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Detailed information for vg0121350364:

Variant ID: vg0121350364 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 21350364
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGAAACATAGACATTATTAATTATTTGCTACATTTCATTCATCTAAAAATTTTTAATTTTGAAATCACCTAAAACTACATGCTTCTAAACAGGGAGGAA[C/T]
GTAGCATCAAACTAGAAGTGCTCATCTTTTTCTTCATCTTTTGGCTCCCTCTACTCTTATTCCTTCTTTCCCCTCCCATCTCTCCTCTTTTCCATAGGAA

Reverse complement sequence

TTCCTATGGAAAAGAGGAGAGATGGGAGGGGAAAGAAGGAATAAGAGTAGAGGGAGCCAAAAGATGAAGAAAAAGATGAGCACTTCTAGTTTGATGCTAC[G/A]
TTCCTCCCTGTTTAGAAGCATGTAGTTTTAGGTGATTTCAAAATTAAAAATTTTTAGATGAATGAAATGTAGCAAATAATTAATAATGTCTATGTTTCCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 1.30% 0.00% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 98.30% 1.70% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.80% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 3.40% 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 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0121350364 C -> T LOC_Os01g38130.1 synonymous_variant ; p.Asn89Asn; LOW nonsynonymous_codon Average:45.562; most accessible tissue: Minghui63 panicle, score: 68.46 unknown unknown TOLERATED 1.00