGCAGAAGAAAATACATAACCTTCTGATGTCAGAATCAGATGAGCCGATGACACTTCTTTGTTAAGGAAAGAGATATT[C/A]
TAATTGAACCTTTGAGGAAGAATCAACATGGTGAAAGCAATACCTCATAAGACATGTTGTCAATATCCATTCTCATATCTCTGTGCTGGTCATGCAGGCC

Reverse complement sequence

GGCCTGCATGACCAGCACAGAGATATGAGAATGGATATTGACAACATGTCTTATGAGGTATTGCTTTCACCATGTTGATTCTTCCTCAAAGGTTCAATTA[G/T]
AATATCTCTTTCCTTAACAAAGAAGTGTCATCGGCTCATCTGATTCTGACATCAGAAGGTTATGTATTTTCTTCTGCTTTTCATTTGCTCAGGAACTATT

Allele Frequencies:

Populations Population SizeFrequency of C(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 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.60% 0.40% 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 99.70% 0.30% 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 98.80% 1.20% 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
vg0629060923 C -> A LOC_Os06g48040.1 intron_variant ; MODIFIER N Average:70.118; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N