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Detailed information for vg0135986444:

Variant ID: vg0135986444 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 35986444
Reference Allele: TAAlternative Allele: T,TAA
Primary Allele: TASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGAACACATCATTCAACCGACCTACCTTTGAGCCACACTAATCATTTTCTGGATTTGCCAGTCAATCTATTGGAACCCAATCCCCTCACGTGTTTCCTT[TA/T,TAA]
AAAAAAAATATTAACAGCCAATCGGATGATGAAATTGGGGAAACTACCTGTGAACAGATGAGCTAATTACTTAAAAAAAACGCATATGCTACACTTTACA

Reverse complement sequence

TGTAAAGTGTAGCATATGCGTTTTTTTTAAGTAATTAGCTCATCTGTTCACAGGTAGTTTCCCCAATTTCATCATCCGATTGGCTGTTAATATTTTTTTT[TA/A,TTA]
AAGGAAACACGTGAGGGGATTGGGTTCCAATAGATTGACTGGCAAATCCAGAAAATGATTAGTGTGGCTCAAAGGTAGGTCGGTTGAATGATGTGTTCCG

Allele Frequencies:

Populations Population SizeFrequency of TA(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.80% 47.00% 0.13% 0.00% TAA: 0.06%
All Indica  2759 27.30% 72.60% 0.14% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 40.10% 58.00% 0.74% 0.00% TAA: 1.12%
Indica I  595 12.10% 87.90% 0.00% 0.00% NA
Indica II  465 7.50% 92.50% 0.00% 0.00% NA
Indica III  913 40.90% 59.10% 0.00% 0.00% NA
Indica Intermediate  786 34.70% 64.80% 0.51% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 65.60% 34.40% 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
vg0135986444 TA -> T LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:45.112; most accessible tissue: Callus, score: 74.913 N N N N
vg0135986444 TA -> TAA LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:45.112; most accessible tissue: Callus, score: 74.913 N N N N