Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0327370239:

Variant ID: vg0327370239 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27370239
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATCTCTTCGATAATTAACGGGAAATCCCGCCTAAGATGAAAGTAGCCATCAGTGACGGCCACCTTCTTGAAGTTGATCTCCGCCATCAAGAAGCTGAG[C/G]
CACTTGCTCTTTAGCTCCGGGCAATGGTACCTCTCGGCGTAGGCGCGTAGCCTAGAGTCATCGCCACCGTCTCCACCGACACACTCTCCCACAGCTTCTG

Reverse complement sequence

CAGAAGCTGTGGGAGAGTGTGTCGGTGGAGACGGTGGCGATGACTCTAGGCTACGCGCCTACGCCGAGAGGTACCATTGCCCGGAGCTAAAGAGCAAGTG[G/C]
CTCAGCTTCTTGATGGCGGAGATCAACTTCAAGAAGGTGGCCGTCACTGATGGCTACTTTCATCTTAGGCGGGATTTCCCGTTAATTATCGAAGAGATAA

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 66.00% 33.90% 0.11% 0.00% NA
All Indica  2759 98.60% 1.30% 0.11% 0.00% NA
All Japonica  1512 1.50% 98.50% 0.07% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 98.50% 1.10% 0.43% 0.00% NA
Indica III  913 98.70% 1.20% 0.11% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 0.80% 99.10% 0.13% 0.00% NA
Tropical Japonica  504 2.00% 98.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 64.40% 34.40% 1.11% 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
vg0327370239 C -> G LOC_Os03g48120.1 missense_variant ; p.Trp164Cys; MODERATE nonsynonymous_codon ; W164C Average:78.061; most accessible tissue: Zhenshan97 panicle, score: 86.788 probably damaging -3.421 TOLERATED 1.00