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Detailed information for vg0321793674:

Variant ID: vg0321793674 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21793674
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATGCCAACCGAGCAGCAAGTCCCGTCGTCGTCGTGCATAAGAGGCCGACACCGGAGACGGAGAAGGAGCAGGATCAGGAGCCGCCACGACAGAGGCGCC[G/T]
CACAGGAGACAGTGCCGCACAAGACTAGCGAGCTCATGTCGATCGCCACTTAATTTGTCATTATTAGTTAGTAGGTAGATTACCATGTGCTCTTTTTTTT

Reverse complement sequence

AAAAAAAAGAGCACATGGTAATCTACCTACTAACTAATAATGACAAATTAAGTGGCGATCGACATGAGCTCGCTAGTCTTGTGCGGCACTGTCTCCTGTG[C/A]
GGCGCCTCTGTCGTGGCGGCTCCTGATCCTGCTCCTTCTCCGTCTCCGGTGTCGGCCTCTTATGCACGACGACGACGGGACTTGCTGCTCGGTTGGCATC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 0.70% 0.68% 0.00% NA
All Indica  2759 97.80% 1.10% 1.09% 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 92.80% 3.20% 4.03% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.10% 0.64% 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 97.80% 0.00% 2.22% 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
vg0321793674 G -> T LOC_Os03g39240.1 missense_variant ; p.Arg272Leu; MODERATE nonsynonymous_codon ; R272L Average:38.309; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 unknown unknown DELETERIOUS 0.03